title: Deep RNA-Seq uncovers the peach transcriptome landscape.
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.
authors.affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China, wanglu@wbgcas.cn.
authors.forename: Lu
authors.initials: L
authors.lastname: Wang
authors.forename: Shuang
authors.initials: S
authors.lastname: Zhao
authors.forename: Chao
authors.initials: C
authors.lastname: Gu
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhou
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Ma
authors.forename: Jun
authors.initials: J
authors.lastname: Cheng
authors.forename: Yuepeng
authors.initials: Y
authors.lastname: Han
mesh_terms: D017398:Alternative Splicing; D002874:Chromosome Mapping; D005091:Exons / Q000235:genetics; D035264:Flowers / Q000235:genetics; D005638:Fruit / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D018515:Plant Leaves / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D027861:Prunus / Q000235:genetics*; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018749:RNA, Plant; D022661:RNA, Untranslated