Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution

Xiaomin Wang; Shengyi Bai; Zhaolei Zhang; Fushun Zheng; Lina Song; Lu Wen; Meng Guo; Guoxin Cheng; Wenkong Yao; Yanming Gao; Jianshe Li

doi:10.3389/fpls.2023.1179009

Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution

Front Plant Sci. 2023 May 9:14:1179009. doi: 10.3389/fpls.2023.1179009. eCollection 2023.

Authors

Xiaomin Wang^{1

2

3}, Shengyi Bai¹, Zhaolei Zhang⁴, Fushun Zheng¹, Lina Song¹, Lu Wen¹, Meng Guo^{1

2

3}, Guoxin Cheng^{1

2

3}, Wenkong Yao^{1

2

3}, Yanming Gao^{1

2

3}, Jianshe Li^{1

2

3}

Affiliations

¹ College of Enology and Horticultrue, Ningxia University, Yinchuan, China.
² Ningxia Modern Facility Horticulture Engineering Technology Research Center, Ningxia Facility Horticulture (Ningxia University) Technology Innovation Center, Yinchuan, China.
³ Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Ningxia University, Yinchuan, China.
⁴ Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China.

Abstract

In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average K _A/K _S ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.

Keywords: adaptive evolution; chloroplast genome; germplasm; phylogenetic; tomato.

Grants and funding

This research was funded by Ningxia Hui Autonomous Region Agricultural Special and Dominant Industry Breeding Project (NXNYYZ20200104).