Deep RNA-Seq uncovers the peach transcriptome landscape

Deep RNA-Seq uncovers the peach transcriptome landscape Peach (Prunus persica) 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Molecular Biology Springer Journals

Deep RNA-Seq uncovers the peach transcriptome landscape

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Publisher
Springer Journals
Copyright
Copyright © 2013 by Springer Science+Business Media Dordrecht
Subject
Life Sciences; Plant Sciences; Biochemistry, general; Plant Pathology
ISSN
0167-4412
eISSN
1573-5028
D.O.I.
10.1007/s11103-013-0093-5
Publisher site
See Article on Publisher Site

Abstract

Peach (Prunus persica) 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.

Journal

Plant Molecular BiologySpringer Journals

Published: Jun 20, 2013

References

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