The Comparative Study on Molecular Phylogenetics and Development of Microsatellite Primers From Durian Chloroplast Genomes

Tran Gia Huy, Pham Thanh Phuc, Nguyen Pham Anh Thi, Tran Van Be Nam, Do Tan Khang

Ecol Evol.; 2025 Oct 7; 15(10):e72245. doi: 10.1002/ece3.72245.

Abstract

Durian, or Durio zibethinus, is an exotic fruit with high economic value in Southeast Asia. This study aims to determine the genetic variants based on the chloroplast genome between species and cultivars in the Durio genus and design the molecular marker based on microsatellite resources. The research was conducted by collecting the data of 8 chloroplast genomes followed by the genome structure and organization analysis, variants analysis, phylogenetic relationship analysis, and possibly, primer designing. The results illustrate that regions with high Pi values for the nucleotide diversity analysis were the regions in ycf1, psbZ-rps14, accD, and rpl33-rps18. Although the nucleotide diversity analysis had shown various hotspots from the current data of complete chloroplast genomes of the Durio genus, the accD gene was shown to have a high Pi value between species but failed to distinguish between variants of the same species. Furthermore, 13 primer SSR regions were selected from 135 SSRs, and the corresponding primer pairs were designed for amplification. Durio zibethinus cv. Ri6 has a close relationship to other Durio zibethinus cultivars but has high genetic divergence from other Durio genus species. Both the phylogenetic trees constructed from SNPs/InDels and from CDS data produced concordant clustering results, revealing consistent genetic relationships among species within the genus Durio. The cp genomes are stated to be a useful tool in studying the phylogenetic relationship. In conclusion, the cp genomes are a useful tool and could be further utilized for molecular markers designing and the evolution history of the Durio genus.

See https://pubmed.ncbi.nlm.nih.gov/41063781/

Figure 4

Number of long repeats in chloroplast genomes of species in the Durio genus. (A) Repeat unit size. (B) Length of repeat.