Abstract
Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.
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References
Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664
Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K (2011) Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol 52(2):274–282
Augustus software. [http://bioinf.uni-greifswald.de/augustus/]
Blackman CJ, Brodribb TJ, Jordan GJ (2010) Leaf hydraulic vulnerability is related to conduit dimensions and drought resistance across a diverse range of woody angiosperms. New Phytol 188(4):1113–1123
Cao K, Zheng ZJ, Wang LR, Liu X, Zhu GR, Fang WC, Cheng SF, Zeng P, Chen CW, Wang XW, Xie M, Zhong X, Wang XL, Zhao P, Bian C, Zhu YL, Zhang JH, Ma GS, Chen CX, Li YJ, Hao FG, Li Y, Huang GD, Li YX, Li HY, Guo J, Xu X, Wang J (2014) Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biol 15:415
Cao K, Zhou ZK, Wang Q, Guo J, Zhao P, Zhu GR, Fang WC, Chen CW, Wang XW, Wang XL, Tian ZX, Wang LR (2016) Genome-wide association study of 12 agronomic traits in peach. Nat Commun 7:13246
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang QY, Locke DP, Shi XQ, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6:677–681
Conesa A, Gotz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 619832
Felsenstein J (1989) PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164–166
Hacke UG, Spicer R, Schreiber SG, Plavcova L (2016) An ecophysiological and developmental perspective on variation in vessel diameter. Plant Cell Environ 40:831–845
Harris RS (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University
Hu HH, Xiong LZ (2014) Genetic engineering and breeding of drought-resistant crops. Annu Rev Plant Biol 65:715–741
InterPro database. [https://www.ebi.ac.uk/interpro/]
Janick J (2011) Origin and dissemination of Prunus crops - Peach, Cherry, Apricot, Plum, Almond. Scripta Horticulturae, No 11, The American Pomological Society, Leuven
Kyoto Encyclopedia of Genes and Genomes database. [http://www.genome.jp/kegg/].
Luo RB, Liu BH, Xie YL, Li ZY, Huang WH, Yuan JY, He GZ, Chen YX, Pan Q, Liu YJ, Tang JB, Wu GX, Zhang H, Shi YJ, Liu Y, Yu C, Wang B, Lu Y, Han CL, Cheung DW, Yiu SM, Peng SL, Zhu XQ, Liu GM, Liao XK, Li YR, Yang HM, Wang J, Lam T, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The genome analysis toolkit: a map reduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303
Mowrey BD, Wemer DJ, Byrne DH (1990) Isozyme survey of various species of Prunus in the subgenus Amygdalus. Sci Hortic 44:251–260
Okie WR (2001) Plum crazy: rediscovering our lost Prunus resources. HortSci 36:209–213
Park S, Yu HJ, Mun JH, Lee SC (2010) Genome-wide discovery of DNA polymorphism in Brassica rapa. Mol Gen Genomics 283(2):135–145
Scoffoni C, Albuquerque C, Brodersen CR, Townes SV, John GP, Cochard H, Buckley TN, McElrone AJ, Sack L (2017) Leaf vein xylem conduit diameter influences susceptibility to embolism and hydraulic decline. New Phytol 213(3):1076–1092
Sun LD, Zhang QX, Xu ZD, Yang WR, Guo Y, Lu JX, Pan HT, Cheng TR, Cai M (2013) Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.). BMC Genet 14:98
SwissProt database. [http://www.uniprot.org/].
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 45:487–494
Vcftools software. [https://vcftools.github.io/index.html]
Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu SQ, Grimwood J, Tartarini S, Dettori MT, Schmutz J (2017) The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics 18:225
Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:293–297
Yoon J, Liu DC, Song W, Liu WS, Zhang AM, Li SH (2006) Genetic diversity and ecogeographical phylogenetic relationships among peach and nectarine cultivars based on simple sequence repeat (SSR) markers. J Am Soc Hortic Sci 131:513–521
Yoon JH, Yang DC, Liu DC, Song WS, Zhang AM, Li SH (2009) Phylogenetic relationships among cultivars of Prunus persica based on internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA. J Horticult Sci Biotechnol 84:167–174
Yu DJ (1979) Taxonomy of Chinese fruit tree. Agriculture press, Beijing, pp 25–81 (in Chinese)
Zhang JS, Zhang H, Srivastava AK, Pan YJ, Bai JJ, Fang JJ, Shi HZ, Zhu JK (2018) Knock-down of rice microRNA166 confers drought resistance by causing leaf rolling and altering stem xylem development. Plant Physiol. https://doi.org/10.1104/pp.17.01432
Zheng YF, Crawford GW, Chen XG (2014) Archaeological evidence for peach (Prunus persica) cultivation and domestication in China. PLoS One 9(9):e106595
Data archiving statement
Supporting data of Data S1, and S2S2 are included as additional files in the manuscript. All raw sequences of the 15 peach accessions have been deposited in the Sequence Read Archive (SRA) of National Center for Biotechnology Information with accession codes SRX268334, SRX268357, SRX268316, SRX268383, SRX268318, SRX268336, SRX268343, SRX268329, SRX268315, and SRX268324 or in Figshare database (https://figshare.com/s/e92fc6a391cfa2c67150). The high-depth sequencing data of two accessions and resequencing data of 31 accessions for population structure analysis have been deposited into the NCBI Sequence Read Archive (SRA) under accession SRP168153. All other relevant data are available from the corresponding author on request.
Funding
This work was supported by the Chinese Academy of Agricultural Sciences (Grant CAAS-ASTIP-2017-ZFRI-01), the Ministry of Science and Technology of China (2013AA102606), and the Ministry of Agriculture of China (2016NWB041). Each of the funding bodies granted the funds based on a research proposal. They had no influence over the experimental design, data analysis or interpretation, or writing of the manuscript.
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LW and KC designed research. WF carried out the experimental work. CC and XW contributed reagents/materials/analysis tools. GZ carried out the interpretation of results and critical revision of the manuscript. KC analyzed all the data and wrote the manuscript. All the authors read and approved the final manuscript.
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Communicated by V. Decroocq
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Supplementary Table 1
The description of peach samples used in this study and its sequencing results to perform phylogenetic and population analysis (XLSX 12 kb)
Data S1
Specific gene in assembling sequence using unmapped reads of ‘Xia Miao 1’ (Prunus persica) (FA 1512 kb)
Data S2
Specific gene in assembling sequence using unmapped reads of ‘Xia Miao 1’ (Prunus persica) (FA 701 kb)
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Cao, K., Wang, L., Zhu, G. et al. High-throughput sequencing of Prunus ferganensis indicates that it is a geographical population of P. persica. Tree Genetics & Genomes 14, 92 (2018). https://doi.org/10.1007/s11295-018-1303-8
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DOI: https://doi.org/10.1007/s11295-018-1303-8