Deep RNA-Seq uncovers the peach transcriptome landscape View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2013-06-20

AUTHORS

Lu Wang, Shuang Zhao, Chao Gu, Ying Zhou, Hui Zhou, Juanjuan Ma, Jun Cheng, Yuepeng Han

ABSTRACT

Peach (Prunuspersica) is one of the most important of deciduous fruit trees worldwide. To facilitate isolation of genes controlling important horticultural traits of peach, transcriptome sequencing was conducted in this study. A total of 133 million pair-end RNA-Seq reads were generated from leaf, flower, and fruit, and 90 % of reads were mapped to the peach draft genome. Sequence assembly revealed 1,162 transcription factors and 2,140 novel transcribed regions (NTRs). Of these 2,140 NTRs, 723 contain an open reading frame, while the rest 1,417 are non-coding RNAs. A total of 9,587 SNPs were identified across six peach genotypes, with an average density of one SNP per ~5.7 kb. The top of chromosome 2 has higher density of expressed SNPs than the rest of the peach genome. The average density of SSR is 312.5/Mb, with tri-nucleotide repeats being the most abundant. Most of the detected SSRs are AT-rich repeats and the most common di-nucleotide repeat is CT/TC. The predominant type of alternative splicing (AS) events in peach is exon-skipping isoforms, which account for 43 % of all the observed AS events. In addition, the most active transcribed regions in peach genome were also analyzed. Our study reveals for the first time the complexity of the peach transcriptome, and our results will be helpful for functional genomics research in peach. More... »

PAGES

365-377

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    http://scigraph.springernature.com/pub.10.1007/s11103-013-0093-5

    DOI

    http://dx.doi.org/10.1007/s11103-013-0093-5

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23783411


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