Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction
Identifieur interne : 001085 ( Main/Exploration ); précédent : 001084; suivant : 001086Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction
Auteurs : Hyungtaek Jung [Australie] ; Byung-Ha Yoon [Corée du Sud] ; Woo-Jin Kim ; Dong-Wook Kim ; David A. Hurwood ; Russell E. Lyons ; Krishna R. Salin ; Heui-Soo Kim ; Ilseon Baek ; Vincent Chand ; Peter B. MatherSource :
- International Journal of Molecular Sciences [ 1422-0067 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical : Genetic Markers.
- genetics : Decapoda, Reproduction.
- metabolism : Decapoda.
- methods : Molecular Sequence Annotation, Sequence Analysis, RNA.
- physiology : Decapoda.
- Algorithms, Animals, Genome, Polymorphism, Single Nucleotide, Transcriptome.
Abstract
The giant freshwater prawn,
Url:
DOI: 10.3390/ijms17050690
PubMed: 27164098
PubMed Central: 4881516
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Optimizing Hybrid <italic>de Novo</italic> Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (<italic>Macrobrachium rosenbergii</italic>): The Identification of Genes and Markers Associated with Reproduction</title><author><name sortKey="Jung, Hyungtaek" sort="Jung, Hyungtaek" uniqKey="Jung H" first="Hyungtaek" last="Jung">Hyungtaek Jung</name><affiliation wicri:level="1"><nlm:aff id="af1-ijms-17-00690">Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000</wicri:regionArea><wicri:noRegion>Queensland 4000</wicri:noRegion></affiliation></author><author><name sortKey="Yoon, Byung Ha" sort="Yoon, Byung Ha" uniqKey="Yoon B" first="Byung-Ha" last="Yoon">Byung-Ha Yoon</name><affiliation><nlm:aff id="af2-ijms-17-00690">Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305806, Korea;<email>cogate@kribb.re.kr</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-17-00690">Department of Bioinformatics, University of Science and Technology, Daejeon 305333, Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Bioinformatics, University of Science and Technology, Daejeon 305333</wicri:regionArea><wicri:noRegion>Daejeon 305333</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Woo Jin" sort="Kim, Woo Jin" uniqKey="Kim W" first="Woo-Jin" last="Kim">Woo-Jin Kim</name><affiliation><nlm:aff id="af4-ijms-17-00690">Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea;<email>wj2464@korea.kr</email></nlm:aff></affiliation></author><author><name sortKey="Kim, Dong Wook" sort="Kim, Dong Wook" uniqKey="Kim D" first="Dong-Wook" last="Kim">Dong-Wook Kim</name><affiliation><nlm:aff id="af5-ijms-17-00690">All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302729, Korea;<email>kdw9017@naver.com</email></nlm:aff></affiliation></author><author><name sortKey="Hurwood, David A" sort="Hurwood, David A" uniqKey="Hurwood D" first="David A." last="Hurwood">David A. Hurwood</name><affiliation><nlm:aff id="af6-ijms-17-00690">Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia;<email>d.hurwood@qut.edu.au</email> (D.A.H.);<email>v.chand@qut.edu.au</email> (V.C.);<email>p.mather@qut.edu.au</email> (P.B.M.)</nlm:aff></affiliation></author><author><name sortKey="Lyons, Russell E" sort="Lyons, Russell E" uniqKey="Lyons R" first="Russell E." last="Lyons">Russell E. Lyons</name><affiliation><nlm:aff id="af7-ijms-17-00690">School of Veterinary Science, University of Queensland, Queensland 4067, Australia;<email>r.lyons2@uq.edu.au</email></nlm:aff></affiliation></author><author><name sortKey="Salin, Krishna R" sort="Salin, Krishna R" uniqKey="Salin K" first="Krishna R." last="Salin">Krishna R. Salin</name><affiliation><nlm:aff id="af8-ijms-17-00690">School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120, Thailand;<email>salinkr@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Kim, Heui Soo" sort="Kim, Heui Soo" uniqKey="Kim H" first="Heui-Soo" last="Kim">Heui-Soo Kim</name><affiliation><nlm:aff id="af9-ijms-17-00690">Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735, Korea;<email>khs307@pusan.ac.kr</email></nlm:aff></affiliation></author><author><name sortKey="Baek, Ilseon" sort="Baek, Ilseon" uniqKey="Baek I" first="Ilseon" last="Baek">Ilseon Baek</name><affiliation><nlm:aff id="af10-ijms-17-00690">Division of Marine Technology, Chonnam National University, Yeosu 550250, Korea;<email>chitago@naver.com</email></nlm:aff></affiliation></author><author><name sortKey="Chand, Vincent" sort="Chand, Vincent" uniqKey="Chand V" first="Vincent" last="Chand">Vincent Chand</name><affiliation><nlm:aff id="af6-ijms-17-00690">Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia;<email>d.hurwood@qut.edu.au</email> (D.A.H.);<email>v.chand@qut.edu.au</email> (V.C.);<email>p.mather@qut.edu.au</email> (P.B.M.)</nlm:aff></affiliation></author><author><name sortKey="Mather, Peter B" sort="Mather, Peter B" uniqKey="Mather P" first="Peter B." last="Mather">Peter B. Mather</name><affiliation><nlm:aff id="af6-ijms-17-00690">Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia;<email>d.hurwood@qut.edu.au</email> (D.A.H.);<email>v.chand@qut.edu.au</email> (V.C.);<email>p.mather@qut.edu.au</email> (P.B.M.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27164098</idno><idno type="pmc">4881516</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881516</idno><idno type="RBID">PMC:4881516</idno><idno type="doi">10.3390/ijms17050690</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000097</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000097</idno><idno type="wicri:Area/Pmc/Curation">000097</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000097</idno><idno type="wicri:Area/Pmc/Checkpoint">000A51</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000A51</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:27164098</idno><idno type="wicri:Area/PubMed/Corpus">001127</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001127</idno><idno type="wicri:Area/PubMed/Curation">001127</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001127</idno><idno type="wicri:Area/PubMed/Checkpoint">000F56</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000F56</idno><idno type="wicri:Area/Ncbi/Merge">001618</idno><idno type="wicri:Area/Ncbi/Curation">001618</idno><idno type="wicri:Area/Ncbi/Checkpoint">001618</idno><idno type="wicri:Area/Main/Merge">001089</idno><idno type="wicri:Area/Main/Curation">001085</idno><idno type="wicri:Area/Main/Exploration">001085</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Optimizing Hybrid <italic>de Novo</italic> Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (<italic>Macrobrachium rosenbergii</italic>): The Identification of Genes and Markers Associated with Reproduction</title><author><name sortKey="Jung, Hyungtaek" sort="Jung, Hyungtaek" uniqKey="Jung H" first="Hyungtaek" last="Jung">Hyungtaek Jung</name><affiliation wicri:level="1"><nlm:aff id="af1-ijms-17-00690">Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000</wicri:regionArea><wicri:noRegion>Queensland 4000</wicri:noRegion></affiliation></author><author><name sortKey="Yoon, Byung Ha" sort="Yoon, Byung Ha" uniqKey="Yoon B" first="Byung-Ha" last="Yoon">Byung-Ha Yoon</name><affiliation><nlm:aff id="af2-ijms-17-00690">Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305806, Korea;<email>cogate@kribb.re.kr</email></nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-ijms-17-00690">Department of Bioinformatics, University of Science and Technology, Daejeon 305333, Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Bioinformatics, University of Science and Technology, Daejeon 305333</wicri:regionArea><wicri:noRegion>Daejeon 305333</wicri:noRegion></affiliation></author><author><name sortKey="Kim, Woo Jin" sort="Kim, Woo Jin" uniqKey="Kim W" first="Woo-Jin" last="Kim">Woo-Jin Kim</name><affiliation><nlm:aff id="af4-ijms-17-00690">Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea;<email>wj2464@korea.kr</email></nlm:aff></affiliation></author><author><name sortKey="Kim, Dong Wook" sort="Kim, Dong Wook" uniqKey="Kim D" first="Dong-Wook" last="Kim">Dong-Wook Kim</name><affiliation><nlm:aff id="af5-ijms-17-00690">All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302729, Korea;<email>kdw9017@naver.com</email></nlm:aff></affiliation></author><author><name sortKey="Hurwood, David A" sort="Hurwood, David A" uniqKey="Hurwood D" first="David A." last="Hurwood">David A. Hurwood</name><affiliation><nlm:aff id="af6-ijms-17-00690">Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia;<email>d.hurwood@qut.edu.au</email> (D.A.H.);<email>v.chand@qut.edu.au</email> (V.C.);<email>p.mather@qut.edu.au</email> (P.B.M.)</nlm:aff></affiliation></author><author><name sortKey="Lyons, Russell E" sort="Lyons, Russell E" uniqKey="Lyons R" first="Russell E." last="Lyons">Russell E. Lyons</name><affiliation><nlm:aff id="af7-ijms-17-00690">School of Veterinary Science, University of Queensland, Queensland 4067, Australia;<email>r.lyons2@uq.edu.au</email></nlm:aff></affiliation></author><author><name sortKey="Salin, Krishna R" sort="Salin, Krishna R" uniqKey="Salin K" first="Krishna R." last="Salin">Krishna R. Salin</name><affiliation><nlm:aff id="af8-ijms-17-00690">School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120, Thailand;<email>salinkr@gmail.com</email></nlm:aff></affiliation></author><author><name sortKey="Kim, Heui Soo" sort="Kim, Heui Soo" uniqKey="Kim H" first="Heui-Soo" last="Kim">Heui-Soo Kim</name><affiliation><nlm:aff id="af9-ijms-17-00690">Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735, Korea;<email>khs307@pusan.ac.kr</email></nlm:aff></affiliation></author><author><name sortKey="Baek, Ilseon" sort="Baek, Ilseon" uniqKey="Baek I" first="Ilseon" last="Baek">Ilseon Baek</name><affiliation><nlm:aff id="af10-ijms-17-00690">Division of Marine Technology, Chonnam National University, Yeosu 550250, Korea;<email>chitago@naver.com</email></nlm:aff></affiliation></author><author><name sortKey="Chand, Vincent" sort="Chand, Vincent" uniqKey="Chand V" first="Vincent" last="Chand">Vincent Chand</name><affiliation><nlm:aff id="af6-ijms-17-00690">Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia;<email>d.hurwood@qut.edu.au</email> (D.A.H.);<email>v.chand@qut.edu.au</email> (V.C.);<email>p.mather@qut.edu.au</email> (P.B.M.)</nlm:aff></affiliation></author><author><name sortKey="Mather, Peter B" sort="Mather, Peter B" uniqKey="Mather P" first="Peter B." last="Mather">Peter B. Mather</name><affiliation><nlm:aff id="af6-ijms-17-00690">Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia;<email>d.hurwood@qut.edu.au</email> (D.A.H.);<email>v.chand@qut.edu.au</email> (V.C.);<email>p.mather@qut.edu.au</email> (P.B.M.)</nlm:aff></affiliation></author></analytic><series><title level="j">International Journal of Molecular Sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Decapoda (genetics)</term><term>Decapoda (metabolism)</term><term>Decapoda (physiology)</term><term>Genetic Markers</term><term>Genome</term><term>Molecular Sequence Annotation (methods)</term><term>Polymorphism, Single Nucleotide</term><term>Reproduction (genetics)</term><term>Sequence Analysis, RNA (methods)</term><term>Transcriptome</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ARN ()</term><term>Animaux</term><term>Annotation de séquence moléculaire ()</term><term>Génome</term><term>Marqueurs génétiques</term><term>Polymorphisme de nucléotide simple</term><term>Reproduction (génétique)</term><term>Transcriptome</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Decapoda</term><term>Reproduction</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Reproduction</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Decapoda</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Molecular Sequence Annotation</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Decapoda</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Genome</term><term>Polymorphism, Single Nucleotide</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ARN</term><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Génome</term><term>Marqueurs génétiques</term><term>Polymorphisme de nucléotide simple</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The giant freshwater prawn, <italic>Macrobrachium rosenbergii</italic>, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the <italic>M. rosenbergii</italic> sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from <italic>M. rosenbergii</italic> applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple <italic>k</italic>-mer methods respectively, were used to analyse the data. The influence of multiple <italic>k</italic>-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, <italic>de novo</italic> assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in <italic>M. rosenbergii</italic>, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on <italic>M</italic>. <italic>rosenbergii</italic> and can be applied more widely on other freshwater prawn species in the genus <italic>Macrobrachium</italic>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jung, H" uniqKey="Jung H">H. Jung</name></author><author><name sortKey="Lyons, R E" uniqKey="Lyons R">R.E. Lyons</name></author><author><name sortKey="Hurwood, D A" uniqKey="Hurwood D">D.A. Hurwood</name></author><author><name sortKey="Mather, P B" uniqKey="Mather P">P.B. Mather</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y. 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Durbin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>Corée du Sud</li></country></list><tree><noCountry><name sortKey="Baek, Ilseon" sort="Baek, Ilseon" uniqKey="Baek I" first="Ilseon" last="Baek">Ilseon Baek</name><name sortKey="Chand, Vincent" sort="Chand, Vincent" uniqKey="Chand V" first="Vincent" last="Chand">Vincent Chand</name><name sortKey="Hurwood, David A" sort="Hurwood, David A" uniqKey="Hurwood D" first="David A." last="Hurwood">David A. Hurwood</name><name sortKey="Kim, Dong Wook" sort="Kim, Dong Wook" uniqKey="Kim D" first="Dong-Wook" last="Kim">Dong-Wook Kim</name><name sortKey="Kim, Heui Soo" sort="Kim, Heui Soo" uniqKey="Kim H" first="Heui-Soo" last="Kim">Heui-Soo Kim</name><name sortKey="Kim, Woo Jin" sort="Kim, Woo Jin" uniqKey="Kim W" first="Woo-Jin" last="Kim">Woo-Jin Kim</name><name sortKey="Lyons, Russell E" sort="Lyons, Russell E" uniqKey="Lyons R" first="Russell E." last="Lyons">Russell E. Lyons</name><name sortKey="Mather, Peter B" sort="Mather, Peter B" uniqKey="Mather P" first="Peter B." last="Mather">Peter B. Mather</name><name sortKey="Salin, Krishna R" sort="Salin, Krishna R" uniqKey="Salin K" first="Krishna R." last="Salin">Krishna R. Salin</name></noCountry><country name="Australie"><noRegion><name sortKey="Jung, Hyungtaek" sort="Jung, Hyungtaek" uniqKey="Jung H" first="Hyungtaek" last="Jung">Hyungtaek Jung</name></noRegion></country><country name="Corée du Sud"><noRegion><name sortKey="Yoon, Byung Ha" sort="Yoon, Byung Ha" uniqKey="Yoon B" first="Byung-Ha" last="Yoon">Byung-Ha Yoon</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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