Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species

Ru Yi; Wenquan Bao; Dun Ao; Yu-E Bai; Lin Wang; Ta-Na Wuyun

doi:10.3390/genes14101959

Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species

Genes (Basel). 2023 Oct 18;14(10):1959. doi: 10.3390/genes14101959.

Authors

Ru Yi¹, Wenquan Bao¹, Dun Ao¹, Yu-E Bai¹, Lin Wang^{2

3}, Ta-Na Wuyun^{2

3}

Affiliations

¹ College of Forestry, Inner Mongolia Agricultural University, Hohhot 010018, China.
² State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China.
³ Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China.

Abstract

The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and kernel consumption apricot were sequenced, characterized, and phylogenetically analyzed. The three chloroplast (cp) genomes ranged from 157,951 to 158,224 bp, and 131 genes were identified, including 86 protein-coding genes, 37 rRNAs, and 8 tRNAs. The GC content ranged from 36.70% to 36.75%. Of the 170 repetitive sequences detected, 42 were shared by all three species, and 53-57 simple sequence repeats were detected with AT base preferences. Comparative genomic analysis revealed high similarity in overall structure and gene content as well as seven variation hotspot regions, including psbA-trnK-UUU, rpoC1-rpoB, rpl32-trnL-UAG, trnK-rps16, ndhG-ndhI, ccsA-ndhD, and ndhF-trnL. Phylogenetic analysis showed that the three apricot species clustered into one group, and the genetic relationship between P. armeniaca and kernel consumption apricot was the closest. The results of this study provide a theoretical basis for further research on the genetic diversity of apricots and the development and utilization of molecular markers for the genetic engineering and breeding of apricots.

Keywords: Rosaceae; chloroplast genome; comparative genomics; phylogenetic relationship; repetitive sequence.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Chloroplast*
Genomics / methods
Phylogeny
Plant Breeding
Prunus armeniaca* / genetics

Grants and funding

This research was supported by the Inner Mongolia Agricultural University Young Teachers Scientific Research Ability Promotion Project, grant number BR220114; the National Natural Science Foundation of CHINA, grant number 32360400; and the Program of Research and Demonstration of Key Technology of High-efficient Production in Kernel-aprico and Almond, grant number 2013BAD14B02.