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 : 000F56 ( PubMed/Checkpoint ); précédent : 000F55; suivant : 000F57Optimizing 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 [Corée du Sud] ; Dong-Wook Kim [Corée du Sud] ; David A. Hurwood [Australie] ; Russell E. Lyons [Australie] ; Krishna R. Salin [Thaïlande] ; Heui-Soo Kim [Corée du Sud] ; Ilseon Baek [Corée du Sud] ; Vincent Chand [Australie] ; Peter B. Mather [Australie]Source :
- 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, Macrobrachium rosenbergii, 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 M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii 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 k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo 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 M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.
DOI: 10.3390/ijms17050690
PubMed: 27164098
Affiliations:
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Hurwood</name><affiliation wicri:level="1"><nlm:affiliation>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. d.hurwood@qut.edu.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000</wicri:regionArea><wicri:noRegion>Queensland 4000</wicri:noRegion></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 wicri:level="1"><nlm:affiliation>School of Veterinary Science, University of Queensland, Queensland 4067, Australia. r.lyons2@uq.edu.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>School of Veterinary Science, University of Queensland, Queensland 4067</wicri:regionArea><wicri:noRegion>Queensland 4067</wicri:noRegion></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 wicri:level="1"><nlm:affiliation>School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120, Thailand. salinkr@gmail.com.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120</wicri:regionArea><wicri:noRegion>Pathumthani 12120</wicri:noRegion></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 wicri:level="1"><nlm:affiliation>Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735, Korea. khs307@pusan.ac.kr.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735</wicri:regionArea><wicri:noRegion>Busan 609735</wicri:noRegion></affiliation></author><author><name sortKey="Baek, Ilseon" sort="Baek, Ilseon" uniqKey="Baek I" first="Ilseon" last="Baek">Ilseon Baek</name><affiliation wicri:level="1"><nlm:affiliation>Division of Marine Technology, Chonnam National University, Yeosu 550250, Korea. chitago@naver.com.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Division of Marine Technology, Chonnam National University, Yeosu 550250</wicri:regionArea><wicri:noRegion>Yeosu 550250</wicri:noRegion></affiliation></author><author><name sortKey="Chand, Vincent" sort="Chand, Vincent" uniqKey="Chand V" first="Vincent" last="Chand">Vincent Chand</name><affiliation wicri:level="1"><nlm:affiliation>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. v.chand@qut.edu.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000</wicri:regionArea><wicri:noRegion>Queensland 4000</wicri:noRegion></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 wicri:level="1"><nlm:affiliation>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. p.mather@qut.edu.au.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000</wicri:regionArea><wicri:noRegion>Queensland 4000</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of molecular sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2016" type="published">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">The giant freshwater prawn, Macrobrachium rosenbergii, 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 M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii 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 k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo 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 M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27164098</PMID><DateCompleted><Year>2017</Year><Month>03</Month><Day>09</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>5</Issue><PubDate><Year>2016</Year><Month>May</Month><Day>07</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>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.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms17050690</ELocationID><ELocationID EIdType="pii" ValidYN="Y">E690</ELocationID><Abstract><AbstractText>The giant freshwater prawn, Macrobrachium rosenbergii, 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 M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii 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 k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo 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 M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jung</LastName><ForeName>Hyungtaek</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Centre for Tropical Crops and Biocommodities, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. h7.jung@qut.edu.au.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yoon</LastName><ForeName>Byung-Ha</ForeName><Initials>BH</Initials><AffiliationInfo><Affiliation>Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305806, Korea. cogate@kribb.re.kr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Bioinformatics, University of Science and Technology, Daejeon 305333, Korea. cogate@kribb.re.kr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Woo-Jin</ForeName><Initials>WJ</Initials><AffiliationInfo><Affiliation>Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea. wj2464@korea.kr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Dong-Wook</ForeName><Initials>DW</Initials><AffiliationInfo><Affiliation>All Bio Technology Co., LTD, Internet Business Incubation Center, Mokweon University, Daejeon 302729, Korea. kdw9017@naver.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hurwood</LastName><ForeName>David A</ForeName><Initials>DA</Initials><AffiliationInfo><Affiliation>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. d.hurwood@qut.edu.au.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lyons</LastName><ForeName>Russell E</ForeName><Initials>RE</Initials><AffiliationInfo><Affiliation>School of Veterinary Science, University of Queensland, Queensland 4067, Australia. r.lyons2@uq.edu.au.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salin</LastName><ForeName>Krishna R</ForeName><Initials>KR</Initials><AffiliationInfo><Affiliation>School of Environment, Resources and Development, Asian Institute of Technology, Pathumthani 12120, Thailand. salinkr@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Heui-Soo</ForeName><Initials>HS</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609735, Korea. khs307@pusan.ac.kr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baek</LastName><ForeName>Ilseon</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Division of Marine Technology, Chonnam National University, Yeosu 550250, Korea. chitago@naver.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chand</LastName><ForeName>Vincent</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. v.chand@qut.edu.au.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mather</LastName><ForeName>Peter B</ForeName><Initials>PB</Initials><AffiliationInfo><Affiliation>Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Queensland 4000, Australia. p.mather@qut.edu.au.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>05</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Int J Mol Sci</MedlineTA><NlmUniqueID>101092791</NlmUniqueID><ISSNLinking>1422-0067</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D033364" MajorTopicYN="N">Decapoda</DescriptorName><QualifierName UI="Q000235" 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UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Macrobrachium rosenbergii</Keyword><Keyword MajorTopicYN="N">crustacean</Keyword><Keyword MajorTopicYN="N">de novo assembly</Keyword><Keyword MajorTopicYN="N">hybrid transcriptome</Keyword><Keyword MajorTopicYN="N">optimization</Keyword><Keyword MajorTopicYN="N">prawn</Keyword><Keyword MajorTopicYN="N">reproduction</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>03</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2016</Year><Month>04</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>04</Month><Day>29</Day></PubMedPubDate><PubMedPubDate 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Mather</name></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><name sortKey="Baek, Ilseon" sort="Baek, Ilseon" uniqKey="Baek I" first="Ilseon" last="Baek">Ilseon Baek</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></country><country name="Thaïlande"><noRegion><name sortKey="Salin, Krishna R" sort="Salin, Krishna R" uniqKey="Salin K" first="Krishna R" last="Salin">Krishna R. Salin</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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