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Tree Genetics & Genomes

, 14:92 | Cite as

High-throughput sequencing of Prunus ferganensis indicates that it is a geographical population of P. persica

  • Ke Cao
  • Lirong Wang
  • Gengrui Zhu
  • Weichao Fang
  • Changwen Chen
  • Xinwei Wang
Original Article
  • 68 Downloads
Part of the following topical collections:
  1. Population structure

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.

Keywords

Collinearity Genetic variation Prunus ferganensis Short reads 

Notes

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.

Author contributions

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.

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.

Supplementary material

11295_2018_1303_MOESM1_ESM.xlsx (13 kb)
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)
11295_2018_1303_MOESM2_ESM.fa (1.5 mb)
Data S1 Specific gene in assembling sequence using unmapped reads of ‘Xia Miao 1’ (Prunus persica) (FA 1512 kb)
11295_2018_1303_MOESM3_ESM.fa (702 kb)
Data S2 Specific gene in assembling sequence using unmapped reads of ‘Xia Miao 1’ (Prunus persica) (FA 701 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouChina

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