Chloroplast genome data of five Amygdalus species: Clarifying genome structure and phylogenetic relationships

Yixiao Chen; Wenquan Bao; Dun Ao; Yue Bai; Haiguang Huang; Rong Yang; Lin Wang; Ta-Na Wuyun

doi:10.1016/j.dib.2024.110077

Chloroplast genome data of five Amygdalus species: Clarifying genome structure and phylogenetic relationships

Data Brief. 2024 Jan 24:53:110077. doi: 10.1016/j.dib.2024.110077. eCollection 2024 Apr.

Authors

Yixiao Chen¹, Wenquan Bao¹, Dun Ao¹, Yue Bai¹, Haiguang Huang², Rong Yang², Lin Wang³, Ta-Na Wuyun³

Affiliations

¹ Inner Mongolia Agricultural University, 010000, Hohhot, China.
² Inner Mongolia Academy of Forestry Science, 010000, Hohhot, China.
³ State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, 450003, Zhengzhou, China.

Abstract

Amygdalus species have considerable ecological and economic value, however, the phylogenetic relationships among Amygdalus remain controversy. In this study, we sequenced and assembled the chloroplast (cp) genomes of five Amygdalus species: Prunus communis, P. mongolica, P. pedunculata, P. triloba, and P. mira. We then conducted comparative genomic analyses and constructed their phylogenetic relationships. The genome length ranged from 157,870 to 158,451 bp, and 131 genes were annotated (86 protein-coding genes, 37 tRNAs, and 8 rRNAs). Additionally, 49-57 simple sequence repeats were detected, with most in the large single-copy region and with AT base preferences. Comparative genomic analyses revealed high similarities in structure, order, and gene content. However, we identified four highly divergent sequences: trnR-UCU-atpA, nbdhC-trnV-UAC, ycf4-cemA, and rpl32-trnL-UAG. The phylogenomic relationship analysis suggested that the Amygdalus species were grouped together, in which P. pedunculata, P. triloba, and Prunus tangutica were categorized into a branch, P. mongolica and Prunus davidiana were clustered a branch. This study provides an improved understanding of the genetic relationships among the Amygdalus and provides a basis for the development and utilization of Amygdalus resources.

Keywords: Amygdalus; Comparative genomics; Phylogenetic relationships; Sequence divergence.