Skip to main content

ORIGINAL RESEARCH article

Front. Genet.
Sec. Genomics of Plants and the Phytoecosystem
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1468596
This article is part of the Research Topic Applied Research on Plant Organelle Genomes and Key Genes View all articles

Chloroplast Genome Sequencing and Divergence Analysis of 18 Pyrus Species: Insights into Intron Length Polymorphisms and Evolutionary Processes

Provisionally accepted
Jung Sun Kim Jung Sun Kim 1*Hoyong Chung Hoyong Chung 2Bohyeon Park Bohyeon Park 2Karpagam Veerappan Karpagam Veerappan 2Yoon-Kyung Kim Yoon-Kyung Kim 3
  • 1 Rural Development Administration (South Korea), Jeonju, Republic of Korea
  • 2 3BIGS Co. Ltd., Hwaseong, South Korea, Hwaseong, Republic of Korea
  • 3 Pear Research Institute, National Institute of Horticultural and Herbal Science, Republic Korea, Naju, Republic of Korea

The final, formatted version of the article will be published soon.

    Pears, an essential temperate crop, are primarily produced through interspecific hybridization due to their self-incompatibility, which complicates their breeding history. To address this, we sequenced the complete chloroplast (cp) genomes of 18 Pyrus species and 1 Malus species using the Illumina HiSeq4000 platform. The cp genomes, which ranged from 159,885 to 160,153 bp, exhibited a conserved circular DNA structure with an average GC content of 36.5%. Each cp genome contained 127 genes, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Divergence analysis with mVISTA showed high conservation in coding regions and notable variation in non-coding regions. All species shared 17 intron-containing genes, with ycf3 and clpP each having two introns. Five introncontaining genes (ndhB, rpl2, rps12, trnA-UGC, and trnE-UUC) were located in IR regions, while trnL-UAA was in the LSC region, with conserved intron lengths across Pomoideae. We identified polymorphic intron sequences in rpl22, petB, clpP, ndhA, and rps16, and designed primers for these regions. Notably, the two Pyrus ussuriensis accessions, Doonggeullebae and Cheongdangrori, showed intron length polymorphisms despite being classified as the same species. Phylogenetic analysis of cp genome sequences revealed two major clusters, indicating distinct maternal lineages and evolutionary origins. This study underscores the importance of cp gene polymorphisms in P. fauriei, P. calleryana, P. ussuriensis, and P. pyrifolia, providing valuable insights into Pyrus evolution and aiding in the conservation and breeding of pear germplasm.

    Keywords: Chloroplast genome, Pyrus ussuriensis, Pyrus pyrifolia, phylogeny, Next-generation sequencing

    Received: 22 Jul 2024; Accepted: 26 Sep 2024.

    Copyright: © 2024 Kim, Chung, Park, Veerappan and Kim. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Jung Sun Kim, Rural Development Administration (South Korea), Jeonju, Republic of Korea

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.