WillowV1, Main, Corpus, bibRecord, 001295

Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis).

Identifieur interne : 001295 ( Main/Corpus ); précédent : 001294; suivant : 001296

Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis).

Auteurs : Jingjing Liu ; Tongming Yin ; Ning Ye ; Yingnan Chen ; Tingting Yin ; Min Liu ; Danial Hassani

Source :

PloS one [ 1932-6203 ] ; 2013.

RBID : pubmed:23560075

English descriptors

Abstract

BACKGROUND

The dioecious system is relatively rare in plants. Shrub willow is an annual flowering dioecious woody plant, and possesses many characteristics that lend it as a great model for tracking the missing pieces of sex determination evolution. To gain a global view of the genes differentially expressed in the male and female shrub willows and to develop a database for further studies, we performed a large-scale transcriptome sequencing of flower buds which were separately collected from two types of sexes.

RESULTS

Totally, 1,201,931 high quality reads were obtained, with an average length of 389 bp and a total length of 467.96 Mb. The ESTs were assembled into 29,048 contigs, and 132,709 singletons. These unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 291 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified 806 differentially expressed genes between the male and female flower buds. And 33 of them located on the incipient sex chromosome of Salicaceae, among which, 12 genes might involve in plant sex determination empirically. These genes were worthy of special notification in future studies.

CONCLUSIONS

In this study, a large number of EST sequences were generated from the flower buds of a male and a female shrub willow. We also reported the differentially expressed genes between the two sex-type flowers. This work provides valuable information and sequence resources for uncovering the sex determining genes and for future functional genomics analysis of Salicaceae spp.

DOI: 10.1371/journal.pone.0060181
PubMed: 23560075
PubMed Central: PMC3613397

Links to Exploration step

pubmed:23560075

Le document en format XML

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<author><name sortKey="Liu, Jingjing" sort="Liu, Jingjing" uniqKey="Liu J" first="Jingjing" last="Liu">Jingjing Liu</name>
<affiliation><nlm:affiliation>Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, China.</nlm:affiliation>
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<author><name sortKey="Yin, Tongming" sort="Yin, Tongming" uniqKey="Yin T" first="Tongming" last="Yin">Tongming Yin</name>
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<author><name sortKey="Ye, Ning" sort="Ye, Ning" uniqKey="Ye N" first="Ning" last="Ye">Ning Ye</name>
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<author><name sortKey="Chen, Yingnan" sort="Chen, Yingnan" uniqKey="Chen Y" first="Yingnan" last="Chen">Yingnan Chen</name>
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<author><name sortKey="Yin, Tingting" sort="Yin, Tingting" uniqKey="Yin T" first="Tingting" last="Yin">Tingting Yin</name>
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<author><name sortKey="Liu, Min" sort="Liu, Min" uniqKey="Liu M" first="Min" last="Liu">Min Liu</name>
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<author><name sortKey="Hassani, Danial" sort="Hassani, Danial" uniqKey="Hassani D" first="Danial" last="Hassani">Danial Hassani</name>
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<affiliation><nlm:affiliation>Key Lab of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, China.</nlm:affiliation>
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<author><name sortKey="Chen, Yingnan" sort="Chen, Yingnan" uniqKey="Chen Y" first="Yingnan" last="Chen">Yingnan Chen</name>
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<author><name sortKey="Yin, Tingting" sort="Yin, Tingting" uniqKey="Yin T" first="Tingting" last="Yin">Tingting Yin</name>
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<author><name sortKey="Liu, Min" sort="Liu, Min" uniqKey="Liu M" first="Min" last="Liu">Min Liu</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Plant (MeSH)</term>
<term>Databases, Genetic (MeSH)</term>
<term>Expressed Sequence Tags (MeSH)</term>
<term>Flowers (genetics)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Microsatellite Repeats (MeSH)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Salix (genetics)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
<term>Transcriptome (MeSH)</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Flowers</term>
<term>Salix</term>
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<keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Plant</term>
<term>Databases, Genetic</term>
<term>Expressed Sequence Tags</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation, Plant</term>
<term>Genome, Plant</term>
<term>Microsatellite Repeats</term>
<term>Molecular Sequence Annotation</term>
<term>Sequence Analysis, DNA</term>
<term>Transcriptome</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>The dioecious system is relatively rare in plants. Shrub willow is an annual flowering dioecious woody plant, and possesses many characteristics that lend it as a great model for tracking the missing pieces of sex determination evolution. To gain a global view of the genes differentially expressed in the male and female shrub willows and to develop a database for further studies, we performed a large-scale transcriptome sequencing of flower buds which were separately collected from two types of sexes.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>Totally, 1,201,931 high quality reads were obtained, with an average length of 389 bp and a total length of 467.96 Mb. The ESTs were assembled into 29,048 contigs, and 132,709 singletons. These unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases and assigned with Gene Ontology (GO) terms. A biochemical pathway database containing 291 predicted pathways was also created based on the annotations of the unigenes. Digital expression analysis identified 806 differentially expressed genes between the male and female flower buds. And 33 of them located on the incipient sex chromosome of Salicaceae, among which, 12 genes might involve in plant sex determination empirically. These genes were worthy of special notification in future studies.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>In this study, a large number of EST sequences were generated from the flower buds of a male and a female shrub willow. We also reported the differentially expressed genes between the two sex-type flowers. This work provides valuable information and sequence resources for uncovering the sex determining genes and for future functional genomics analysis of Salicaceae spp.</p>
</div>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The dioecious system is relatively rare in plants. Shrub willow is an annual flowering dioecious woody plant, and possesses many characteristics that lend it as a great model for tracking the missing pieces of sex determination evolution. To gain a global view of the genes differentially expressed in the male and female shrub willows and to develop a database for further studies, we performed a large-scale transcriptome sequencing of flower buds which were separately collected from two types of sexes.</AbstractText>
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Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis).

Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis).

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