文献类型：期刊文献

英文题名：Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella

作者：Qin, Yue[1] Zhao, Han[1] Han, Hongwei[2] Zhu, Gaopu[1] Wang, Zhaoshan[3] Li, Fangdong[1]

第一作者：Qin, Yue

通信作者：Zhu, GP[1];Wang, ZS[2]

机构：[1]Chinese Acad Forestry, Res Inst Nontimber Forestry, Zhengzhou 450003, Peoples R China;[2]Xinjiang Acad Forestry, Econ Forest Res Inst, Urumqi 830000, Peoples R China;[3]Chinese Acad Forestry, Res Inst Forestry, Beijing 100091, Peoples R China

年份：2023

卷号：24

期号：14

外文期刊名：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

收录：;Scopus(收录号：2-s2.0-85165993663);WOS:【SCI-EXPANDED(收录号:WOS:001035919200001)】；

语种：英文

外文关键词：P; tenella; genome; assembly; almond; population genetic structure

摘要：Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.