Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.
Identifieur interne : 000407 ( PubMed/Checkpoint ); précédent : 000406; suivant : 000408Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.
Auteurs : Matthew C. Hale [États-Unis] ; Cory R. Mccormick ; James R. Jackson ; J Andrew DewoodySource :
- BMC genomics [ 1471-2164 ] ; 2009.
English descriptors
- KwdEn :
- MESH :
- genetics : Fishes.
- metabolism : Gonads.
- methods : Gene Expression Profiling, Sequence Analysis, DNA.
- Animals, Expressed Sequence Tags, Female, Gene Library, Male, Pilot Projects, Polymorphism, Single Nucleotide.
Abstract
Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads.
DOI: 10.1186/1471-2164-10-203
PubMed: 19402907
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.</title><author><name sortKey="Hale, Matthew C" sort="Hale, Matthew C" uniqKey="Hale M" first="Matthew C" last="Hale">Matthew C. Hale</name><affiliation wicri:level="2"><nlm:affiliation>Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA. mchale@purdue.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907</wicri:regionArea><placeName><region type="state">Indiana</region></placeName></affiliation></author><author><name sortKey="Mccormick, Cory R" sort="Mccormick, Cory R" uniqKey="Mccormick C" first="Cory R" last="Mccormick">Cory R. Mccormick</name></author><author><name sortKey="Jackson, James R" sort="Jackson, James R" uniqKey="Jackson J" first="James R" last="Jackson">James R. Jackson</name></author><author><name sortKey="Dewoody, J Andrew" sort="Dewoody, J Andrew" uniqKey="Dewoody J" first="J Andrew" last="Dewoody">J Andrew Dewoody</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19402907</idno><idno type="pmid">19402907</idno><idno type="doi">10.1186/1471-2164-10-203</idno><idno type="wicri:Area/PubMed/Corpus">000434</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000434</idno><idno type="wicri:Area/PubMed/Curation">000434</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000434</idno><idno type="wicri:Area/PubMed/Checkpoint">000434</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000434</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.</title><author><name sortKey="Hale, Matthew C" sort="Hale, Matthew C" uniqKey="Hale M" first="Matthew C" last="Hale">Matthew C. Hale</name><affiliation wicri:level="2"><nlm:affiliation>Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA. mchale@purdue.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907</wicri:regionArea><placeName><region type="state">Indiana</region></placeName></affiliation></author><author><name sortKey="Mccormick, Cory R" sort="Mccormick, Cory R" uniqKey="Mccormick C" first="Cory R" last="Mccormick">Cory R. Mccormick</name></author><author><name sortKey="Jackson, James R" sort="Jackson, James R" uniqKey="Jackson J" first="James R" last="Jackson">James R. Jackson</name></author><author><name sortKey="Dewoody, J Andrew" sort="Dewoody, J Andrew" uniqKey="Dewoody J" first="J Andrew" last="Dewoody">J Andrew Dewoody</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Expressed Sequence Tags</term><term>Female</term><term>Fishes (genetics)</term><term>Gene Expression Profiling (methods)</term><term>Gene Library</term><term>Gonads (metabolism)</term><term>Male</term><term>Pilot Projects</term><term>Polymorphism, Single Nucleotide</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fishes</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Gonads</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Expressed Sequence Tags</term><term>Female</term><term>Gene Library</term><term>Male</term><term>Pilot Projects</term><term>Polymorphism, Single Nucleotide</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19402907</PMID><DateCreated><Year>2009</Year><Month>06</Month><Day>01</Day></DateCreated><DateCompleted><Year>2009</Year><Month>06</Month><Day>05</Day></DateCompleted><DateRevised><Year>2014</Year><Month>12</Month><Day>09</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2009</Year><Month>Apr</Month><Day>29</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.</ArticleTitle><Pagination><MedlinePgn>203</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-10-203</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (approximately 19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from > 50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hale</LastName><ForeName>Matthew C</ForeName><Initials>MC</Initials><AffiliationInfo><Affiliation>Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA. mchale@purdue.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McCormick</LastName><ForeName>Cory R</ForeName><Initials>CR</Initials></Author><Author ValidYN="Y"><LastName>Jackson</LastName><ForeName>James R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Dewoody</LastName><ForeName>J Andrew</ForeName><Initials>JA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType 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Version="1">18266620</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol. 2008 Apr;17(7):1629-31</RefSource><PMID Version="1">18284566</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Sex Dev. 2007;1(2):85-99</RefSource><PMID Version="1">18391519</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2008;9:312</RefSource><PMID Version="1">18590545</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>PLoS One. 2008;3(7):e2837</RefSource><PMID Version="1">18665231</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2008 Nov 1;24(21):2498-504</RefSource><PMID Version="1">18779233</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genetics. 2000 Apr;154(4):1907-12</RefSource><PMID Version="1">10747078</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2000 May;25(1):25-9</RefSource><PMID Version="1">10802651</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Biotechniques. 2001 Apr;30(4):892-7</RefSource><PMID Version="1">11314272</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genetics. 2001 Jul;158(3):1203-15</RefSource><PMID Version="1">11454768</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol. 2002 Nov;11(11):2445-9</RefSource><PMID Version="1">12406254</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2003 Sep;13(9):2164-70</RefSource><PMID Version="1">12952883</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioorg Khim. 2005 Mar-Apr;31(2):186-94</RefSource><PMID Version="1">15889793</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2005;6:107</RefSource><PMID Version="1">16095544</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2005 Sep 15;437(7057):376-80</RefSource><PMID Version="1">16056220</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genetics. 2006 Jan;172(1):569-77</RefSource><PMID Version="1">16219784</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Plant Biol. 2006;6:17</RefSource><PMID Version="1">16934154</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2006;7:246</RefSource><PMID Version="1">17010196</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2006;7:275</RefSource><PMID Version="1">17067373</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Genomics. 2006;7:272</RefSource><PMID Version="1">17062153</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Ecol. 2007 Mar;16(5):907-24</RefSource><PMID Version="1">17305850</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Bioinformatics. 2007;8 Suppl 1:S22</RefSource><PMID Version="1">17430567</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Science. 2007 Oct 19;318(5849):441-4</RefSource><PMID Version="1">17901299</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005399" MajorTopicYN="N">Fishes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006066" MajorTopicYN="N">Gonads</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010865" MajorTopicYN="N">Pilot Projects</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC2688523</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2008</Year><Month>12</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2009</Year><Month>04</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>5</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>5</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>6</Month><Day>9</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19402907</ArticleId><ArticleId IdType="pii">1471-2164-10-203</ArticleId><ArticleId IdType="doi">10.1186/1471-2164-10-203</ArticleId><ArticleId IdType="pmc">PMC2688523</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Indiana</li></region></list><tree><noCountry><name sortKey="Dewoody, J Andrew" sort="Dewoody, J Andrew" uniqKey="Dewoody J" first="J Andrew" last="Dewoody">J Andrew Dewoody</name><name sortKey="Jackson, James R" sort="Jackson, James R" uniqKey="Jackson J" first="James R" last="Jackson">James R. Jackson</name><name sortKey="Mccormick, Cory R" sort="Mccormick, Cory R" uniqKey="Mccormick C" first="Cory R" last="Mccormick">Cory R. Mccormick</name></noCountry><country name="États-Unis"><region name="Indiana"><name sortKey="Hale, Matthew C" sort="Hale, Matthew C" uniqKey="Hale M" first="Matthew C" last="Hale">Matthew C. Hale</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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