High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia. An, X., Gao, K., Chen, Z., Li, J., Yang, X., Yang, X., Zhou, J., Guo, T., Zhao, T., Huang, S., Miao, D., Ullah Khan, W., Rao, P., Ye, M., Lei, B., Liao, W., Wang, J., Ji, L., Li, Y., Guo, B., Siddig Mustafa, N., Li, S., Yun, Q., Keller, S. R., Mao, J., Zhang, R., & Strauss, S. H. Molecular Ecology Resources, 22(2):786–802, 2022. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13507
High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia [link]Paper  doi  abstract   bibtex   
Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. 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 throughout the genus. 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, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.
@article{an_high_2022,
	title = {High quality haplotype-resolved genome assemblies of {Populus} tomentosa {Carr}., a stabilized interspecific hybrid species widespread in {Asia}},
	volume = {22},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13507},
	doi = {10.1111/1755-0998.13507},
	abstract = {Populus has a wide ecogeographical range spanning the Northern Hemisphere, and interspecific hybrids are common. 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 throughout the genus. 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, with an origin of approximately 3.93 Ma. Although highly colinear, significant structural variation was found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.},
	language = {en},
	number = {2},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {An, Xinmin and Gao, Kai and Chen, Zhong and Li, Juan and Yang, Xiong and Yang, Xiaoyu and Zhou, Jing and Guo, Ting and Zhao, Tianyun and Huang, Sai and Miao, Deyu and Ullah Khan, Wasif and Rao, Pian and Ye, Meixia and Lei, Bingqi and Liao, Weihua and Wang, Jia and Ji, Lexiang and Li, Ying and Guo, Bin and Siddig Mustafa, Nada and Li, Shanwen and Yun, Quanzheng and Keller, Stephen R. and Mao, Jian-Feng and Zhang, Ren-Gang and Strauss, Steven H.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13507},
	keywords = {PacBio long-read sequencing, Populus tomentosa, forest biotechnology, haplotype-resolved genome assembly, hybridization},
	pages = {786--802},
}
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