De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.).
Identifieur interne : 000422 ( PubMed/Corpus ); précédent : 000421; suivant : 000423De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.).
Auteurs : Hui Xue ; Shangyin Cao ; Haoxian Li ; Jie Zhang ; Juan Niu ; Lina Chen ; Fuhong Zhang ; Diguang ZhaoSource :
- PloS one [ 1932-6203 ] ; 2017.
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Abstract
Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.
DOI: 10.1371/journal.pone.0178809
PubMed: 28594931
PubMed Central: PMC5464567
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sort="Zhang, Jie" uniqKey="Zhang J" first="Jie" last="Zhang">Jie Zhang</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Niu, Juan" sort="Niu, Juan" uniqKey="Niu J" first="Juan" last="Niu">Juan Niu</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Lina" sort="Chen, Lina" uniqKey="Chen L" first="Lina" last="Chen">Lina Chen</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Fuhong" sort="Zhang, Fuhong" uniqKey="Zhang F" first="Fuhong" last="Zhang">Fuhong Zhang</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Diguang" sort="Zhao, Diguang" uniqKey="Zhao D" first="Diguang" last="Zhao">Diguang Zhao</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28594931</idno><idno type="pmid">28594931</idno><idno type="doi">10.1371/journal.pone.0178809</idno><idno type="pmc">PMC5464567</idno><idno type="wicri:Area/PubMed/Corpus">000422</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000422</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.).</title><author><name sortKey="Xue, Hui" sort="Xue, Hui" uniqKey="Xue H" first="Hui" last="Xue">Hui Xue</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Cao, Shangyin" sort="Cao, Shangyin" uniqKey="Cao S" first="Shangyin" last="Cao">Shangyin Cao</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Haoxian" sort="Li, Haoxian" uniqKey="Li H" first="Haoxian" last="Li">Haoxian Li</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Jie" sort="Zhang, Jie" uniqKey="Zhang J" first="Jie" last="Zhang">Jie Zhang</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Niu, Juan" sort="Niu, Juan" uniqKey="Niu J" first="Juan" last="Niu">Juan Niu</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Lina" sort="Chen, Lina" uniqKey="Chen L" first="Lina" last="Chen">Lina Chen</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Fuhong" sort="Zhang, Fuhong" uniqKey="Zhang F" first="Fuhong" last="Zhang">Fuhong Zhang</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Diguang" sort="Zhao, Diguang" uniqKey="Zhao D" first="Diguang" last="Zhao">Diguang Zhao</name><affiliation><nlm:affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (MeSH)</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Lythraceae (genetics)</term><term>Reverse Transcriptase Polymerase Chain Reaction (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gene Expression Regulation, Plant</term><term>Lythraceae</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28594931</PMID><DateCompleted><Year>2017</Year><Month>09</Month><Day>19</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>6</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.).</ArticleTitle><Pagination><MedlinePgn>e0178809</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0178809</ELocationID><Abstract><AbstractText>Pomegranate (Punica granatum L.) belongs to Punicaceae, and is valued for its social, ecological, economic, and aesthetic values, as well as more recently for its health benefits. The 'Tunisia' variety has softer seeds and big arils that are easily swallowed. It is a widely popular fruit; however, the molecular mechanisms of the formation of hard and soft seeds is not yet clear. We conducted a de novo assembly of the seed transcriptome in P. granatum L. and revealed differential gene expression between the soft-seed and hard-seed pomegranate varieties. A total of 35.1 Gb of data were acquired in this study, including 280,881,106 raw reads. Additionally, de novo transcriptome assembly generated 132,287 transcripts and 105,743 representative unigenes; approximately 13,805 unigenes (37.7%) were longer than 1,000 bp. Using bioinformatics annotation libraries, a total of 76,806 unigenes were annotated and, among the high-quality reads, 72.63% had at least one significant match to an existing gene model. Gene expression and differentially expressed genes were analyzed. The seed formation of the two pomegranate cultivars involves lignin biosynthesis and metabolism, including some genes encoding laccase and peroxidase, WRKY, MYB, and NAC transcription factors. In the hard-seed pomegranate, lignin-related genes and cellulose synthesis-related genes were highly expressed; in soft-seed pomegranates, expression of genes related to flavonoids and programmed cell death was slightly higher. We validated selection of the identified genes using qRT-PCR. This is the first transcriptome analysis of P. granatum L. This transcription sequencing greatly enriched the pomegranate molecular database, and the high-quality SSRs generated in this study will aid the gene cloning from pomegranate in the future. It provides important insights into the molecular mechanisms underlying the formation of soft seeds in pomegranate.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xue</LastName><ForeName>Hui</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Shangyin</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Haoxian</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jie</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Niu</LastName><ForeName>Juan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Lina</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Fuhong</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Diguang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Zhengzhou Fruit Research Institute, CAAS, Zhengzhou, 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