J Syst Evol ›› 2020, Vol. 58 ›› Issue (2): 118-132.DOI: 10.1111/jse.12492

• Research Articles • Previous Articles     Next Articles

Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships

Umar Zeb1†, Wan-Lin Dong1†, Ting-Ting Zhang1, Ruo-Nan Wang1, Khurram Shahzad1, Xiong-Feng Ma2*, and Zhong-Hu Li1*   

  1. 1Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
    2Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China
  • Received:2018-06-20 Accepted:2019-03-05 Online:2019-03-25 Published:2020-03-01


Pinus L. is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms. However, our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny. Thus, we analyzed the sequences of 97 Pinus plastid genomes, including four newly sequenced genomes and 93 previously published plastomes, to explore the evolution and phylogenetic relationships in the genus Pinus. The complete chloroplast genomes of Pinus species ranged in size from 109 640 bp (P. cembra L.) to 121 976 bp (P. glabra Walter), and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms. We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983 (44%), followed by tandem repeats with 2999 (33%), and then palindromic repeats with 2126 (23%). Sixteen divergence hotspot regions were identified in Pinus plastid genomes, which could be useful molecular markers for future population genetics studies. Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus (single needle section) and Pinus (double needles section). Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous. The two subgenera subsequently split 85.86 Mya, which was largely consistent with the other molecular results based on partial DNA markers. These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes.

Key words: divergence time, molecular evolution, phylogenetic relationship, Pinus, plastid genome