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High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species that is widespread in Asia
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  • Xinmin An,
  • Kai Gao,
  • Zhong Chen,
  • Juan Li,
  • Xiong Yang,
  • Xiaoyu Yang,
  • Jing Zhou,
  • Ting Guo,
  • Tianyun Zhao,
  • Sai Huang,
  • Deyu Miao,
  • Wasif Ullah Khan,
  • Pian Rao,
  • Meixia Ye,
  • Bingqi Lei,
  • Weihua Liao,
  • Jia Wang,
  • Lexiang Ji,
  • Ying Li,
  • Bin Guo,
  • Nada Siddig Mustafa,
  • Shanwen Li,
  • Quanzheng Yun,
  • Stephen Keller,
  • Jianfeng Mao,
  • Rengang Zhang,
  • Steven Strauss
Xinmin An
Beijing Forestry University
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Kai Gao
Beijing Forestry University
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Zhong Chen
Beijing Forestry University
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Juan Li
Beijing Forestry University
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Xiong Yang
Beijing Forestry University
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Xiaoyu Yang
Beijing Forestry University
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Jing Zhou
Beijing Forestry University
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Ting Guo
Beijing Forestry University
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Tianyun Zhao
Beijing Forestry University
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Sai Huang
Beijing Forestry University
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Deyu Miao
Beijing Forestry University
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Wasif Ullah Khan
Beijing Forestry University
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Pian Rao
Beijing Forestry University
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Meixia Ye
Beijing Forestry University
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Bingqi Lei
Beijing Forestry University
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Weihua Liao
Beijing Forestry University
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Jia Wang
Beijing Forestry University
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Lexiang Ji
Beijing Forestry University
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Ying Li
Beijing Forestry University
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Bin Guo
Beijing Forestry University
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Nada Siddig Mustafa
Beijing Forestry University
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Shanwen Li
Shandong Academy of Forestry
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Quanzheng Yun
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Stephen Keller
University of Vermont
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Jianfeng Mao
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Rengang Zhang
Beijing Ori-Gene Science and Technology Co.,Ltd.
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Steven Strauss
Oregon State University
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Abstract

Populus has a wide ecogeographical range spanning the Northern Hemisphere, and exhibits abundant distinct species and hybrids globally. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo, chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n=2x=38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, approximately 3.93 Mya. Although highly colinear, significant structural variation was also found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.

Peer review status:UNDER REVIEW

23 Apr 2021Submitted to Molecular Ecology Resources
01 Jun 2021Assigned to Editor
01 Jun 2021Submission Checks Completed
09 Jun 2021Reviewer(s) Assigned