Qin, Y.; Zhao, H.; Han, H.; Zhu, G.; Wang, Z.; Li, F. Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella. Int. J. Mol. Sci.2023, 24, 11735.
Qin, Y.; Zhao, H.; Han, H.; Zhu, G.; Wang, Z.; Li, F. Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella. Int. J. Mol. Sci. 2023, 24, 11735.
Qin, Y.; Zhao, H.; Han, H.; Zhu, G.; Wang, Z.; Li, F. Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella. Int. J. Mol. Sci.2023, 24, 11735.
Qin, Y.; Zhao, H.; Han, H.; Zhu, G.; Wang, Z.; Li, F. Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella. Int. J. Mol. Sci. 2023, 24, 11735.
Abstract
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 of 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, 231Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32088 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 exhibit many presence/absence variants. Moreover, a large inversion at the 7,588 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 protecting, developing, and utilizing P. tenella germplasm resources.
Keywords
Prunus tenella; genome; assembly; almond; population genetic structure
Subject
Biology and Life Sciences, Horticulture
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
