ArticlePlant molecular biology2013
Deep RNA-Seq uncovers the peach transcriptome landscape.
Article in Plant molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 104 citations in OpenAlex.
- Transcriptome analysis of critical genes related to flowering in Mikania micrantha at different altitudes provides insights for a potential control.BMC genomics · 2023Article
- PpHYH is responsible for light-induced anthocyanin accumulation in fruit peel of Prunus persica.Tree physiology · 2022Article
- The Genome-Wide Identification of Long Non-Coding RNAs Involved in Floral Thermogenesis inInternational journal of molecular sciences · 2022Article
- Alternative splicing during fruit development among fleshy fruits.BMC genomics · 2021Article
- A candidate PpRPH gene of the D locus controlling fruit acidity in peach.Plant molecular biology · 2021Article
- Potential Association of Reactive Oxygen Species With Male Sterility in Peach.Frontiers in plant science · 2021Article
- Molecular Bases of Fruit Quality inInternational journal of molecular sciences · 2020Review
- A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding.G3 (Bethesda, Md.) · 2020Article
- Identification of EIL and ERF Genes Related to Fruit Ripening in Peach.International journal of molecular sciences · 2020Article
- Functional Analysis Reveals the Regulatory Role ofInternational journal of molecular sciences · 2020Article
- Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Frontiers in plant science · 2020Article
- Stone Fruit as Biofactories of Phytochemicals With Potential Roles in Human Nutrition and Health.Frontiers in plant science · 2020Review
- Detection and application of genome-wide variations in peach for association and genetic relationship analysis.BMC genetics · 2019Article
- Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway.Scientific reports · 2019Article
- Genome-wide discovery and characterization of flower development related long non-coding RNAs in Prunus mume.BMC plant biology · 2019Article
- Identification of phloem-associated translatome alterations during leaf development inHorticulture research · 2019Article
- Two amino acid changes in the R3 repeat cause functional divergence of two clustered MYB10 genes in peach.Plant molecular biology · 2018Article
- Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress.Molecular genetics and genomics : MGG · 2018Article
- Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima.PloS one · 2018Article
- Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics.GigaScience · 2017Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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