Study on the differences of gene expression between pear and apple wild cultivation materials based on RNA-seq technique

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1. Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA. Phylogeny and classifcation of Rosaceae. Plant Syst Evol. 2007;266(1–2):5–43. 2. Jang JT. Identifcation of Pyrus species by leaf peroxidase isozyme phenotypes. J Jpn Soc Horticult Sci. 1992;61(2):273–86. 3. Silva GJ, Souza TM, Barbieri RL, Oliveira. Origin, domestication, and dispersing of pear (Pyrus spp.). Adv Agric. 2014;2014(1):1–8. 4. Zheng X, Cai D, Yao L, Teng Y. Non-concerted ITS evolution, early origin and phylogenetic utility of ITS pseudogenes in Pyrus. Mol Phylogenet Evol. 2008;48(3):892–903. 5. Tamura F, Tanabe K, Itai A, Morimoto M. Variations in the chilling requirements for breaking leaf bud endodormancy in wild pear species and pear cultivars. J Jpn Soc Horticult Sci. 2008;70(5):596–8. 6. Vavilov NI. Studies on the origin of cultivated plants. Trudy Byuro Prikl Bot. 1926;16:139–245. 7. Duan N, Yang B, Sun H, Nan W, Chen X. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nat Commun. 2017;8(1):249. 8. Pinhas. Domestication of fruit trees. Dev Agric. 1986;16:201. 9. Voltas J, Pemán J, Fusté F. Phenotypic diversity and delimitation between wild and cultivated forms of the genus Pyrus in North-eastern Spain based on morphometric analyses. Genet Resour Crop Evol. 2007;54(7):1473–87. 10. Li WM, Dita M, Rouard M, Wu W, Ge XJ. Deep RNA-seq analysis reveals key responding aspects of wild banana relative resistance to Fusarium oxysporum f. sp. cubense tropical race 4. Funct Integr Genomics. 2020;20:551–62. 11. Li M, Li L, Dunwell JM, Qiao X, Liu X, Zhang S. Characterization of the lipoxygenase (LOX) gene family in the Chinese white pear (Pyrus bretschneideri ) and comparison with other members of the Rosaceae. BMC Genomics. 2014;15(1):444. 12. Zhang XJ, Wang LX, Liu YL, Chen XX, Yang YZ, Zhao ZY. Diferential gene expression analysis of ‘Granny Smith’ apple (Malus domestica Borkh.) during fruit skin coloration. S Afr J Bot. 2013;88:125–31. 13. Li M, Li P, Ma F, Dandekar AM, Cheng L. Sugar metabolism and accumulation in the fruit of transgenic apple trees with decreased sorbitol synthesis. Horticult Res. 2018;5(1):1. 14. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23(2):396–408. 15. Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, Henri V, Bianco L, Micheletti D, Velasco R. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet. 2017;49(7):1099. 16. Zhang L, Hu J, Han X, Li J, Gao Y, Richards CM, Zhang C, Tian Y, Liu G, Gul H. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat Commun. 2019;10(1):1494. 17. Velasco R, Zharkikh A, Afourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Genetics DP. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet. 2010;42(10):833–9. 18. Zhen Q, Fang T, Peng Q, Liao L, Zhao L, Owiti A, Han Y. Developing genetagged molecular markers for evaluation of genetic association of apple SWEET genes with fruit sugar accumulation. Horticult Res. 2018;5(1):14. 19. Vimolmangkang S, Han Y, Wei G, Korban SS. An apple MYB transcription factor, MdMYB3, is involved in regulation of anthocyanin biosynthesis and fower development. BMC Plant Biol. 2013;13(1):176. 20. Chagnã D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P. The draft genome sequence of European pear (Pyrus communis L. ’Bartlett’). Plos One. 2014;9(4):e92644. 21. Wu J, Li LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL. High-density genetic linkage map construction and identifcation of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot. 2014;65(20):5771–81. 22. Potts SM, Khan MA, Han Y, Kushad MM, Korban SS. Identifcation of Quantitative Trait Loci (QTLs) for Fruit Quality Traits in Apple. Plant Mol Biol Rep. 2013;32(1):109–16. 23. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57. 24. Haas BJ, Zody MC. Advancing RNA-Seq analysis. Nat Biotechnol. 2010;28:421–3. 25. Zhen Z, Sun A, Yu C, Sheng B, Cheng YJ. Agrobacterium-mediated transformation of the apple rootstock Malus micromalus Makino with the Rolc gene. Vitro Cell Dev Biol Plant. 2006;42(6):491–7. 26. Li X, Ling K, Zhang J, Xie Y, Wang L, Yan Y, Na W, Xu J, Li C, Wang W. Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica ). Gigascience. 2016;5(1):1–5. 27. Yao GF, Zhang SL, Cao YF, Liu J, Wu J, Yuan J, Zhang HP, Xiao CC. Characteristics of components and contents of soluble sugars in pear fruits from diferent species. Scientia Agricultura Sinica. 2010;43(20):4229–37. 28. Sha S, Li J, Wu J, Zhang S. Characteristics of organic acids in the fruit of diferent pear species. Afr J Agric Res. 2011;6(10):2403. 29. Ernst J, Barjoseph Z. STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics. 2006;7(1):191. 30. Minoru K, Michihiro A, Susumu G, Masahiro H, Mika H, Masumi I, Toshiaki K, Shuichi K, Shujiro O, Toshiaki TJ. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36(Database issue):480–4. 31. Peter L, Steve H. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559. 32. Wang L, Feng Z, Wang X, Wang X, Zhang XJ. DEGseq: an R package for identifying diferentially expressed genes from RNA-seq data. Bioinformatics. 2010;26(1):136–8. 33. Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nat Biotechnol. 2012;29(7):572–3. 34. Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002;9:297. 35. Zhang X, Koo J, Eun JB. Antioxidant Activities of Methanol Extracts and phenolic compounds in Asian pear at diferent stages of maturity. Food Sci Biotechnol. 2006;15(1):44–50. 36. He CY, Cui K, Zhang JG, Duan AG, Zeng YF. Next-generation sequencingbased mRNA and microRNA expression profling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo. BMC Plant Biol. 2013;13(1):119. 37. Gofnet MC, Robinson TL, Lakso AN. A comparison of “Empire” apple fruit size and anatomy in unthinned and hand-thinned trees. J Pomology Horticult Sci. 1995;70(3):375–87. 38. Liao MA, Liu X, Deng GT, Chen SB, Ren YJ, Liu WG. Studies on the changes of endogenous hormones during fruit growth and development of two pear cultivars. J Fruit Sci. 2009;26:25–31. 39. Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Nat Rev Mol Cell Biol. 2006;7(11):847–59. 40. Love J, Bioerklund S, Vahala J, Hertzberg M, Kangasjaervi J, Sundberg B. Ethylene is an endogenous stimulator of cell division in the cambial meristem of Populus. Proc Natl Acad Sci USA. 2009;106(14):5984–9. 41. Zelitch I. Photosynthesis, photorespiration and plant productivity. Q Rev Biol. 1971;301–37. 42. Cha-Um S, Charoenpanich A, Roytrakul S, Kirdmanee C. Sugar accumulation, photosynthesis and growth of two indica rice varieties in response to salt stress. Acta Physiol Plant. 2009;31(3):477–86. 43. Tsuchihira A, Hanba YT, Kato N, Doi T, Maeshima M. Efect of overexpression of radish plasma membrane aquaporins on water-use efciency, photosynthesis and growth of Eucalyptus trees. Tree Physiol. 2010;30(3):417–30. 44. Hetherington Suzan EJ. Profling photosyrithetic competence in mango fruit. J Pomology Horticult Sci. 2015;72(5):755–63. 45. Karanjalker GR, Ravishankar KV, Shivashankara KS, Dinesh MR, Roy TK, Sudhakar Rao DV. A study on the expression of genes involved in Carotenoids and Anthocyanins during ripening in fruit peel of green, yellow, and red colored mango cultivars. Appl Biochem Biotechnol. 2018;184:140. 46. Pearce GW, Streeter LR. A report on the efect of light on pigment formation in apples. J Biol Chem. 1931;92:743–9. 47. Ban Y, Honda C, Hatsuyama Y, Igarashi M, Bessho H, Moriguchi T. Isolation and functional analysis of a MYB transcription factor gene that is a key regulator for the development of red coloration in apple skin. Plant Cell Physiology. 2007;48(7):958. 48. Takos AM, Felix WJ, Jacob SR, Jochen B, Robinson SP, Walker AR. Lightinduced expression of a MYB gene regulates anthocyanin biosynthesis in red apples. Plant Physiol. 2018;142(3):1216–32. 49. Gunasekera D, Santakumari M, Glinka Z, Berkowitz GA. Wild and cultivated barley genotypes demonstrate varying ability to acclimate to plant water defcits. Plant Sci. 1994;99(2):125–34. 50. Jiang W. Screening and utilization of wild rice with blast resistance genes. Entia Agricutura Sinica. 1996;29(6):21–28. 51. Qiang X, Liu Y, Zhu A, Wu X, Ye J, Yu K, Guo W, Deng X. Discovery and comparative profling of microRNAs in a sweet orange red-fesh mutant and its wild type. BMC Genomics. 2010;11(1):246. 52. Li Kun, Wang Yongzhang, Qu Haiyong. RNA-Seq analysis of compatible and incompatible styles of Pyrus species at the beginning of pollination. Plant Mol Biol. 2020;102(3):287–306. 53. Tikhomirov MM, Khorlin AY, Voelter W, Bauer H. High-performance liquid chromatographic investigation of the amino acid, amino sugar and neutral sugar content in glycoproteins. J Chromatogr A. 1978;167(DEC):197–203. 54. Young M, Wakefeld MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2):R14–R14.