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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative <italic>in silico</italic> analysis of EST-SSRs in angiosperm and gymnosperm tree genera</title><author><name sortKey="Ranade, Sonali Sachin" sort="Ranade, Sonali Sachin" uniqKey="Ranade S" first="Sonali Sachin" last="Ranade">Sonali Sachin Ranade</name><affiliation><nlm:aff id="Aff1">Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden</nlm:aff></affiliation></author><author><name sortKey="Lin, Yao Cheng" sort="Lin, Yao Cheng" uniqKey="Lin Y" first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name><affiliation><nlm:aff id="Aff2">Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium</nlm:aff></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation><nlm:aff id="Aff3">Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy</nlm:aff></affiliation><affiliation><nlm:aff id="Aff4">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation><nlm:aff id="Aff2">Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium</nlm:aff></affiliation><affiliation><nlm:aff id="Aff5">Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa</nlm:aff></affiliation></author><author><name sortKey="Garcia Gil, Maria Del Rosario" sort="Garcia Gil, Maria Del Rosario" uniqKey="Garcia Gil M" first="María Del Rosario" last="García-Gil">María Del Rosario García-Gil</name><affiliation><nlm:aff id="Aff1">Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25143005</idno><idno type="pmc">4160553</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160553</idno><idno type="RBID">PMC:4160553</idno><idno type="doi">10.1186/s12870-014-0220-8</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000614</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative <italic>in silico</italic> analysis of EST-SSRs in angiosperm and gymnosperm tree genera</title><author><name sortKey="Ranade, Sonali Sachin" sort="Ranade, Sonali Sachin" uniqKey="Ranade S" first="Sonali Sachin" last="Ranade">Sonali Sachin Ranade</name><affiliation><nlm:aff id="Aff1">Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden</nlm:aff></affiliation></author><author><name sortKey="Lin, Yao Cheng" sort="Lin, Yao Cheng" uniqKey="Lin Y" first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name><affiliation><nlm:aff id="Aff2">Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium</nlm:aff></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation><nlm:aff id="Aff3">Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy</nlm:aff></affiliation><affiliation><nlm:aff id="Aff4">Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</nlm:aff></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation><nlm:aff id="Aff2">Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium</nlm:aff></affiliation><affiliation><nlm:aff id="Aff5">Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa</nlm:aff></affiliation></author><author><name sortKey="Garcia Gil, Maria Del Rosario" sort="Garcia Gil, Maria Del Rosario" uniqKey="Garcia Gil M" first="María Del Rosario" last="García-Gil">María Del Rosario García-Gil</name><affiliation><nlm:aff id="Aff1">Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden</nlm:aff></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).</p></sec><sec><title>Results</title><p>Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.</p></sec><sec><title>Conclusions</title><p>Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-014-0220-8) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Tautz, D" uniqKey="Tautz D">D Tautz</name></author><author><name sortKey="Renz, M" uniqKey="Renz M">M Renz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zane, L" uniqKey="Zane L">L Zane</name></author><author><name sortKey="Bargelloni, L" uniqKey="Bargelloni L">L 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Plant Biol</journal-id><journal-id journal-id-type="iso-abbrev">BMC Plant Biol</journal-id><journal-title-group><journal-title>BMC Plant Biology</journal-title></journal-title-group><issn pub-type="epub">1471-2229</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25143005</article-id><article-id pub-id-type="pmc">4160553</article-id><article-id pub-id-type="publisher-id">220</article-id><article-id pub-id-type="doi">10.1186/s12870-014-0220-8</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Comparative <italic>in silico</italic> analysis of EST-SSRs in angiosperm and gymnosperm tree genera</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ranade</surname><given-names>Sonali Sachin</given-names></name><address><email>Sonali.Ranade@slu.se</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Yao-Cheng</given-names></name><address><email>yao-cheng.lin@psb.vib-ugent.be</email></address><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author"><name><surname>Zuccolo</surname><given-names>Andrea</given-names></name><address><email>azuccolo@appliedgenomics.org</email></address><xref ref-type="aff" rid="Aff3"></xref><xref ref-type="aff" rid="Aff4"></xref></contrib><contrib contrib-type="author"><name><surname>Van de Peer</surname><given-names>Yves</given-names></name><address><email>yves.vandepeer@psb.vib-ugent.be</email></address><xref ref-type="aff" rid="Aff2"></xref><xref ref-type="aff" rid="Aff5"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>García-Gil</surname><given-names>María del Rosario</given-names></name><address><email>M.Rosario.Garcia@slu.se</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><aff id="Aff1"><label></label>Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden</aff><aff id="Aff2"><label></label>Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium</aff><aff id="Aff3"><label></label>Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy</aff><aff id="Aff4"><label></label>Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy</aff><aff id="Aff5"><label></label>Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa</aff></contrib-group><pub-date pub-type="epub"><day>21</day><month>8</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>21</day><month>8</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>14</volume><elocation-id>220</elocation-id><history><date date-type="received"><day>7</day><month>4</month><year>2014</year></date><date date-type="accepted"><day>5</day><month>8</month><year>2014</year></date></history><permissions><copyright-statement>© Ranade et al.; licensee BioMed Central Ltd. 2014</copyright-statement><license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><sec><title>Background</title><p>Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera).</p></sec><sec><title>Results</title><p>Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera.</p></sec><sec><title>Conclusions</title><p>Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-014-0220-8) contains supplementary material, which is available to authorized users.</p></sec></abstract><kwd-group xml:lang="en"><title>Keywords</title><kwd>Angiosperms</kwd><kwd>Gymnosperms</kwd><kwd>Expressed sequence tags</kwd><kwd>Simple sequence repeats (SSR)</kwd><kwd>Microsatellites</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2014</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="Sec1" sec-type="introduction"><title>Background</title><p>Microsatellites, also called SSRs (simple sequence repeats) or STRs (short tandem repeats), are 1-6 bp tandem repeat motifs present in both the coding and non-coding fractions of eukaryotic and prokaryotic genomes [<xref ref-type="bibr" rid="CR1">1</xref>-<xref ref-type="bibr" rid="CR3">3</xref>]. SSRs are especially abundant in transcribed regions of the genome making them a valuable molecular marker for genetic studies in plants [<xref ref-type="bibr" rid="CR4">4</xref>]. SSRs result from mutations due to DNA-polymerase slippage during replication and unequal recombination [<xref ref-type="bibr" rid="CR5">5</xref>]. SSRs are widely used in plant genetic research because of their co-dominant inheritance, relative abundance, multi-allelic nature, high reproducibility and ease of detection [<xref ref-type="bibr" rid="CR6">6</xref>].</p><p>Expressed sequence tags (ESTs) are segments of expressed genes generated by single-pass sequencing of cDNA libraries [<xref ref-type="bibr" rid="CR7">7</xref>]. In contrast to the genomic SSRs, EST-SSRs represent functional markers located in the coding fractions of the genome and changes in EST-SSRs length can cause a phenotypic effect, irrespective of the mutation site, whether it occurs in 5′- or 3′-UnTranslated Regions (UTRs) or in the Open Reading Frames (ORFs) [<xref ref-type="bibr" rid="CR8">8</xref>]. The significance of EST-SSRs as a molecular tool in population genetic studies has been known for long [<xref ref-type="bibr" rid="CR9">9</xref>]. In woody trees, EST-SSRs have been applied in population studies and analysis of genetic diversity in <italic>Cycas</italic> [<xref ref-type="bibr" rid="CR10">10</xref>], <italic>Picea</italic> [<xref ref-type="bibr" rid="CR11">11</xref>,<xref ref-type="bibr" rid="CR12">12</xref>], <italic>Prunus</italic> [<xref ref-type="bibr" rid="CR13">13</xref>,<xref ref-type="bibr" rid="CR14">14</xref>], <italic>Eucalyptus</italic> [<xref ref-type="bibr" rid="CR15">15</xref>,<xref ref-type="bibr" rid="CR16">16</xref>] and <italic>Populus</italic> [<xref ref-type="bibr" rid="CR17">17</xref>]; in hybrid selection in e.g., <italic>Citrus</italic> [<xref ref-type="bibr" rid="CR18">18</xref>]; and also in genetic mapping in <italic>Citrus</italic> [<xref ref-type="bibr" rid="CR19">19</xref>], <italic>Quercus</italic> [<xref ref-type="bibr" rid="CR20">20</xref>,<xref ref-type="bibr" rid="CR21">21</xref>] and <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR22">22</xref>]. Furthermore, unlike the genomic SSRs, EST-SSRs are easily transferable across species [<xref ref-type="bibr" rid="CR23">23</xref>], therefore allowing studying polymorphism and genetic diversity in related species [<xref ref-type="bibr" rid="CR9">9</xref>]. However, EST-SSRs have some disadvantages over genomic SSRs as EST-SSRs are known to be less variable than the genomic SSRs [<xref ref-type="bibr" rid="CR24">24</xref>] and the amplicon size can also differ from the predicted size due to the effect of presence of introns in the flanking fractions [<xref ref-type="bibr" rid="CR25">25</xref>].</p><p>With the advent of genomics, the availability of ESTs in the public databases, such as NCBI’s dbEST, has increased exponentially allowing for the identification of large numbers of EST-SSRs. For example, characterisation and comparative analysis of EST microsatellites in woody trees have been carried out in <italic>Citrus</italic> [<xref ref-type="bibr" rid="CR26">26</xref>-<xref ref-type="bibr" rid="CR28">28</xref>], <italic>Betula</italic> [<xref ref-type="bibr" rid="CR29">29</xref>], <italic>Fagus</italic> [<xref ref-type="bibr" rid="CR30">30</xref>], <italic>Prunus</italic> [<xref ref-type="bibr" rid="CR31">31</xref>], <italic>Quercus</italic> [<xref ref-type="bibr" rid="CR20">20</xref>], <italic>Populus</italic> [<xref ref-type="bibr" rid="CR17">17</xref>,<xref ref-type="bibr" rid="CR32">32</xref>], <italic>Eucalyptus</italic> [<xref ref-type="bibr" rid="CR33">33</xref>-<xref ref-type="bibr" rid="CR35">35</xref>], <italic>Cryptomeria</italic> [<xref ref-type="bibr" rid="CR36">36</xref>,<xref ref-type="bibr" rid="CR37">37</xref>], <italic>Cycas</italic> [<xref ref-type="bibr" rid="CR38">38</xref>-<xref ref-type="bibr" rid="CR40">40</xref>], <italic>Ginkgo</italic> [<xref ref-type="bibr" rid="CR41">41</xref>], <italic>Picea</italic> [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR12">12</xref>] and <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR42">42</xref>]. However, analysis of SSRs for each individual EST genomic fraction (i.e., 5′- and 3′-UTR, and ORF) has only been carried out in <italic>Quercus</italic> [<xref ref-type="bibr" rid="CR20">20</xref>], <italic>Cryptomeria</italic> [<xref ref-type="bibr" rid="CR37">37</xref>] and <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR43">43</xref>]. Unfortunately, most of the results in those three studies are presented for the entire EST, which can lead to inaccurate results. For example, in <italic>Cryptomeria</italic> dimers are the most common motif in the 3′UTR fraction; moreover, when all three EST fractions are considered together, trimers are concluded to be the most frequent motif across the entire EST [<xref ref-type="bibr" rid="CR37">37</xref>]. Furthermore, AT was shown to be the most frequent dimer motif as an overall result, whereas analysis of each EST fraction separately revealed AG as the most frequent dimer in the ORF fraction [<xref ref-type="bibr" rid="CR37">37</xref>]. These results demonstrate that SSR characterization on the whole EST sequence as a unit will provide only partial information, which may be misleading and result in discrepancies across studies.</p><p>Other discrepancies in EST-SSRs motif abundance and distribution across different plant studies can be attributed to the parameter setup [<xref ref-type="bibr" rid="CR25">25</xref>], annotation deficiency [<xref ref-type="bibr" rid="CR44">44</xref>], and the selected EST-SSR analysis algorithm [<xref ref-type="bibr" rid="CR20">20</xref>]. For example, higher abundance of EST-SSR dimers was reported in <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR45">45</xref>,<xref ref-type="bibr" rid="CR46">46</xref>], whereas Yan et al. [<xref ref-type="bibr" rid="CR47">47</xref>] reported trimers as the most abundant in the same genus. Thus, comparative EST-SSRs studies will be more reliable when the EST data sets are analysed by applying the same bioinformatics procedure. In this study, we performed a comparative analysis of SSRs in each genomic fraction of EST separately (5′UTR, ORF and 3′UTR), across selected angiosperm and gymnosperm genera with a focus on woody trees. The aim was to present highly comparable data on SSR-EST abundance, composition and distribution; for genomes that diverged ~350 Myr [<xref ref-type="bibr" rid="CR48">48</xref>].</p></sec><sec id="Sec2" sec-type="results"><title>Results</title><p>Table <xref rid="Tab1" ref-type="table">1</xref> shows values for EST-SSRs length and EST-SSR counts per genus across the 5′UTR, ORF and 3′UTR fractions (see also Additional file <xref rid="MOESM1" ref-type="media">1</xref>: Table S1).<table-wrap id="Tab1"><label>Table 1</label><caption><p>EST-SSR Counts per Mbp in each genomic fraction in: (a) Angiosperms and (b) Gymnosperms</p></caption><table frame="hsides" rules="groups"><thead><tr valign="top"><th colspan="2"><bold>(a)</bold></th><th colspan="2"><bold>5′UTR</bold></th><th colspan="2"><bold>ORF</bold></th><th colspan="2"><bold>3′UTR</bold></th></tr><tr valign="top"><th><bold>Genus</bold></th><th><bold>Mean Genome size (pg)</bold></th><th><bold>Motif length* (bp)</bold></th><th><bold>Counts Mbp</bold></th><th><bold>Motif length* (bp)</bold></th><th><bold>Counts Mpb</bold></th><th><bold>Motif length* (bp)</bold></th><th><bold>Counts Mbp</bold></th></tr></thead><tbody><tr valign="top"><td><italic>Populus</italic></td><td>0.52</td><td>24.8 (6.04)</td><td>1483</td><td>25.7 (8.10)</td><td>580</td><td>24.8 (7.60)</td><td>653</td></tr><tr valign="top"><td><italic>Eucalyptus</italic></td><td>0.6</td><td>25.5 (5.31)</td><td>2267</td><td>25.1 (5.48)</td><td>1248</td><td>25.3 (5.83)</td><td>638</td></tr><tr valign="top"><td><italic>Betula</italic></td><td>0.62</td><td>23.1 (3.34)</td><td>1404</td><td>22.7 (3.02)</td><td>893</td><td>21.4 (1.51)</td><td>945</td></tr><tr valign="top"><td><italic>Fagus</italic></td><td>0.56</td><td>24 (5.36)</td><td>1698</td><td>25.2 (7.01)</td><td>465</td><td>23.9 (4.90)</td><td>622</td></tr><tr valign="top"><td><italic>Quercus</italic></td><td>0.87</td><td>24.2 (5.27)</td><td>2739</td><td>25.2 (7.98)</td><td>949</td><td>24.3 (6.78)</td><td>1109</td></tr><tr valign="top"><td><italic>Citrus</italic></td><td>0.44</td><td>24.7 (6.75)</td><td>503</td><td>25.2 (8.15)</td><td>247</td><td>24.6 (6.87)</td><td>210</td></tr><tr valign="top"><td><italic>Prunus</italic></td><td>0.57</td><td>27.5 (8.95)</td><td>7965</td><td>29.5 (11.38)</td><td>3089</td><td>26.9 (8.57)</td><td>4537</td></tr><tr valign="top"><td><italic>Fraxinus</italic></td><td>0.93</td><td>24.2 (3.38)</td><td>551</td><td>28.7 (10.23)</td><td>183</td><td>22.4 (4.17)</td><td>236</td></tr><tr valign="top"><td colspan="2"><bold>(b)</bold></td><td colspan="2"><bold>5′UTR</bold></td><td colspan="2"><bold>ORF</bold></td><td colspan="2"><bold>3′UTR</bold></td></tr><tr valign="top"><td><bold>Genus</bold></td><td><bold>Mean Genome size (pg)</bold></td><td><bold>Motif Length* (bp)</bold></td><td><bold>Counts Mbp</bold></td><td><bold>Motif Length* (bp)</bold></td><td><bold>Counts Mbp</bold></td><td><bold>Motif Length* (bp)</bold></td><td><bold>Counts Mbp</bold></td></tr><tr valign="top"><td><italic>Picea</italic></td><td>18.1</td><td>29.7 (19.49)</td><td>247</td><td>32.1 (23.20)</td><td>206</td><td>28.6 (13.59)</td><td>250</td></tr><tr valign="top"><td><italic>Pinus</italic></td><td>26.4</td><td>30.2 (17.80)</td><td>216</td><td>32.4 (19.09)</td><td>184</td><td>27.4 (11.98)</td><td>187</td></tr><tr valign="top"><td><italic>Cryptomeria</italic></td><td>11.2</td><td>22.8 (3.95)</td><td>223</td><td>26.2 (10.37)</td><td>218</td><td>24.4 (8.40)</td><td>240</td></tr><tr valign="top"><td><italic>Gnetum</italic></td><td>3.4</td><td>23.5 (4.22)</td><td>632</td><td>24.8 (7.96)</td><td>664</td><td>22.7 (3.64)</td><td>549</td></tr><tr valign="top"><td><italic>Cycas</italic></td><td>14.7</td><td>23.8 (6.34)</td><td>173</td><td>26.4 (11.59)</td><td>109</td><td>24.9 (7.05)</td><td>399</td></tr><tr valign="top"><td><italic>Zamia</italic></td><td>17</td><td>25.8 (6.55)</td><td>610</td><td>29.0 (12.64)</td><td>701</td><td>26.3 (8.4)</td><td>734</td></tr><tr valign="top"><td><italic>Ginkgo</italic></td><td>11.8</td><td>24.5 (4.37)</td><td>386</td><td>29.2 (19.69)</td><td>210</td><td>27.1 (8.11)</td><td>539</td></tr></tbody></table><table-wrap-foot><p>*Standard deviation for EST-SSR length is in between parenthesis.</p></table-wrap-foot></table-wrap></p><sec id="Sec3"><title>EST-SSR length and complexity</title><p>There were no significant differences observed regarding EST-SSRs length between the three genomic fractions within and between taxa. In angiosperms, there was no significant association between genome size and EST-SSRs length for any of the EST fractions. In gymnosperms, however, there was a positive and significant association (r = 0.6; P-value < 0.03) between genome size and EST-SSRs motif length for all three EST fractions.</p><p>Perfect EST-SSRs were more frequent than compound ones in both taxa and in all three genomic fractions (Additional file <xref rid="MOESM1" ref-type="media">1</xref>: Table S2). In angiosperms, <italic>Eucalyptus</italic> (ORF) had the highest percentage of compound EST-SSR motifs (7.4%), while <italic>Cycas</italic> (3′UTR) had the highest percentage of compound SSR motifs (6.8%) in gymnosperms. None of the statistical tests made to compare proportions of complex EST-SSRs within and between taxa were significant. Furthermore, complexity was not significantly associated to genome size.</p></sec><sec id="Sec4"><title>EST-SSR abundance (motif counts per Mbp)</title><sec id="Sec5"><title>(i) Overall</title><p>In angiosperms, SSR counts showed a wide range across genera, with <italic>Prunus</italic> having an exceptional high abundance. EST-SSR counts were significantly higher in the 5′UTR fraction and lower in the ORFs. In gymnosperms, the SSR counts range was narrower than in angiosperms with <italic>Zamia</italic> and <italic>Gnetum</italic> having the highest values. EST-SSRs were significantly more abundant in the 3′UTR fraction, while there was a non-significant difference in abundance between the 5′UTR and ORF fractions. EST-SSRs were significantly more abundant in angiosperms than in gymnosperms. No association was found between density and genome size in any of the two taxa.</p></sec><sec id="Sec6"><title>(ii) By motif size</title><p>The distribution of counts per Mbp for each of the EST-SSRs, according to motif size, is shown in Table <xref rid="Tab2" ref-type="table">2</xref>. In angiosperms and gymnosperms, dimer motifs showed significantly higher number of counts in all three genomic fractions, followed by trimers, with the exception of <italic>Citrus</italic> (ORF, trimers > dimers), <italic>Cryptomeria</italic> (ORF, trimers > dimers) and <italic>Gnetum</italic> (5′UTR and ORF, trimers > dimers and trimers > hexamers, respectively). Non-significant differences between dimers and trimers were found in <italic>Cryptomeria</italic> (5′UTR) and <italic>Gnetum</italic> (3′UTR). In both taxa, the most frequent motif ranking in the ORF was dimer > trimer > hexamer. The same motif ranking was often observed in the UTRs in gymnosperms. Moreover, in angiosperms, hexamers are less often ranked in the third position in the UTRs, supporting a lower representation of hexamers in UTRs in angiosperms. Despite dimers being the motifs with higher number of counts in most of the genera across all three genomic fractions, the proportion of dimers to trimers was clearly lower in the ORF, indicating an enrichment of trimers in the ORF fraction in both taxa. Interestingly, <italic>Gnetum</italic> was the only genus where dimers rank third when it comes to abundance (ORF, trimers > hexamers > dimers); trimers and hexamers being relatively abundant across all three fractions. In <italic>Fraxinus</italic> and <italic>Fagus</italic>, trimers and hexamers were also rather abundant.<table-wrap id="Tab2"><label>Table 2</label><caption><p>Counts per Mbp of different SSR motifs in each genomic fraction in: (a) Angiosperms and (b) Gymnosperms</p></caption><table frame="hsides" rules="groups"><thead><tr valign="top"><th rowspan="2"><bold>(a)</bold></th><th colspan="3"><bold>Populus</bold></th><th colspan="3"><bold>Eucalyptus</bold></th><th colspan="3"><bold>Betula</bold></th><th colspan="3"><bold>Fagus</bold></th><th colspan="3"><bold>Quercus</bold></th><th colspan="3"><bold>Citrus</bold></th><th colspan="3"><bold>Prunus</bold></th><th colspan="3"><bold>Fraxinus</bold></th></tr><tr valign="top"><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th></tr></thead><tbody><tr valign="top"><td>Dimer</td><td>948</td><td>272</td><td>379</td><td>1821</td><td>699</td><td>459</td><td>1131</td><td>649</td><td>880</td><td>1304</td><td>230</td><td>397</td><td>2193</td><td>530</td><td>832</td><td>318</td><td>96</td><td>122</td><td>6854</td><td>2403</td><td>3568</td><td>522</td><td>124</td><td>143</td></tr><tr valign="top"><td>Trimer</td><td>250</td><td>209</td><td>146</td><td>232</td><td>412</td><td>91</td><td>151</td><td>181</td><td>0</td><td>172</td><td>161</td><td>77</td><td>232</td><td>286</td><td>126</td><td>190</td><td>104</td><td>43</td><td>329</td><td>413</td><td>388</td><td>0</td><td>19</td><td>57</td></tr><tr valign="top"><td>Tetramer</td><td>85</td><td>16</td><td>42</td><td>77</td><td>27</td><td>27</td><td>47</td><td>10</td><td>41</td><td>65</td><td>7</td><td>21</td><td>97</td><td>15</td><td>49</td><td>32</td><td>7</td><td>15</td><td>204</td><td>32</td><td>133</td><td>0</td><td>0</td><td>8</td></tr><tr valign="top"><td>Pentamer</td><td>97</td><td>16</td><td>35</td><td>49</td><td>15</td><td>23</td><td>0</td><td>34</td><td>0</td><td>39</td><td>3</td><td>35</td><td>88</td><td>15</td><td>45</td><td>24</td><td>4</td><td>9</td><td>182</td><td>65</td><td>163</td><td>0</td><td>4</td><td>12</td></tr><tr valign="top"><td>Hexamer</td><td>68</td><td>54</td><td>28</td><td>43</td><td>67</td><td>17</td><td>0</td><td>8</td><td>0</td><td>60</td><td>56</td><td>49</td><td>70</td><td>91</td><td>26</td><td>17</td><td>27</td><td>7</td><td>94</td><td>85</td><td>82</td><td>18</td><td>35</td><td>12</td></tr><tr valign="top"><td>Heptamer</td><td>27</td><td>7</td><td>18</td><td>29</td><td>14</td><td>14</td><td>57</td><td>6</td><td>24</td><td>52</td><td>2</td><td>41</td><td>50</td><td>7</td><td>25</td><td>16</td><td>5</td><td>9</td><td>196</td><td>39</td><td>120</td><td>11</td><td>0</td><td>5</td></tr><tr valign="top"><td>Octamer</td><td>6</td><td>2</td><td>2</td><td>2</td><td>4</td><td>5</td><td>0</td><td>0</td><td>0</td><td>3</td><td>1</td><td>0</td><td>3</td><td>1</td><td>3</td><td>4</td><td>1</td><td>2</td><td>67</td><td>18</td><td>49</td><td>0</td><td>0</td><td>0</td></tr><tr valign="top"><td>Novamer</td><td>1</td><td>3</td><td>1</td><td>7</td><td>5</td><td>1</td><td>0</td><td>6</td><td>0</td><td>0</td><td>3</td><td>0</td><td>1</td><td>3</td><td>1</td><td>1</td><td>2</td><td>1</td><td>15</td><td>26</td><td>16</td><td>0</td><td>0</td><td>0</td></tr><tr valign="top"><td>Decamer</td><td>3</td><td>2</td><td>2</td><td>7</td><td>6</td><td>2</td><td>19</td><td>0</td><td>0</td><td>4</td><td>2</td><td>1</td><td>5</td><td>1</td><td>2</td><td>2</td><td>2</td><td>2</td><td>23</td><td>7</td><td>18</td><td>0</td><td>0</td><td>0</td></tr><tr valign="top"><td rowspan="2"><bold>(b)</bold></td><td colspan="3"><bold>Picea</bold></td><td colspan="3"><bold>Pinus</bold></td><td colspan="3"><bold>Cryptomeria</bold></td><td colspan="3"><bold>Gnetum</bold></td><td colspan="3"><bold>Cycas</bold></td><td colspan="3"><bold>Zamia</bold></td><td colspan="3"><bold>Ginkgo</bold></td><td colspan="3"></td></tr><tr valign="top"><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td colspan="3"></td></tr><tr valign="top"><td>Dimer</td><td>183</td><td>128</td><td>199</td><td>169</td><td>121</td><td>140</td><td>46</td><td>58</td><td>116</td><td>133</td><td>104</td><td>182</td><td>118</td><td>84</td><td>354</td><td>503</td><td>504</td><td>578</td><td>319</td><td>164</td><td>483</td><td colspan="3"></td></tr><tr valign="top"><td>Trimer</td><td>14</td><td>41</td><td>12</td><td>5</td><td>30</td><td>8</td><td>43</td><td>85</td><td>47</td><td>260</td><td>355</td><td>169</td><td>10</td><td>13</td><td>12</td><td>35</td><td>143</td><td>60</td><td>52</td><td>24</td><td>12</td><td colspan="3"></td></tr><tr valign="top"><td>Tetramer</td><td>6</td><td>1</td><td>10</td><td>6</td><td>2</td><td>11</td><td>17</td><td>1</td><td>9</td><td>78</td><td>15</td><td>69</td><td>17</td><td>1</td><td>12</td><td>36</td><td>18</td><td>52</td><td>8</td><td>4</td><td>13</td><td colspan="3"></td></tr><tr valign="top"><td>Pentamer</td><td>24</td><td>5</td><td>12</td><td>12</td><td>4</td><td>8</td><td>41</td><td>8</td><td>20</td><td>45</td><td>31</td><td>41</td><td>9</td><td>1</td><td>6</td><td>11</td><td>9</td><td>21</td><td>7</td><td>1</td><td>17</td><td colspan="3"></td></tr><tr valign="top"><td>Hexamer</td><td>9</td><td>26</td><td>6</td><td>14</td><td>23</td><td>8</td><td>27</td><td>54</td><td>22</td><td>111</td><td>154</td><td>74</td><td>10</td><td>7</td><td>13</td><td>10</td><td>17</td><td>3</td><td>0</td><td>17</td><td>14</td><td colspan="3"></td></tr><tr valign="top"><td>Heptamer</td><td>8</td><td>1</td><td>8</td><td>7</td><td>2</td><td>6</td><td>37</td><td>8</td><td>22</td><td>0</td><td>2</td><td>5</td><td>7</td><td>2</td><td>2</td><td>15</td><td>8</td><td>19</td><td>0</td><td>0</td><td>0</td><td colspan="3"></td></tr><tr valign="top"><td>Octamer</td><td>2</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>8</td><td>1</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td colspan="3"></td></tr><tr valign="top"><td>Novamer</td><td>1</td><td>3</td><td>1</td><td>1</td><td>2</td><td>2</td><td>0</td><td>3</td><td>0</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td>0</td><td>1</td><td>0</td><td>0</td><td>0</td><td>0</td><td colspan="3"></td></tr><tr valign="top"><td>Decamer</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>2</td><td>4</td><td>1</td><td>2</td><td>5</td><td>0</td><td>8</td><td>0</td><td>0</td><td>0</td><td>0</td><td>2</td><td>0</td><td>0</td><td>0</td><td>0</td><td colspan="3"></td></tr></tbody></table></table-wrap></p></sec><sec id="Sec7"><title>(iii) By dimer and trimer nucleotide composition</title><p>The counts for dimer and trimer nucleotide composition across genomic fractions and genera are shown in Table <xref rid="Tab3" ref-type="table">3</xref>. In angiosperms, the AG/CT dimer motif showed the highest number of counts per Mbp in all genomic fractions and genera, followed by the AT/AT motif, with exception of <italic>Betula</italic> (AT/AT and AG/CT were present in similar numbers), <italic>Citrus</italic> (3′UTR; AT/AT) and <italic>Populus</italic> (3′UTR; AT/AT). In gymnosperms, AT/AT was the most abundant dimer motif in the 3′UTR fraction, with the exception of <italic>Cryptomeria</italic>, <italic>Cycas</italic> and <italic>Gnetum</italic> where AT/AT and AG/CT were present in similar numbers. In the 5′UTR and ORF fractions in gymnosperms, AG/CT was the most abundant motif in most of the genera, with the exception of <italic>Cycas</italic> (5′UTR), <italic>Ginkgo</italic> (ORF) and <italic>Zamia</italic> (ORF), where AT/AT and AG/CT were present in similar numbers; and <italic>Ginkgo</italic> (5′UTR), <italic>Zamia</italic> (5′UTR) and <italic>Cycas</italic> (ORF), where AT/AT was the most abundant. Overall, AT/AT was often the most abundant dimer in gymnosperms. The dimer motif CG/CG was absent in most of the genera and only present at low density in the ORF of <italic>Populus</italic> and <italic>Quercus</italic>.<table-wrap id="Tab3"><label>Table 3</label><caption><p>Counts per Mbp of dimer and trimer motifs in all three genomic fractions in: (a) Angiosperms and (b) Gymnosperms</p></caption><table frame="hsides" rules="groups"><thead><tr valign="top"><th colspan="25"><bold>(a)</bold></th></tr><tr valign="top"><th><bold>Motif</bold></th><th colspan="3"><bold><italic>Populus</italic></bold></th><th colspan="3"><bold><italic>Eucalyptus</italic></bold></th><th colspan="3"><bold><italic>Betula</italic></bold></th><th colspan="3"><bold><italic>Fagus</italic></bold></th><th colspan="3"><bold><italic>Quercus</italic></bold></th><th colspan="3"><bold><italic>Citrus</italic></bold></th><th colspan="3"><bold><italic>Prunus</italic></bold></th><th colspan="3"><bold><italic>Fraxinus</italic></bold></th></tr><tr valign="top"><th></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th><th><bold>5′UTR</bold></th><th><bold>ORF</bold></th><th><bold>3′UTR</bold></th></tr></thead><tbody><tr valign="top"><td>AC/GT</td><td>53</td><td>22</td><td>53</td><td>27</td><td>7</td><td>12</td><td>-</td><td>-</td><td>98</td><td>61</td><td>11</td><td>7</td><td>103</td><td>27</td><td>43</td><td>27</td><td>8</td><td>18</td><td>165</td><td>48</td><td>101</td><td>91</td><td>6</td><td>34</td></tr><tr valign="top"><td>AG/CT</td><td>822</td><td>185</td><td>148</td><td>1788</td><td>684</td><td>431</td><td>1131</td><td>649</td><td>350</td><td>1173</td><td>181</td><td>262</td><td>1885</td><td>439</td><td>471</td><td>230</td><td>73</td><td>47</td><td>5992</td><td>2226</td><td>2655</td><td>431</td><td>113</td><td>109</td></tr><tr valign="top"><td>AT/AT</td><td>73</td><td>57</td><td>178</td><td>7</td><td>8</td><td>15</td><td>-</td><td>-</td><td>432</td><td>69</td><td>38</td><td>128</td><td>205</td><td>63</td><td>317</td><td>60</td><td>16</td><td>57</td><td>697</td><td>129</td><td>811</td><td>-</td><td>6</td><td>-</td></tr><tr valign="top"><td>CG/CG</td><td>-</td><td>8</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr valign="top"><td>ACG/CGT</td><td>27</td><td>42</td><td>14</td><td>29</td><td>63</td><td>11</td><td>-</td><td>-</td><td>-</td><td>6</td><td>10</td><td>-</td><td>5</td><td>18</td><td>1</td><td>6</td><td>17</td><td>2</td><td>15</td><td>63</td><td>9</td><td>-</td><td>-</td><td>-</td></tr><tr valign="top"><td>ACT/AGT</td><td>23</td><td>23</td><td>14</td><td>17</td><td>4</td><td>9</td><td>66</td><td>34</td><td>-</td><td>13</td><td>24</td><td>5</td><td>27</td><td>38</td><td>29</td><td>6</td><td>9</td><td>4</td><td>29</td><td>114</td><td>136</td><td>-</td><td>4</td><td>21</td></tr><tr valign="top"><td>AAC/GTT</td><td>10</td><td>12</td><td>9</td><td>5</td><td>1</td><td>-</td><td>85</td><td>57</td><td>-</td><td>15</td><td>30</td><td>10</td><td>39</td><td>55</td><td>17</td><td>3</td><td>10</td><td>1</td><td>40</td><td>43</td><td>22</td><td>-</td><td>-</td><td>-</td></tr><tr valign="top"><td>AAG/CTT</td><td>93</td><td>46</td><td>43</td><td>98</td><td>63</td><td>28</td><td>-</td><td>77</td><td>-</td><td>111</td><td>52</td><td>22</td><td>125</td><td>91</td><td>31</td><td>38</td><td>28</td><td>12</td><td>168</td><td>90</td><td>86</td><td>-</td><td>4</td><td>11</td></tr><tr valign="top"><td>AAT/ATT</td><td>30</td><td>11</td><td>51</td><td>-</td><td>5</td><td>3</td><td>-</td><td>14</td><td>-</td><td>13</td><td>11</td><td>36</td><td>24</td><td>14</td><td>42</td><td>29</td><td>16</td><td>21</td><td>34</td><td>26</td><td>41</td><td>-</td><td>4</td><td>25</td></tr><tr valign="top"><td>ACC/GGT</td><td>26</td><td>35</td><td>7</td><td>-</td><td>25</td><td>3</td><td>-</td><td>57</td><td>-</td><td>-</td><td>12</td><td>5</td><td>6</td><td>45</td><td>3</td><td>5</td><td>10</td><td>1</td><td>7</td><td>33</td><td>5</td><td>-</td><td>4</td><td>-</td></tr><tr valign="top"><td>AGG/CCT</td><td>33</td><td>32</td><td>7</td><td>26</td><td>63</td><td>12</td><td>-</td><td>-</td><td>-</td><td>13</td><td>22</td><td>-</td><td>5</td><td>20</td><td>3</td><td>2</td><td>7</td><td>1</td><td>36</td><td>33</td><td>26</td><td>-</td><td>-</td><td>-</td></tr><tr valign="top"><td>CCG/CCG</td><td>4</td><td>7</td><td>1</td><td>52</td><td>183</td><td>12</td><td>-</td><td>-</td><td>-</td><td>-</td><td>1</td><td>-</td><td>1</td><td>6</td><td>-</td><td>2</td><td>6</td><td>1</td><td>-</td><td>5</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr valign="top"><td colspan="25"><bold>(b)</bold></td></tr><tr valign="top"><td><bold>Motif</bold></td><td colspan="3"><bold><italic>Picea</italic></bold></td><td colspan="3"><bold><italic>Pinus</italic></bold></td><td colspan="3"><bold><italic>Cryptomeria</italic></bold></td><td colspan="3"><bold><italic>Gnetum</italic></bold></td><td colspan="3"><bold><italic>Cycas</italic></bold></td><td colspan="3"><bold><italic>Zamia</italic></bold></td><td colspan="3"><bold><italic>Ginkgo</italic></bold></td><td colspan="3"></td></tr><tr valign="top"><td></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td><bold>5′UTR</bold></td><td><bold>ORF</bold></td><td><bold>3′UTR</bold></td><td colspan="3"></td></tr><tr valign="top"><td>AC/GT</td><td>3</td><td>3</td><td>4</td><td>1</td><td>2</td><td>1</td><td>19</td><td>-</td><td>9</td><td>36</td><td>-</td><td>-</td><td>-</td><td>11</td><td>51</td><td>79</td><td>116</td><td>88</td><td>40</td><td>44</td><td>17</td><td colspan="3"></td></tr><tr valign="top"><td>AG/CT</td><td>95</td><td>93</td><td>37</td><td>101</td><td>80</td><td>40</td><td>19</td><td>46</td><td>55</td><td>76</td><td>60</td><td>91</td><td>54</td><td>33</td><td>143</td><td>170</td><td>194</td><td>182</td><td>120</td><td>60</td><td>120</td><td colspan="3"></td></tr><tr valign="top"><td>AT/AT</td><td>85</td><td>31</td><td>157</td><td>67</td><td>39</td><td>100</td><td>8</td><td>12</td><td>53</td><td>20</td><td>45</td><td>91</td><td>64</td><td>40</td><td>160</td><td>254</td><td>194</td><td>308</td><td>346</td><td>60</td><td>346</td><td colspan="3"></td></tr><tr valign="top"><td>CG/CG</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>ACG/CGT</td><td>1</td><td>10</td><td>1</td><td>-</td><td>8</td><td>-</td><td>-</td><td>14</td><td>7</td><td>76</td><td>172</td><td>48</td><td>-</td><td>2</td><td>-</td><td>-</td><td>38</td><td>-</td><td>-</td><td>10</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>ACT/AGT</td><td>1</td><td>1</td><td>2</td><td>-</td><td>3</td><td>-</td><td>9</td><td>8</td><td>7</td><td>38</td><td>31</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>14</td><td>11</td><td>-</td><td>-</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>AAC/GTT</td><td>1</td><td>3</td><td>-</td><td>1</td><td>2</td><td>1</td><td>5</td><td>5</td><td>-</td><td>13</td><td>13</td><td>12</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>AAG/CTT</td><td>1</td><td>6</td><td>2</td><td>1</td><td>7</td><td>-</td><td>6</td><td>26</td><td>10</td><td>76</td><td>57</td><td>86</td><td>10</td><td>9</td><td>-</td><td>8</td><td>32</td><td>16</td><td>-</td><td>5</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>AAT/ATT</td><td>4</td><td>3</td><td>5</td><td>2</td><td>2</td><td>5</td><td>5</td><td>3</td><td>20</td><td>-</td><td>4</td><td>12</td><td>-</td><td>2</td><td>5</td><td>18</td><td>31</td><td>33</td><td>40</td><td>8</td><td>12</td><td colspan="3"></td></tr><tr valign="top"><td>ACC/GGT</td><td>1</td><td>2</td><td>-</td><td>1</td><td>2</td><td>-</td><td>11</td><td>-</td><td>-</td><td>27</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>9</td><td>-</td><td>-</td><td>-</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>AGG/CCT</td><td>5</td><td>13</td><td>1</td><td>-</td><td>4</td><td>1</td><td>8</td><td>19</td><td>-</td><td>29</td><td>37</td><td>12</td><td>-</td><td>-</td><td>6</td><td>8</td><td>14</td><td>-</td><td>12</td><td>-</td><td>-</td><td colspan="3"></td></tr><tr valign="top"><td>CCG/CCG</td><td>1</td><td>4</td><td>-</td><td>-</td><td>2</td><td>-</td><td>-</td><td>10</td><td>4</td><td>-</td><td>14</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td colspan="3"></td></tr></tbody></table></table-wrap></p><p>In the 3′UTR fraction in angiosperms and gymnosperms AAT/ATT was the most abundant trimer motif in all the genera with the exception of <italic>Eucalyptus</italic> (AAG/CTT, AGG/CTT and CCG/CCG were present in similar numbers), <italic>Fraxinus</italic> (AAT/AAT and ACT/AGT were present in similar numbers), <italic>Prunus</italic> (ACT/AGT most abundant) and <italic>Gnetum</italic> (AAG/CTT most abundant). In the 5′UTR and ORF fractions in angiosperms, AAG/CTT was the most abundant in all genera except in <italic>Betula</italic> (5′UTR; AAC/GTT and ACT/AGT were present in similar numbers), <italic>Betula</italic> (ORF; AAG/CTT, AAC/GTT and ACC/GGT were present in similar numbers), <italic>Eucalyptus</italic> (ORF; CCG/CCG most abundant), <italic>Fraxinus</italic> (ORF; AAG/CCT, ACT/AGT, AAT/ATT and ACC/GGT were present in similar numbers) and <italic>Prunus</italic> (ORF; ACT/AGT most abundant). Moreover, in the 5′UTR and ORF in gymnosperms, there was not a single trimer motif that ranked first, instead it varied across genera.</p></sec></sec></sec><sec id="Sec8" sec-type="discussion"><title>Discussion</title><p>In this study we have investigated the occurrence of EST-SSRs in three EST genomic fractions (5′UTR, ORF and 3′UTR), in a genus-wise analysis in woody trees of two taxa, angiosperms and gymnosperms. Genus-wise EST-SSRs analysis for EST genomic fractions separately supports the unequal distribution of EST-SSR motifs across the EST sequences. EST-SSR length is positively associated with genome size in gymnosperms (i.e. larger genomes have longer EST-SSRs). However, EST-SSR density is not proportional to genome size; instead other factors seem to have contributed to the EST-SSR density in gymnosperms. We observed two main differences between angiosperm and gymnosperm genera, which may reflect evolutionary differences following their divergence 350 Myr [<xref ref-type="bibr" rid="CR48">48</xref>], such as the increased presence of hexamers and AT-rich motifs in the gymnosperm genera.</p><sec id="Sec9"><title>Low contribution of EST-SSRs to genome size diversity</title><p>Our EST-SSRs length values are in accordance with those previously reported in the literature [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR27">27</xref>,<xref ref-type="bibr" rid="CR45">45</xref>]. In gymnosperms, we observe a positive and significant association between the EST-SSRs length and genome size. Thus, the largest genomes (<italic>Pinus</italic> and <italic>Picea</italic>) also have, on average, the longest EST-SSRs. Although this suggests a higher relaxation towards genome enlargement in those two genera, the yet small differences in length between the studied gymnosperm genera suggests that EST-SSRs length contribution to <italic>Pinus</italic> and <italic>Picea</italic> genome obesity may be only modest. Instead, EST-SSRs length has been suggested to be mainly the result of a balance between slippage events and point mutation [<xref ref-type="bibr" rid="CR8">8</xref>], which have resulted in a rather homogeneous EST-SSRs length, as suggested before [<xref ref-type="bibr" rid="CR45">45</xref>]. Unlike in gymnosperms, our analysis does not support an association between the EST-SSRs length and genome size in angiosperms. A potential association however could be masked by the multiple polyploidization events and their role in genome size diversification in angiosperms [<xref ref-type="bibr" rid="CR49">49</xref>]. Although other factors may have played a role in genome size diversity in angiosperms; transposable element (TE) expansion seems to be the most determinant factor [<xref ref-type="bibr" rid="CR50">50</xref>]. Conifer genome expansion can also be attributed to a large extent to TE expansion [<xref ref-type="bibr" rid="CR51">51</xref>,<xref ref-type="bibr" rid="CR52">52</xref>], although its role in genome size diversification is yet to be proven within the gymnosperm taxon.</p><p>Our values for percentage of perfect and compound EST-SSRs in <italic>Gnetum</italic> and <italic>Pinus</italic> agree with those reported by Victoria et al. [<xref ref-type="bibr" rid="CR46">46</xref>] and are not correlated with genome size in any of the taxa. Our data also does not support the contribution of overall EST-SSRs abundance to genome size expansion. Instead, angiosperm genera with smaller genomes compared to those in gymnosperms show, on average a significantly higher abundance (four order of magnitude higher) of EST-SSRs. The lower density of EST-SSRs in gymnosperm compared to angiosperm species is in agreement with previous reports [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR45">45</xref>,<xref ref-type="bibr" rid="CR47">47</xref>] and does not support a possible constant abundance of SSRs in the transcribed portions of the genome across species as suggested by Morgante et al. [<xref ref-type="bibr" rid="CR4">4</xref>]. Several studies have concluded that EST-SSRs abundance is inversely related to the genome size [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR37">37</xref>], while others attribute EST-SSRs abundance partly to the action of selection and the effectiveness of mechanisms for regulating slippage errors [<xref ref-type="bibr" rid="CR44">44</xref>,<xref ref-type="bibr" rid="CR53">53</xref>]. Our more extensive investigation however does not support a simple linear relationship between EST-SSR abundance and genome size. For example, two gymnosperm genera such as <italic>Gnetum</italic> and <italic>Zamia</italic> have similar or even higher frequencies of SSRs than angiosperm genera such as <italic>Citrus</italic>, which has a smaller genome size. This suggests that other factors affecting genome evolution in both taxa need to be considered to explain EST-SSR abundance diversity in the plant kingdom.</p><p>EST-SSR abundance across EST fractions also differs between gymnosperm and angiosperms. In angiosperms, EST-SSRs are significantly more abundant in the 5′UTR fraction, while in gymnosperms there is on an average a higher abundance of EST-SSRs in the 3′UTR fraction. In angiosperms, a higher density of EST-SSRs in the UTR fractions has been reported previously [<xref ref-type="bibr" rid="CR4">4</xref>,<xref ref-type="bibr" rid="CR20">20</xref>,<xref ref-type="bibr" rid="CR54">54</xref>,<xref ref-type="bibr" rid="CR55">55</xref>]; while other studies support a higher abundance in the ORF fraction [<xref ref-type="bibr" rid="CR44">44</xref>]. A higher EST-SSR abundance in the 5′UTR could be attributed to a regulatory role [<xref ref-type="bibr" rid="CR56">56</xref>,<xref ref-type="bibr" rid="CR57">57</xref>]. In <italic>Cryptomeria</italic>, a higher density of EST-SSRs in the ORF fraction has also been shown [<xref ref-type="bibr" rid="CR37">37</xref>]. However, due to the limited number of studies performed on each EST fraction separately, a generalization on the relative abundance of SSRs across those fractions warrants further investigation.</p></sec><sec id="Sec10"><title>Motif size: while dimers dominate, hexamers are more common in the gymnosperm EST sequences</title><p>Our study reveals an overall higher abundance of dimers across all three genomic fractions (with six exceptions). In an EST-SSRs analysis that included lower and upper plant species, Victoria et al. [<xref ref-type="bibr" rid="CR46">46</xref>] reported that trimers are more frequent in the majority of groups of higher plants; while individual studies in angiosperm trees have shown dimers as the most abundant motif in genera such as <italic>Populus</italic> [<xref ref-type="bibr" rid="CR17">17</xref>,<xref ref-type="bibr" rid="CR45">45</xref>] and <italic>Eucalyptus</italic> [<xref ref-type="bibr" rid="CR16">16</xref>,<xref ref-type="bibr" rid="CR34">34</xref>]. In <italic>Quercus</italic>, trimers were reported as the most abundant motif in the ORF fraction, while dimers were more frequent in the UTR fractions [<xref ref-type="bibr" rid="CR20">20</xref>]. Trimers were the most common motif in <italic>Citrus</italic> according to some studies [<xref ref-type="bibr" rid="CR19">19</xref>,<xref ref-type="bibr" rid="CR27">27</xref>] whereas Palmieri et al. [<xref ref-type="bibr" rid="CR28">28</xref>] described dimers as the most abundant motifs in the same genus. In gymnosperms, a higher abundance of EST-SSR dimers has previously reported in <italic>Pinus</italic>, <italic>Picea</italic>, and <italic>Ginkgo</italic> [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR24">24</xref>,<xref ref-type="bibr" rid="CR45">45</xref>,<xref ref-type="bibr" rid="CR46">46</xref>]; while Yan et al. [<xref ref-type="bibr" rid="CR47">47</xref>] reported trimers as the most abundant in <italic>Pinus</italic>. Similarly, trimers were the most frequent in the ORF in <italic>Pinus</italic>, while dimers were the most common in the 3′UTR fraction [<xref ref-type="bibr" rid="CR43">43</xref>]. In agreement with our study, increased representation of trimers in the ORF was shown before in <italic>Cryptomeria</italic> [<xref ref-type="bibr" rid="CR37">37</xref>]. Trimers and hexamers were reported to be more common in the ORF compared to the UTRs in <italic>Quercus</italic> [<xref ref-type="bibr" rid="CR20">20</xref>] and <italic>Cryptomeria</italic> [<xref ref-type="bibr" rid="CR37">37</xref>]. Similarly, we also observe trimers and hexamers as common in both taxa with reference to ORF.</p><p>Our data shows that despite the fact that dimers are the most frequent repeats in majority of the genera in all the three genomic fractions, the proportion of dimers to trimers (dimers/trimers) decreases significantly in the ORF fraction. Predominance of trimers in the coding regions was reported previously in animals and plants [<xref ref-type="bibr" rid="CR58">58</xref>]. ORF enrichment in trimers is expected considering that dimers alter the frameshift (i.e., nucleotide triplet or codon is the unit for translation), which should be avoided if the correct translation of the ORF into a protein should be maintained. Presence of SSR dimers in the ORF fraction can potentially affect gene amino acid sequences consequently altering their function due to frameshift mutations, while SSRs in the UTR fractions will affect transcription, translation or splicing of gene products [<xref ref-type="bibr" rid="CR8">8</xref>]. Moreover, if the number of dimer repeats is divisible by three, it will result in the alternation of two amino acids (e.g., (AT)<sub>6</sub>: ATA-TAT-ATA-TAT: Ile-Tyr-Ile-Tyr), thus potentially leaving the reading frame un-altered, as previously suggested by Kantety et al. in cereal species [<xref ref-type="bibr" rid="CR59">59</xref>].</p></sec><sec id="Sec11"><title>Dimer/Trimer nucleotide composition: AT-rich motifs are common in gymnosperms</title><p>Our study reveals a low abundance of AC/GT motif in all studied genera. Unlike as in mammals, the AC/GT motif is known to occur at low frequency in plants [<xref ref-type="bibr" rid="CR4">4</xref>,<xref ref-type="bibr" rid="CR60">60</xref>]. The difference between plants and mammals has been attributed to differences in methylation patterns. AC/GT abundance in animals was suggested as the result of transition of methylated C residue to T (CG/CG → AC/GT), while the absence of a C-hotspot in plants could have prevented the predominance of AC/GT repeats [<xref ref-type="bibr" rid="CR4">4</xref>,<xref ref-type="bibr" rid="CR60">60</xref>]. In agreement with previous works, the CG/CG motif (which creates CpG islands acting as regulatory elements through methylation) is almost absent in all our studied genera across all three genomic fractions. There is however an overall predominance of AG/CT (all three genomic fractions) and AAG/CTT (5′UTR and ORF) motifs in angiosperms, which are also target for methylation in plants [<xref ref-type="bibr" rid="CR61">61</xref>]. In gymnosperms, AG/CT is also the most abundant motif in the 5′UTR and ORF fractions (with few genera where AT/AT is more abundant). In the 3′UTR regions, there is predominance of AT/AT (gymnosperms) and AAT/ATT (both taxa), which are not the target for methylation [<xref ref-type="bibr" rid="CR62">62</xref>]. An increased content in A + T nucleotides in the 3′UTR fraction has been reported before in vertebrates [<xref ref-type="bibr" rid="CR63">63</xref>], mammals [<xref ref-type="bibr" rid="CR64">64</xref>], yeast [<xref ref-type="bibr" rid="CR65">65</xref>] and <italic>Arabidopsis</italic> [<xref ref-type="bibr" rid="CR4">4</xref>], which seems to be related to the UTR processing signal composition.</p><p>An overall predominance of AG/CT and AT/AT dimer motifs in EST sequences was supported by previous studies in angiosperms [<xref ref-type="bibr" rid="CR20">20</xref>,<xref ref-type="bibr" rid="CR34">34</xref>,<xref ref-type="bibr" rid="CR47">47</xref>] and gymnosperms [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR46">46</xref>,<xref ref-type="bibr" rid="CR47">47</xref>]. In angiosperms, AG/CT was reported as the most abundant in <italic>Eucalyptus</italic> [<xref ref-type="bibr" rid="CR16">16</xref>,<xref ref-type="bibr" rid="CR34">34</xref>,<xref ref-type="bibr" rid="CR47">47</xref>], <italic>Citrus</italic> [<xref ref-type="bibr" rid="CR26">26</xref>-<xref ref-type="bibr" rid="CR28">28</xref>] and <italic>Populus</italic> [<xref ref-type="bibr" rid="CR45">45</xref>,<xref ref-type="bibr" rid="CR47">47</xref>,<xref ref-type="bibr" rid="CR66">66</xref>]. In <italic>Quercus</italic>, AC/GT was shown as the most abundant dimer [<xref ref-type="bibr" rid="CR20">20</xref>]. In agreement with an overall enrichment in AT/AT motif gymnosperms (specially in the 3′UTR fraction), other studies have also reported AT/AT as the most frequent dimer in <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR43">43</xref>,<xref ref-type="bibr" rid="CR45">45</xref>-<xref ref-type="bibr" rid="CR47">47</xref>], <italic>Picea</italic> [<xref ref-type="bibr" rid="CR5">5</xref>,<xref ref-type="bibr" rid="CR24">24</xref>,<xref ref-type="bibr" rid="CR45">45</xref>] and <italic>Ginkgo</italic> [<xref ref-type="bibr" rid="CR45">45</xref>]. Berube et al. [<xref ref-type="bibr" rid="CR5">5</xref>] also demonstrate a similar finding with a higher abundance of AT/AT dimers in the 3′ sequenced ESTs in <italic>Pinus</italic> and <italic>Picea</italic>. The motif AG/CT was shown to be the most abundant in <italic>Cycas</italic> [<xref ref-type="bibr" rid="CR45">45</xref>] and <italic>Gnetum</italic> [<xref ref-type="bibr" rid="CR46">46</xref>]; the latter being also supported by our data. In <italic>Cryptomeria</italic>, AT/AT was shown to be the most abundant in the UTR fractions, while AG/CT was the most abundant in the ORF [<xref ref-type="bibr" rid="CR37">37</xref>].</p><p>In agreement with our results, previous studies also support a higher abundance of the AAG/CTT motif in angiosperms. In gymnosperms, our study reveals predominance of the AAT/ATT motif in the 3′UTR fraction; moreover, trimer predominance in the other two fractions seems genus dependent. In angiosperms, AAG/CTT was ranked first in frequency in <italic>Eucalyptus</italic> [<xref ref-type="bibr" rid="CR16">16</xref>,<xref ref-type="bibr" rid="CR47">47</xref>], <italic>Citrus</italic> [<xref ref-type="bibr" rid="CR26">26</xref>-<xref ref-type="bibr" rid="CR28">28</xref>] and <italic>Poplar</italic> [<xref ref-type="bibr" rid="CR45">45</xref>,<xref ref-type="bibr" rid="CR47">47</xref>,<xref ref-type="bibr" rid="CR66">66</xref>]. In <italic>Eucalyptus</italic>, other studies reported AGG/CCT [<xref ref-type="bibr" rid="CR34">34</xref>] as the most abundant trimer motifs. In <italic>Quercus</italic>, AAT/ATT was shown to be the most common trimer motif [<xref ref-type="bibr" rid="CR20">20</xref>]. In gymnosperms, AAT/ATT was shown to be the most abundant trimer in <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR45">45</xref>]. Other studies report AAG/CTT as the most common trimer in <italic>Pinus</italic> [<xref ref-type="bibr" rid="CR43">43</xref>,<xref ref-type="bibr" rid="CR47">47</xref>], <italic>Picea</italic> [<xref ref-type="bibr" rid="CR24">24</xref>] and <italic>Cycas</italic> [<xref ref-type="bibr" rid="CR45">45</xref>]. Also ACG/CGT was presented as the most abundant trimer in <italic>Pinus</italic> and <italic>Picea</italic> [<xref ref-type="bibr" rid="CR5">5</xref>]. In <italic>Cryptomeria</italic>, our trimer motif dominance across the EST fractions corresponds with that reported by [<xref ref-type="bibr" rid="CR37">37</xref>] (i.e., AGG, 5′UTR; AAG, ORF; AAT, 3′UTR).</p></sec></sec><sec id="Sec12" sec-type="conclusion"><title>Conclusions</title><p>Our EST-SSR comparative analysis in eight angiosperm genera and seven gymnosperm genera has revealed interesting differential features among both taxa. While dimers dominate, hexamers are more common in the gymnosperm EST sequences than the angiosperms, and AT-rich motifs among the dimers are the most abundant in gymnosperms. These results provide the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.</p></sec><sec id="Sec13" sec-type="materials|methods"><title>Methods</title><sec id="Sec14"><title>Genomic resources and bioinformatics</title><p>Description of the EST resources analysed in this study is represented in Additional file <xref rid="MOESM1" ref-type="media">1</xref>: Table S1. ESTs from 40 species from eight genera in angiosperms and 17 species from seven genera in gymnosperms were considered for the EST-SSR analysis in this study. EST sequences of the selected species were retrieved from the dbEST database of the NCBI. The criterion for species selection, analysis and the results presented in this work was based on the availability of the sequence data in the EST databank. To remove redundancy, EST sequences were assembled into contigs and singlets, species-wise, using the sequence assembly program CAP3 with its default setting [<xref ref-type="bibr" rid="CR67">67</xref>]. For each genus, the species-wise assembled contigs and singlets were pooled together and the sequence redundancy at genus level was removed using CD-HIT [<xref ref-type="bibr" rid="CR68">68</xref>] with a cut off value of 90% (ensuring 90% sequence identity). The ORF detection is based on the same principle as the generic eukaryotic gene prediction program used for searching the coding regions from a given nucleotide sequence. Based on the coding potential profiles trained from Angiosperms (Arabidopsis) and Gymnosperms (Norway spruce) protein coding genes, we used AUGUSTUS [<xref ref-type="bibr" rid="CR69">69</xref>] to distinguish the coding and the UTR regions, and the coding direction of a given transcript sequence. The main feature in detecting ORF on transcript sequence is that the ORF is located in an intron-less, single exon coding region. However, due to the unexpected higher coding potential in the UTR region, one transcript might contain more than one ORF. In such cases, we have selected the longest ORF as the true coding region and the adjacent nucleotide sequence as the UTR region. Thus the longest ORF was selected from each of the EST sequence from the genus-wise collection of sequences and the 5′UTR and 3′UTR fractions of the sequence were assigned based on the coordinate direction of the ORF. Three groups of sequences were thus created with reference to each genus, namely 5′UTR, ORF and 3′UTR. SSRLocatorI v.1 [<xref ref-type="bibr" rid="CR70">70</xref>] was used to retrieve the SSR information at the genus level from each of the three groups derived. SSRLocator was used with the following settings, SSR repeat motifs and number of repeats shown respectively, dimer-10, trimer-7, tetramer-5, pentamer-4, hexamer-4, heptamer-3, octamer-3, nonamer-3, decamer-2. The space between compound SSRs was set to 100 bp. Thus repetitions that occurred in the adjacent regions lower than 100 bp, were considered as compound SSRs. These settings are in compliance with the search parameters for repetitive elements in class I (≥20 bp) described as more efficient molecular markers followed by Temnykh et al. [<xref ref-type="bibr" rid="CR71">71</xref>]. Mononucleotide repeats can be difficult to accurately assay and are generally eliminated from the SSR analysis [<xref ref-type="bibr" rid="CR45">45</xref>,<xref ref-type="bibr" rid="CR72">72</xref>-<xref ref-type="bibr" rid="CR74">74</xref>] and consequently these repeats were excluded from this study. Therefore, in this article we discuss the occurrence of microsatellites specific to 5′UTR, ORF or 3′UTR fractions of the ESTs. While recording the count of a particular repeat motif, circular permutations and/or reverse complements of each other were clustered together (e.g. AC = GT = CA = TG, ACG = CGA = GCA = TGC = GCT = CGT = AGC = TCG = CAG = GTC = TGC = GAC and AAC = ACA = CAA = TTG = TGT = GTT) [<xref ref-type="bibr" rid="CR5">5</xref>]. We also screened for perfect and compound SSRs. Perfect SSRs are the repeat motifs that are simple tandem sequence, without any interruptions within the repeat (e.g. TATATATATATATATA or [TA]n); while a compound SSR consists of the sequence containing two adjacent distinct SSRs separated by none to any number of base pairs (e.g. TATATATATAGTGTGTGTGT or [TA]n-[GT]n).</p></sec><sec id="Sec15"><title>Statistical analysis</title><p>A non-parametric Tukey HSD test was carried to compare the means of EST-SSRs length between all categories. We carried out a 2 × 3 contingence <italic>χ</italic>2 test for heterogeneity of microsatellite counts (motif counts/total EST-fraction in Mbp) among the three EST genomic regions. Statistical analyses were all carried out using the R software package [<xref ref-type="bibr" rid="CR75">75</xref>].</p></sec></sec></body><back><app-group><app id="App1"><sec id="Sec16"><title>Additional file</title><p><media position="anchor" xlink:href="12870_2014_220_MOESM1_ESM.docx" id="MOESM1"><label>Additional file 1: Table S1.</label><caption><p>EST database size, number of nucleotides used for SSR analysis and counts of repeat motifs per Mbp in each fraction: (a) Angiosperms and (b) Gymnosperms. <bold>Table S2</bold> SSR motif complexity in: (a) Angiosperms and (b) Gymnosperms.</p></caption></media></p></sec></app></app-group><glossary><title>Abbreviations</title><def-list><def-list><def-item><term>SSR</term><def><p>Simple sequence repeats</p></def></def-item><def-item><term>EST</term><def><p>Expressed sequence tags</p></def></def-item><def-item><term>UTR</term><def><p>Untranslated region</p></def></def-item><def-item><term>ORF</term><def><p>Open reading frame</p></def></def-item><def-item><term>Myr</term><def><p>Million years</p></def></def-item><def-item><term>TE</term><def><p>Transposable element</p></def></def-item></def-list></def-list></glossary><fn-group><fn><p><bold>Competing interests</bold></p><p>The authors declare that they have no competing interests.</p></fn><fn><p><bold>Authors’ contributions</bold></p><p>SSR was involved in the design of the study and manuscript writing. SSR performed the bioinformatics analysis. MRGG was involved in the design of the study and manuscript writing. MRGG was responsible of the statistical analyses. YCL, AZ and YVdP contributed to the bioinformatics work. All authors read and approved the final manuscript.</p></fn></fn-group><ack><title>Acknowledgements</title><p>SSR salary was supported by the Faculty of Forest Science, SLU, Umeå, Sweden. Travel cost for SSR was covered by the travel grant from FORMAS. YCL was supported by the Wallenbergs Stiftelse, Norway spruce genome project. YCL and YVdP were supported by Ghent University Multidisciplinary Research Partnerships “Bioinformatics: from nucleotides to networks”. 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