An improved draft genome sequence of hybrid Populus alba × Populus glandulosa

• Published in: Journal of forestry research Vol. 32; no. 4; pp. 1663 - 1672
• Main Authors: Huang, Xiong, Chen, Song, Peng, Xiaopeng, Bae, Eun-Kyung, Dai, Xinren, Liu, Guiming, Qu, Guanzheng, Ko, Jae-Heung, Lee, Hyoshin, Chen, Su, Li, Quanzi, Lu, Mengzhu
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 01.08.2021; Springer Nature B.V; Research Institute of Forestry,Chinese Academy of Forestry, Beijing 100091,People's Republic of China%State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University,Harbin 150040, People's Republic of China%Research Institute of Forestry,Chinese Academy of Forestry, Beijing 100091,People's Republic of China%Division of Forest Biotechnology,National Institute of Forest Science,Suwon 441847,Republic of Korea%State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry,Beijing 100091, People's Republic of China%Agro-Biotechnology Research Center,Beijing Academy of Agriculture and Forestry Sciences,Beijing 100097, People's Republic of China%Department of Plant&Environmental New Resources, Kyung Hee University,Yongin 446701,Republic of Korea; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry,Beijing 100091, People's Republic of China
• Subjects: Annotations; Assembly; Biomedical and Life Sciences; China; Coverage; Forestry; Genes; Genetic transformation; genome assembly; Genomes; Heterozygosity; hybrid poplars; Life Sciences; multiomics; Nucleotide sequence; nucleotide sequences; Original Paper; Populus alba; South Korea; trees; Woody plants; South Korea; China; cl. 84 K; Genome assembly; Gene annotation; Hybrid poplar; Populus alba × p. glandulosa cl. 84 K
• ISSN: 1007-662X; 1993-0607
• DOI: 10.1007/s11676-020-01235-2

Populus alba  ×  P. glandulosa clone 84 K, derived from South Korea, is widely cultivated in China and used as a model in the molecular research of woody plants because of high gene transformation efficiency. Here, we combined 63-fold coverage Illumina short reads and 126-fold coverage PacBio long reads to assemble the genome. Due to the high heterozygosity level at 2.1% estimated by k -mer analysis, we exploited TrioCanu for genome assembly. The PacBio clean subreads of P. alba  ×  P. glandulosa were separated into two parts according to the similarities, compared with the parental genomes of P. alba and P. glandulosa . The two parts of the subreads were assembled to two sets of subgenomes comprising subgenome A (405.31 Mb, from P. alba ) and subgenome G (376.05 Mb, from P. glandulosa ) with the contig N50 size of 5.43 Mb and 2.15 Mb, respectively. A high-quality P. alba  ×  P. glandulosa genome assembly was obtained. The genome size was 781.36 Mb with the contig N50 size of 3.66 Mb and the longest contig was 19.47 Mb. In addition, a total of 176.95 Mb (43.7%), 152.37 Mb (40.5%) of repetitive elements were identified and a total of 38,701 and 38,449 protein-coding genes were predicted in subgenomes A and G, respectively. For functional annotation, 96.98% of subgenome A and 96.96% of subgenome G genes were annotated with public databases. This de novo assembled genome will facilitate systematic and comprehensive study, such as multi-omics analysis, in the model tree P. alba  ×  P. glandulosa .