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Transcriptome Sequencing and Analysis of Wild Pear (Pyrus hopeiensis) Using the Illumina Platform

  • Technical Note - Biological Sciences
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Abstract

Pears are cultivated worldwide as an economically valuable fruit of the Rosaceae. Because of the lack of genomic resources, few molecular biology studies have focused on wild pear, which are less abundant than partially cultivated pear species. However, high-throughput transcriptome sequencing technologies enabled the advent of genomic studies requiring shorter time and minimal costs, allowing efficient wild pear research. Pyrus hopeiensis is an endangered and valuable horticultural plant species, and its transcriptome was sequenced in this study. Overall, 25,877,477 high-quality reads and 48,278 unigenes were generated with the Illumina platform from four different tissue samples. A total of 27,005 (55.94 %) unigenes were successfully annotated. Of these, 26,941 and 19,248 unigenes were annotated in the National Center for Biotechnology Information non-redundant (Nr) protein database and the Swiss-Prot protein database, respectively. In addition, 18,590 and 7505 unigenes were assigned to Gene Ontology and Cluster of Orthologous Groups classifications, respectively, and a total of 5104 unigenes were mapped to 123 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 4301 simple sequence repeat markers were identified in P. hopeiensis, which will be used in future research of the genetic diversity of Pyrus. Finally, the results indicated that lignin biosynthesis, secondary metabolism and suberin/cutin/wax biosynthesis were involved in the russet pericarp formation process of P. hopeiensis. Detailed examination of these pathways revealed 54 candidate genes were predicted based on the KEGG pathways, which encoded 10 key enzymes involved in lignin biosynthesis; moreover, 33 additional regulatory genes for pigmentation of wild pear russet pericarp were also summarized. In summary, this effective RNA-Seq study provides comprehensive genetic and genomic insight into the endangered P. hopeiensis species, which will improve future studies on the molecular mechanism of the appearance and quality of this fruit.

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References

  1. Iketani H., Yamamoto T., Katayama H., Uematsu C., Mase N., Sato Y.: Introgression between native and prehistorically naturalized (archaeophytic) wild pear (Pyrus spp.) populations in Northern Tohoku, Northeast Japan. Conserv. Genet. 11, 115–126 (2010)

    Article  Google Scholar 

  2. Xie M., Huang Y., Zhang Y.P., Wang X., Yang H., Yu O., Dai W.H., Fang C.B.: Transcriptome profiling of fruit development and maturation in Chinese white pear (Pyrus bretschneideri Rehd). BMC Genomics 14, 823 (2013)

    Article  Google Scholar 

  3. Wang Y.Z., Zhang S.J., Dai M.S., Shi Z.B.: Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant. Plant Mol. Biol. 85, 123–134 (2013)

    Article  Google Scholar 

  4. Liu G.Q., Li W.S., Zheng P.H., Xu T., Chen L.J., Liu D.F., Hussain S., Teng Y.W.: Transcriptomic analysis of‘Suli’pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq. BMC Genomics 13, 700 (2012)

    Article  Google Scholar 

  5. Li, M.Y.; Wang, F.; Jiang, Q.; Ma, J.; Xiong, A.S.: Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing. Hortic. Res. 1. doi:10.1038/hortres (2014)

  6. Liu Z.P., Chen T.L., Ma L.C., Ma L.C., Zhao Z.G., Patrick X.Z., Nan Z.B., Wang Y.R.: Global transcriptome sequencing using the illumina platform and the development of EST-SSR markers in autotetraploid alfaifa. Plos One 8, e83549 (2013)

    Article  Google Scholar 

  7. Yuan Y., Song L., Li M., Liu G.M., Chu Y.N., Ma L.Y., Zhou Y.Y., Wang X., Gao W., Qin S.S.: Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica Thunb. BMC Genomics 13, 195 (2012)

    Article  Google Scholar 

  8. Yang S.S., Tu J.Z., Cheung F., Xu W.W., Lamb J.A., Jung H.J., Vance C., Gronwald W.J.: Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12, 199 (2011)

    Article  Google Scholar 

  9. Wang Z., Gerstein M., Snyder M.: RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009)

    Article  Google Scholar 

  10. Wang Y.Z., Zhang S.J., Dai M.S., Shi Z.B.: Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color. Plos One 9, e83675 (2013)

    Article  Google Scholar 

  11. Thiel T., Michalek W., Varshney R.K., Graner A.: Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106, 411–422 (2003)

    Google Scholar 

  12. Conesa A., Gotz S., Garcia-Gomez J.M., Terol J., Talon M.: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674–3676 (2005)

    Article  Google Scholar 

  13. Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann. B., Ferro S., Gasteiqer E., Huang H., Lopez R., Maqrane M., Martin M.J., Natale D.A., O’Donovan C., Redaschi N., Yeh L.S.: UniProt; the universal protein knowledgebase[EB/OL]. Nucleic Acids Res. 32, 115 (2004)

    Article  Google Scholar 

  14. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M.: The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–280 (2004)

    Article  Google Scholar 

  15. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)

    Article  Google Scholar 

  16. Manfred G.G., Brian J.H., Moran Y., Joshua Z.L., Dawn A.T., Ido A., Xian A., Lin F.: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011)

    Article  Google Scholar 

  17. Fraser L.G., Harvey C.F., Crowhurst R.N., De Silva H.N.: EST-derived microsatellites from Actinidia species and their potential for mapping. Theor. Appl. Genet. 108, 1010–1016 (2004)

    Article  Google Scholar 

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

    Article  Google Scholar 

  19. Gupta P.K., Varshney R.K.: The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113, 163–185 (2000)

    Article  Google Scholar 

  20. Wei W.L., Qi X.Q., Wang L.H., Zhang Y.X., Hua W., Li D.H., Zhang X.R.: Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12, 451 (2011)

    Article  Google Scholar 

  21. Morton B.R., Wright S.L.: Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana. Mol. Biol. Evol. 24, 122–129 (2007)

    Article  Google Scholar 

  22. Schordeet D.F., Gartler S.M.: Analysis of CpG suppression in methylated and nonmethylated species. Proc. Natl. Acad. Sci. USA 89, 957–961 (1992)

    Article  Google Scholar 

  23. Liu M.Y., Qiao G.R., Jiang J., Yang H.Q., Xie L.H., Xie J.Z.: Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. Plos One 10, e46766 (2012)

    Article  Google Scholar 

  24. Luo H.M., Sun C., Li Y., Wu Q., Song J.Y., Wang D.L., Jia X.C., Li R.T., Chen S.L.: Analysis of expressed sequence tags from the Huperzia serrata leaf for gene discovery in the areas of secondary metabolites biosynthesis and development regulation. Physiol. Plant. 139, 1–12 (2010)

    Article  Google Scholar 

  25. Liu D.F., Sui S.Z., Ma J., Li Z.N., Guo Y.L., Luo D.P., Yang J.F., Li M.Y.: Transcriptomic analysis of flower development in wintersweet (Chimonanthus praecox). Plos One 9, e86976 (2014)

    Article  Google Scholar 

  26. Kenji N., Hirokazu T., Mikio N., Tokurou S.: Transcriptome analysis of giant pear fruit with fruit-specific DNA reduplication on a mutant branch. Jpn Soc Hortic Sci 82, 301–311 (2013)

    Article  Google Scholar 

  27. Heng W., Liu L., Wang M.D., Jia B., Liu P., Ye Z.F., Zhu L.W.: Differentially expressed genes related to the formation of russet fruit skin in a mutant of ‘Dangshansuli’ pear (Pyrus bretchnederi Rehd.) determined by suppression subtractive hybridization. Euphytica 196, 285–297 (2014)

    Article  Google Scholar 

  28. Inoue E., Kasumi M., Sakuma F., Anzai H., Amano K., Hara H.: Identification of RAPD marker linked to fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). Sci. Hortic. Amsterdam 107, 254–258 (2006)

    Article  Google Scholar 

  29. Sattler S.E., Saathoff A.J., Haas E.J., Palruer N.A., Funnell-Harris D.L., Sarath G., Pedersem J.F.: A nonsense mutation in a cinnamyl alcohol dehydrogenase gene is responsible for the sorghum brown midrib6 phenotype. Plant Physiol. 150, 584–595 (2009)

    Article  Google Scholar 

  30. Chen W., VanOpdorp N., Fitzl D., Fitzl D., Tewari J., Friedemann P., Greene T., Thompson S., Kumpatla S.: Transposon insertion in a cinnamyl alcohol dehydrogenase gene is responsible for a brown midrib1 mutation in maize. Plant Mol. Biol. 80, 289–297 (2012)

    Article  Google Scholar 

  31. Kaur H., Shaker K., Heinzel N., Ralph J., Galis I., Balduwin I.T.: Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies. Plant Physiol. 159, 1545–1570 (2012)

    Article  Google Scholar 

  32. Peng Z.H., Lu T.T., Li L.B., Liu X.H., Gao Z.M., Hu T., Yang X.W., Feng Q., Guan J.P., Weng Q.J., Fan D.L., Zhu C.R., Lu Y., Han B., Jiang Z.H.: Genome-wide characterization of the biggest grass, bamboo, based on 10608 putative full-length cDNA sequences. BMC Plant Biol. 10, 116–128 (2010)

    Article  Google Scholar 

  33. Prashant S., Srilakshmi S.M., Pramod S., Pramod S., Gupta R.K., Anil K.S., Rao K.S., Rawal S.K., Kavi Kishor P.B.: Downregulation of Leucaena leucocephala cinnamoyl CoA reductase (LlCCR) gene induces significant changes in phenotype, soluble phenolic pools and lignin in transgenic tobacco. Plant Cell Rep. 230, 2215–2231 (2011)

    Article  Google Scholar 

  34. Wagner A., Donaldson L., Kim H., Zhu H., Zhang L., Zhang Z., Zhang C., Ma Z.: Suppression of 4-coumarate-CoA ligase in the coniferous gymnosperm Pinus radiata. Plant Physiol. 149, 70–383 (2009)

    Article  Google Scholar 

  35. Gil-Amado J.A., Gomez-Jimenez M.C.: Regulation of polyamine metabolism and biosynthetic gene expression during olive mature-fruit abscission. Planta 235, 1221–1237 (2012)

    Article  Google Scholar 

  36. Bird D., Beisson F., Brigham A., Shin J., Greer S.: Characterization of arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J. 52, 485–498 (2007)

    Article  Google Scholar 

  37. Miao Y.C., Liu C.J.: ATP-binding cassette-like transporters are involved in the transport of lignin precursors across plasma and vacuolar membranes. Proc. Natl. Acad. Sci. USA 107, 22728–22733 (2010)

    Article  Google Scholar 

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    Authors and Affiliations

    1. College of Forestry, Shandong Agricultural University, P.O.BOX 271018, Taian, China

      Ting Ting Liang, Yan Ma, Jing Guo & De Kui Zang

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    1. Ting Ting Liang
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    2. Yan Ma
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    3. Jing Guo
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    4. De Kui Zang
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    Correspondence to De Kui Zang.

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    The first author’s Liang Ting Ting and Ma Yan contributed equally to this paper.

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    Liang, T.T., Ma, Y., Guo, J. et al. Transcriptome Sequencing and Analysis of Wild Pear (Pyrus hopeiensis) Using the Illumina Platform. Arab J Sci Eng 41, 45–53 (2016). https://doi.org/10.1007/s13369-015-1725-7

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    • DOI: https://doi.org/10.1007/s13369-015-1725-7

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