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

文献类型： 外文期刊

第一作者： Cao, Ke

作者： Cao, Ke;Wang, Lirong;Zhu, Gengrui;Fang, Weichao;Chen, Changwen;Wang, Xinwei

作者机构：

关键词： Collinearity; Genetic variation; Prunus ferganensis; Short reads

期刊名称：TREE GENETICS & GENOMES （ 影响因子：2.297； 五年影响因子：2.547 ）

ISSN： 1614-2942

年卷期： 2018 年 14 卷 6 期

页码：

收录情况： SCI

摘要： 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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