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Comparative genomic and phylogenetic analyses of Populus section Leuce using complete chloroplast genome sequences

Abstract

Species of Populus section Leuce are distributed throughout most parts of the Northern Hemisphere and have important economic and ecological significance. However, due to frequent hybridization within Leuce, the phylogenetic relationship between species has not been clarified. The chloroplast (cp) genome is characterized by maternal inheritance and relatively conservative mutation rates; thus, it is a powerful tool for building phylogenetic trees. In this study, we used the PacBio SEQUEL software to determine that the cp genome of Populus tomentosa has a length of 156,558 bp including a long single-copy region (84,717 bp), a small single-copy region (16,555 bp), and a pair of inverted repeat regions (27,643 bp). The cp genome contains 131 unique genes, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. We compared the cp genomes of seven species of section Leuce and identified five cp DNA markers with > 1% variable sites. Phylogenetic analyses revealed two evolutionary branches for section Leuce. The species with the closest relationship with P. tomenstosa was P. adenopoda, followed by P. alba. These cp genome data will help to determine the cp evolution of section Leuce and further elucidate the origin of P. tomentosa.

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Funding

This work was supported by the National Key Program on Transgenic Research (2018ZX08020002-002-004), the National Natural Science Foundation of China (31570661), the Graduate Training and Development Program of Beijing Municipal Commission of Education (BLCXY201512), and the medium-long-term project of young teachers (2015ZCQ-SW-01).

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Kai Gao and Xinmin An conceived and revised the experiment; Kai Gao, Tianyun Zhao, and Xiaoyu Yang assembled sequences and analyzed the data; Kai Gao, Juan Li, and Wasif Ullah Khan wrote the manuscript; Xiong Yang and Bin Guo collected the plant materials. All authors have read and approved the final version of the manuscript.

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Correspondence to Xinmin An.

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The authors declare that they have no conflict of interest.

Data archiving statement

The final P. tomentosa cp sequence was submitted to the NCBI database with the GenBank accession number MK251149.

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Gao, K., Li, J., Khan, W.U. et al. Comparative genomic and phylogenetic analyses of Populus section Leuce using complete chloroplast genome sequences. Tree Genetics & Genomes 15, 32 (2019). https://doi.org/10.1007/s11295-019-1342-9

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Keywords

  • Chloroplast genome
  • PacBio SEQUEL
  • Phylogenetic analysis
  • Populus tomentosa