Skip to main content
SpringerLink
Log in

Deep RNA-Seq uncovers the peach transcriptome landscape

  • Published:
Plant Molecular Biology Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martínez-García PJ, Crisosto CH (2011) Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics 12:569

    Article  PubMed  CAS  Google Scholar 

  • Arús P, Verde I, Sosinski B, Zhebentyayeva T, Abbott AG (2012) The peach genome. Tree Genet Genomes 8:1–17

    Article  Google Scholar 

  • Barbazuk WB, Fu Y, McGinnis KM (2008) Genome wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res 18:1381–1392

    Article  PubMed  CAS  Google Scholar 

  • Bonghi C, Trainotti L, Botton A, Tadiello A, Rasori A, Ziliotto F, Zaffalon V, Casadoro G, Ramina A (2011) A microarray approach to identify genes involved in seed-pericarp cross-talk and development in peach. BMC Plant Biol 11:107

    Article  PubMed  CAS  Google Scholar 

  • Boudehri K, Bendahmane A, Cardinet G, Troadec C, Moing A, Dirlewanger E (2009) Phenotypic and fine genetic characterization of the D locus controlling fruit acidity in peach. BMC Plant Biol 19:59

    Article  Google Scholar 

  • Brandi F, Bar E, Mourgues F, Horváth G, Turcsi E, Giuliano G, Liverani A, Tartarini S, Lewinsohn E, Rosati C (2011) Study of ‘Redhaven’ peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism. BMC Plant Biol 11:24

    Article  PubMed  CAS  Google Scholar 

  • Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7:327

    Article  PubMed  Google Scholar 

  • Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 56:847–854

    Google Scholar 

  • Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11:569

    Article  PubMed  Google Scholar 

  • Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EH, Gardiner SE, Korban SS (2008) Development of a set of SNP markers present in expressed genes of the apple. Genomics 92:353–358

    Article  PubMed  Google Scholar 

  • Dirlewanger E, Cosson P, Howad W, Capdeville G, Bosselut N, Claverie M, Voisin R, Poizat C, Lafargue B, Baron O, Laigret F, Kleinhentz M, Arús P, Esmenjaud D (2004) Microsatellite genetic linkage maps of myrobalan plum and an almond-peach hybrid-location of root-knot nematode resistance genes. Theor Appl Genet 109:827–838

    Article  PubMed  CAS  Google Scholar 

  • Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76–79

    Article  PubMed  CAS  Google Scholar 

  • Jiménez S, Li ZG, Reighard GL, Bielenberg DG (2010a) Identification of genes associated with growth cessation and bud dormancy entrance using a dormancy-incapable tree mutant. BMC Plant Biol 10:25

    Article  PubMed  Google Scholar 

  • Jiménez S, Reighard GL, Bielenberg DG (2010b) Gene expression of DAM 5 and DAM6 is suppressed by chilling temperatures and inversely correlated with bud break. Plant Mol Biol 73:157–167

    Article  PubMed  Google Scholar 

  • Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302:2141–2144

    Article  PubMed  CAS  Google Scholar 

  • Joobeur T, Periam N, de Vicente MC, King GJ, Arús P (2000) Development of a second generation linkage map for almond using RAPD and SSR markers. Genome 43:649–655

    Article  PubMed  CAS  Google Scholar 

  • Jung S, Abbott A, Jesudurai C, Tomkins J, Main D (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics 5:136–143

    Article  PubMed  CAS  Google Scholar 

  • Kantety V, Rota L, Matthews E, Sorrells E (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice sorghum and wheat. Plant Mol Biol 48:501–510

    Article  PubMed  CAS  Google Scholar 

  • Khan MA, Han Y, Zhao YF, Korban SS (2012) A high-throughput apple SNP genotyping platform using the GoldenGate™ assay. Gene 494:196–201

    Article  PubMed  CAS  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    Article  PubMed  CAS  Google Scholar 

  • Li ZG, Reighard GL, Abbott AG, Bielenberg DG (2009) Dormancy associated MADS genes from the EVG locus of peach [Prunus persica (L.) Batsch] have distinct seasonal and photoperiodic expression patterns. J Exp Bot 60:3521–3530

    Article  PubMed  CAS  Google Scholar 

  • Lijavetzky D, Cabezas JA, Ibáñez A, Rodríguez V, Martínez-Zapater JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8:424

    Article  PubMed  Google Scholar 

  • Livio T, Tadiello A, Casadoro G (2007) Variations of the peach fruit transcriptome during ripening and in response to hormone treatments. Caryologia 60:156–159

    Article  Google Scholar 

  • Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, Huang X, Han B (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 20:1238–1249

    Article  PubMed  CAS  Google Scholar 

  • Martínez-Gómez P, Crisosto CH, Bonghi C, Rubio M (2011) New approaches to Prunus transcriptome analysis. Genetica 139:755–769

    Article  PubMed  Google Scholar 

  • McHale L, Tan X, Koehl P, Michelmore RW (2006) Plant NBS-LRR proteins: adaptable guards. Genome Biol 7:212

    Article  PubMed  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  PubMed  CAS  Google Scholar 

  • Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EH, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ, Laing WA, McArtney S, Nain B, Ross GS, Snowden KC, Souleyre EJ, Walton EF, Yauk YK (2006) Analyses of expressed sequence tags from apple. Plant Physiol 141:147–166

    Article  PubMed  Google Scholar 

  • Nishiyama R, Le DT, Watanabe Y, Matsui A, Tanaka M et al (2012) Transcriptome analyses of a salt-tolerant cytokinin-deficient mutant reveal differential regulation of salt stress response by cytokinin deficiency. PLoS One 7:e32124

    Article  PubMed  CAS  Google Scholar 

  • Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, Carstens RP, Xing Y (2012) MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40:e61

    Article  PubMed  CAS  Google Scholar 

  • Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arús P, Dandekar AM, Lewers K, Gardiner SE, Potter D, Veilleux E (2008) Multiple models for Rosaceae genomics. Plant Physiol 147:985–1003

    Article  PubMed  CAS  Google Scholar 

  • Socquet-Juglard D, Kamber T, Pothier JF, Christen D, Gessler C, Duffy B, Patocchi A (2013) Comparative RNA-Seq analysis of early-Infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. Pruni. PLoS One 8:e541969

    Article  Google Scholar 

  • Soria-Guerra RE, Rosales-Mendoza S, Gasic K, Wisniewski ME, Band M, Korban SS (2011) Gene expression is highly regulated in early developing fruit of apple. Plant Mol Biol Rep 29:885–897

    Article  CAS  Google Scholar 

  • Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462:799–802

    Article  PubMed  CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • The International Peach Genome Initiative (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. doi:10.1038/ng.2586

    Google Scholar 

  • Tong Z, Gao Z, Wang F, Zhou J, Zang Z (2009) Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol 10:71

    Article  PubMed  Google Scholar 

  • Trainotti L, Bonghi C, Ziliotto F, Zanin D, Rasori A, Casadoro G, Ramina A, Tonutti P (2006) The use of microarray μPEACH1.0 to investigate transcriptome changes during transition from preclimacteric to climacteric phase in peach fruit. Plant Sci 170:606–613

    Article  CAS  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111

    Article  PubMed  CAS  Google Scholar 

  • Vecchietti A (2009) Comparative analysis of expressed sequence tags from tissues in ripening stages of peach. Tree Genet Genomes 5:377–391

    Article  Google Scholar 

  • Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D, Rosyara UR, Cattonaro F, Vendramin E, Main D, Aramini V, Blas AL, Mockler TC, Bryant DW, Wilhelm L, Troggio M, Sosinski B, Aranzana MJ, Arús P, Iezzoni A, Morgante M, Peace C (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7:e35668

    Article  PubMed  CAS  Google Scholar 

  • Wang C, Xu G, Jiang X, Chen G, Wu J, Wu H, Zhang S (2009) S-RNase triggers mitochondrial alteration and DNA degradation in the incompatible pollen tube of Pyruspyrifolia in vitro. Plant J 57:220–229

    Article  PubMed  CAS  Google Scholar 

  • Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:e164

    Article  PubMed  Google Scholar 

  • Xin MM, Wang Y, Yao YY, Song N, Hu ZR, Qin DD, Xie CJ, Peng HR, Ni ZF, Sun QX (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol 11:61–73

    Article  PubMed  CAS  Google Scholar 

  • Yamamoto T, Mochida K, Imai T, Shi IZ, Ogiwara I, Hayashi T (2002) Microsatellite markers in peach [Prunus persica (L.) Batsch] derived from an enriched genomic and cDNA libraries. Mol Ecol Notes 2:298–302

    Article  CAS  Google Scholar 

  • Zhang Q, Ma B, Li H, Chang Y, Han Y, Li J, Wei G, Zhao S, Khan MA, Zhou Y, Gu C, Zhang X, Han Z, Korban SS, Li S, Han Y (2012) Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple. BMC Genomics 13:537

    Article  PubMed  Google Scholar 

  • Zhebentyayeva T, Swire-Clark G, Georgi L, Garay L, Jung S, Forrest S, Blenda A, Blackmon B, Mook J, Horn R, Howad W, Arús P, Main D, Tomkins J, Sosinski B, Baird W, Reighard G, Abbott A (2008) A framework physical map for peach, a model Rosaceae species. Tree Genet Genomics 4:745–756

    Article  Google Scholar 

Download references

Acknowledgments

This project was supported by funds received from the National 863 program of China (No. 2011AA100206), the National 948 Project from the Ministry of Agriculture of China, and the National Natural Science Foundation of China (No. 31201604 and 31000139).

Author information

Authors and Affiliations

  1. 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

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

Authors
  1. Lu Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shuang Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chao Gu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ying Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hui Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Juanjuan Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jun Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yuepeng Han
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuepeng Han.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 1455 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, L., Zhao, S., Gu, C. et al. Deep RNA-Seq uncovers the peach transcriptome landscape. Plant Mol Biol 83, 365–377 (2013). https://doi.org/10.1007/s11103-013-0093-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11103-013-0093-5

Keywords

Search

Navigation