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

## TL;DR

This study sequenced chloroplast genomes of five Amygdalus species to better understand their genetic relationships and structure.

## Contribution

The paper provides new chloroplast genome data and clarifies phylogenetic relationships among five Amygdalus species.

## Key findings

- The chloroplast genomes of five Amygdalus species were sequenced and show high structural similarity.
- Four highly divergent genomic regions were identified, offering insights into genetic variation.
- Phylogenetic analysis grouped the species into distinct branches, aiding in understanding their evolutionary relationships.

## 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.