Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes.
Identifieur interne : 002339 ( PubMed/Curation ); précédent : 002338; suivant : 002340Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes.
Auteurs : Jun Zou [République populaire de Chine] ; Dandan Hu [République populaire de Chine] ; Peifa Liu [République populaire de Chine] ; Harsh Raman [Australie] ; Zhongsong Liu [République populaire de Chine] ; Xianjun Liu [République populaire de Chine] ; Isobel A P. Parkin [Canada] ; Boulos Chalhoub [France] ; Jinling Meng [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2016.
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Abstract
There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, A(r)A(r); B. nigra, B(ni)B(ni); B. oleracea, C(o)C(o)) and the derived allotetraploid species (i.e.: B. juncea, A(j)A(j)B(j)B(j); B. napus, A(n)A(n)C(n)C(n); B. carinata, B(c)B(c)C(c)C(c)). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).
DOI: 10.1186/s12864-015-2343-1
PubMed: 26728943
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes.</title><author><name sortKey="Zou, Jun" sort="Zou, Jun" uniqKey="Zou J" first="Jun" last="Zou">Jun Zou</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. daist82@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea></affiliation></author><author><name sortKey="Hu, Dandan" sort="Hu, Dandan" uniqKey="Hu D" first="Dandan" last="Hu">Dandan Hu</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. hudandan@webmail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Peifa" sort="Liu, Peifa" uniqKey="Liu P" first="Peifa" last="Liu">Peifa Liu</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. 394447475@qq.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. 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Parkin</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea></affiliation></author><author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name><affiliation wicri:level="1"><nlm:affiliation>Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex, France. chalhoub@evry.inra.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex</wicri:regionArea></affiliation></author><author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. jmeng@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. 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R. China, Huazhong Agricultural University, Wuhan, 430070, China. daist82@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea></affiliation></author><author><name sortKey="Hu, Dandan" sort="Hu, Dandan" uniqKey="Hu D" first="Dandan" last="Hu">Dandan Hu</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. hudandan@webmail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Peifa" sort="Liu, Peifa" uniqKey="Liu P" first="Peifa" last="Liu">Peifa Liu</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. 394447475@qq.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea></affiliation></author><author><name sortKey="Raman, Harsh" sort="Raman, Harsh" uniqKey="Raman H" first="Harsh" last="Raman">Harsh Raman</name><affiliation wicri:level="1"><nlm:affiliation>Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia. harsh.raman@dpi.nsw.gov.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Zhongsong" sort="Liu, Zhongsong" uniqKey="Liu Z" first="Zhongsong" last="Liu">Zhongsong Liu</name><affiliation wicri:level="1"><nlm:affiliation>Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China. zsliu48@sohu.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Xianjun" sort="Liu, Xianjun" uniqKey="Liu X" first="Xianjun" last="Liu">Xianjun Liu</name><affiliation wicri:level="1"><nlm:affiliation>Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China. lxxjjz@sina.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128</wicri:regionArea></affiliation></author><author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A P" last="Parkin">Isobel A P. Parkin</name><affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2</wicri:regionArea></affiliation></author><author><name sortKey="Chalhoub, Boulos" sort="Chalhoub, Boulos" uniqKey="Chalhoub B" first="Boulos" last="Chalhoub">Boulos Chalhoub</name><affiliation wicri:level="1"><nlm:affiliation>Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex, France. chalhoub@evry.inra.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex</wicri:regionArea></affiliation></author><author><name sortKey="Meng, Jinling" sort="Meng, Jinling" uniqKey="Meng J" first="Jinling" last="Meng">Jinling Meng</name><affiliation wicri:level="1"><nlm:affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. jmeng@mail.hzau.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Brassica napus (genetics)</term><term>Chromosome Mapping</term><term>Diploidy</term><term>Genetic Linkage</term><term>Genome, Plant (genetics)</term><term>Genotype</term><term>Microsatellite Repeats (genetics)</term><term>Mustard Plant (genetics)</term><term>Quantitative Trait Loci (genetics)</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Arabidopsis (génétique)</term><term>Brassica napus (génétique)</term><term>Cartographie chromosomique</term><term>Diploïdie</term><term>Génome végétal (génétique)</term><term>Génotype</term><term>Liaison génétique</term><term>Locus de caractère quantitatif (génétique)</term><term>Moutarde (plante) (génétique)</term><term>Répétitions microsatellites (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Brassica napus</term><term>Genome, Plant</term><term>Microsatellite Repeats</term><term>Mustard Plant</term><term>Quantitative Trait Loci</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Brassica napus</term><term>Génome végétal</term><term>Locus de caractère quantitatif</term><term>Moutarde (plante)</term><term>Répétitions microsatellites</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Diploidy</term><term>Genetic Linkage</term><term>Genotype</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cartographie chromosomique</term><term>Diploïdie</term><term>Génotype</term><term>Liaison génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, A(r)A(r); B. nigra, B(ni)B(ni); B. oleracea, C(o)C(o)) and the derived allotetraploid species (i.e.: B. juncea, A(j)A(j)B(j)B(j); B. napus, A(n)A(n)C(n)C(n); B. carinata, B(c)B(c)C(c)C(c)). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26728943</PMID><DateCreated><Year>2016</Year><Month>01</Month><Day>05</Day></DateCreated><DateCompleted><Year>2016</Year><Month>09</Month><Day>28</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><PubDate><Year>2016</Year><Month>Jan</Month><Day>05</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes.</ArticleTitle><Pagination><MedlinePgn>18</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-2343-1</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, A(r)A(r); B. nigra, B(ni)B(ni); B. oleracea, C(o)C(o)) and the derived allotetraploid species (i.e.: B. juncea, A(j)A(j)B(j)B(j); B. napus, A(n)A(n)C(n)C(n); B. carinata, B(c)B(c)C(c)C(c)). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A dense genetic linkage map of B. juncea was constructed using an F2 population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of Arabidopsis thaliana, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of B. rapa and B. napus, and marker sequence anchored on the genetic map of B. juncea, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying Brassica species showed that the highest genetic distance were estimated when comparing A(j)-A(n) than between A(n)-A(r) and A(j)-A(r) subgenome pairs.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The development of the dense genetic linkage map of B. juncea with informative DArT-seq marker sequences and availability of the reference sequences of the A(r), and A(n)C(n) genomes allowed us to compare the A subgenome structure of B. juncea (A(j)) . Our results suggest that strong co-linearity exists among the three A Brassica genomes (A(r), A(n) and A(j)) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying Brassica species support the idea that B. juncea has distinct genomic diversity, and/or evolved from a different A genome progenitor of B. napus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zou</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. daist82@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Dandan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. hudandan@webmail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Peifa</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. 394447475@qq.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Raman</LastName><ForeName>Harsh</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Graham Centre for Agricultural Innovation (an alliance between the Charles Sturt University and NSW Department of Primary Industries), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia. harsh.raman@dpi.nsw.gov.au.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Zhongsong</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China. zsliu48@sohu.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Xianjun</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Oilseed Crops Institute, Hunan Agricultural University, Changsha, 410128, China. lxxjjz@sina.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parkin</LastName><ForeName>Isobel A P</ForeName><Initials>IA</Initials><AffiliationInfo><Affiliation>Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. isobel.parkin@agr.gc.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chalhoub</LastName><ForeName>Boulos</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Unité de Recherche en Génomique Végétale (Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essonnes), Organization and Evolution of Plant Genomes, 91057, Evry cedex, France. chalhoub@evry.inra.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Jinling</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture P. R. China, Huazhong Agricultural University, Wuhan, 430070, China. jmeng@mail.hzau.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>01</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2014;9(7):e101673</RefSource><PMID Version="1">25006804</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Mol Evol. 1983;19(2):153-70</RefSource><PMID Version="1">6571220</PMID></CommentsCorrections><CommentsCorrections 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DNA</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4700566</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>04</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>12</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>1</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>1</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26728943</ArticleId><ArticleId IdType="doi">10.1186/s12864-015-2343-1</ArticleId><ArticleId IdType="pii">10.1186/s12864-015-2343-1</ArticleId><ArticleId 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