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Analysis of the chloroplast genomes of four Pinus species in Northeast China: Insights into hybrid speciation and identification of DNA molecular markers

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Abstract

Species of the Pinus genus provide a classical model for studying hybrid speciation. Although studies on two narrowly distributed species (Pinus funebris and P. takahasii) concluded that they originated from two widespread species (P. sylvestris and P. densiflora) via hybrid speciation, the conclusion was based on a low number of informative restriction sites. In this study, we analyzed the sequences of four Pinus chloroplast (cp) genomes (P. sylvestris, P. densiflora, P. funebris and P. takahasii) to clarify whether hybrid speciation was involved. The complete cp-genomes of Pinus species ranged in size from 119,865 to 119,890 bp, similar to other Pinus species. Phylogenetic results based on the whole cp-genomes showed P. sylvestris clustered with P. funebris and P. takahasii, which suggested that P. sylvestris was the paternal parent in hybridization events. In an analysis of simple sequence repeats (SSRs), we detected a total of 69 SSRs repeats among the four Pinus cp-genomes; most were A or T bases. In addition, we identified divergent hotspot regions among the four Pinus cp-genomes (trnE-clpP, cemA-ycf4, petD-rpoA, psbD-trnT, and trnN-chlL), in P. sylvestris (psbD-trnT, trnN-chlL, psbB and rps8) and in P. densiflora (trnE-clpP, petD-rpoA, ycf3 intron, psbD-trnT, and trnN-chlL). The genome information found in this study provides new insights into hybrid speciation in Pinus and contributes to a better understanding of the phylogenetic relationships within the Pinus genus.

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Data availability

The complete chloroplast genome sequence data of the four Pinus species have been submitted to GenBank of NCBI: P. densiflora MT786135, P. sylvestris MT796488, P. takahasii MT786134, P. funebris MT793600. We released the raw data to the National Genomics Data Center (NGDC). The GSA DATA and submission is: CRA003870. The data will be available publicly upon publication.

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Funding

This research was funded by Kunyu Mountain National Nature Reserve Administration.

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Author notes

  1. Tao Yu and Zhiyuan Jia have equally contributed to this work and share the first authorship.

Authors and Affiliations

  1. Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Tao Yu, Zhiyuan Jia & Junqing Li

  2. School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia

    Buddhi Dayananda

  3. Kunyu Mountain National Nature Reserve Administration, Yantai, 264113, People’s Republic of China

    Xiaolei Guo

  4. Yantai Kunyu Mountain Forest Farm, Yantai, 264113, People’s Republic of China

    Liang Shi, Xiaowen Yuan & Yan Gao

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  1. Tao Yu
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Correspondence to Junqing Li.

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Corresponding editor: Yanbo Hu.

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Yu, T., Jia, Z., Dayananda, B. et al. Analysis of the chloroplast genomes of four Pinus species in Northeast China: Insights into hybrid speciation and identification of DNA molecular markers. J. For. Res. 33, 1881–1890 (2022). https://doi.org/10.1007/s11676-021-01432-7

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