# Comparative Plastome Analysis of Artocarpus Species in China: Insight Into Adaptive Evolution and Mutational Hotspot Regions

## TL;DR

This study compares the plastomes of 10 Chinese Artocarpus species to understand their evolution and identify useful genetic markers.

## Contribution

The study identifies 13 genes under positive selection and 12 hypervariable regions as potential molecular markers for Artocarpus species.

## Key findings

- Plastomes of ten Chinese Artocarpus species show typical quadripartite structure with sizes between 160,184 bp and 161,009 bp.
- 13 protein-coding genes were found under positive selection, indicating roles in adaptation and function.
- Phylogenetic analysis divided the genus into two clades with consistent topological structures.

## Abstract

The genus Artocarpus J. R. Forst. & G. Forst., with about 70 species worldwide, contains roughly 15 species in China. Nevertheless, the phylogenetic relationships among these Chinese Artocarpus are incompletely understood. Here, we analyzed plastomes of ten Chinese Artocarpus species. These plastomes have a typical quadripartite structure, and sizes ranging from 160,184 bp to 161,009 bp. Simple sequence repeats (SSRs) numbered 73 to 95, while dispersed repeats ranged from 51 to 81. The protein‐coding genes displayed comparable RSCU patterns with minor variations. The genes ycf1 and ndhF showed varying degrees of expansion and contraction at their boundaries. Analysis of selective pressures in 72 protein‐coding genes revealed a predominance of purifying selection, with an average Ka/Ks ratio of 0.23, as well as evidence of positive selection in specific genes. Positive selection was detected in the genes atpF, rpoC2, rpoC1, cemA, rpl20, clpP, petD, rps8, rps3, rps19, ycf2, ycf1, and ndhD within the plastomes of ten Artocarpus species in China. Phylogenetic analyses demonstrated a high degree of consistency in their main topological structures, dividing the genus Artocarpus into Clade A and Clade B. The highly variable regions trnH‐psbA, trnG‐UCC‐trnR‐UCU, trnS‐UGA, trnT‐UGU‐trnL‐UAA, and rps19 were suggested as molecular markers for distinguishing between these clades. Additionally, the study also identified 12 distinct highly variable regions, which represent potential molecular markers for Artocarpus. These results not only enhance our understanding of the phylogenetic relationships within Chinese Artocarpus but also underscore the utility of these specific molecular markers for future studies in this genus.

The initial comparative plastome analysis of 10 Artocarpus species in China lays the groundwork for regional evolutionary research. Investigated of inverted repeat (lR) boundary variations, particularly the incomplete duplication of the ycf1 gene, elucidating mechanisms underlying genomic divergence. Identification of 13 genes under positive selection reveals their roles in environmental adaptation and functional regulation. Constructed highly supported phylogenetic trees using plastome and protein‐coding genes, establishing two clades within the Artocarpus genus. Assessed genetic diversity and identified hypervariable regions (mutation hotspots), providing new avenues for Artocarpus species identification and systematic studies.