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Comparative study on the chloroplast genomes of five Larix species from the Qinghai-Tibet Plateau and the screening of candidate DNA markers

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Abstract

Five Larix species (L. griffithii, L. speciose, L. himalaica, L. kongboensis, and L. potaninii var. australis), have survived on the Qinghai-Tibet Plateau (QTP) under specific climate conditions for decades. The lack of genomic information seriously hinders research on the evolution, conservation and ecology of these Larix resources. In this study, complete chloroplast (cp) genomes of the 5 species were assembled and compared based on next generation sequencing technology combined with polymerase chain reaction validation. The results show that the 5 cp genomes are relatively conservative in size, gene content and arrangement, and border variation. Phylogenetic analysis showed that the species are closely related as well as to seven other species of the same genus. In addition, the 5 cp genomes contained few simple sequence repeats and relatively low nucleotide variability; thus, 12 candidate polymorphic cp DNA markers will be helpful for further research on relevant population genetics. These results will provide valuable genetic information for the conservation, evolution and ecology of these species and their relatives.

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Authors and Affiliations

  1. Institute for Forest Resources & Environment of Guizhou/College of Forestry, Guizhou University, Guiyang, 550025, People’s Republic of China

    Qiqiang Guo

  2. College of Agriculture, Guizhou University, Guiyang, 550025, People’s Republic of China

    Huie Li

  3. College of Life Sciences, Shaanxi Normal University, Xi’an, 710062, People’s Republic of China

    Zengqiang Qian

  4. Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agriculture & Animal Husbandry University), Ministry of Education, Nyingchi, 860000, Tibet, People’s Republic of China

    Jie Lu & Weilie Zheng

  5. Institute of Tibet Plateau Ecology, Tibet Agriculture & Animal Husbandry University, Nyingchi, 860000, Tibet, People’s Republic of China

    Jie Lu & Weilie Zheng

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  1. Qiqiang Guo
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  2. Huie Li
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  3. Zengqiang Qian
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  4. Jie Lu
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  5. Weilie Zheng
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Correspondence to Qiqiang Guo or Weilie Zheng.

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Project funding: This work was supported by the National Natural Science Foundation of China (31660215), the Construction Project for First-Class Ecology Discipline in Guizhou (GNYL [2017] 007), China, and Major Scientific and Technological Projects of Guizhou Province ([2018]5261), China.

The online version is available at http://www.springerlink.com

Corresponding editor: Yanbo Hu.

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Guo, Q., Li, H., Qian, Z. et al. Comparative study on the chloroplast genomes of five Larix species from the Qinghai-Tibet Plateau and the screening of candidate DNA markers. J. For. Res. 32, 2219–2226 (2021). https://doi.org/10.1007/s11676-020-01279-4

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  • DOI: https://doi.org/10.1007/s11676-020-01279-4

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