Genome sequence and evolution of Betula platyphylla
Su Chen1 , Yucheng Wang1 , Lili Yu2 , Tao Zheng3 , Sui Wang1 , Zhen Yue3 , Jing Jiang1 , Sapna Kumari4 , Chunfang Zheng5 , Haibao Tang6,7 , Jun Li8 , Yuqi Li3 , Jiongjiong Chen9 , Wenbo Zhang1 , Hanhui Kuang9 , Jon S. Robertson10 , Patrick X. Zhao8 , Huiyu Li1 , Shengqiang Shu11 , Yordan S. Yordanov12 , Haijiao Huang1 , David M. Goodstein11 , Ying Gai13 , Qi Qi13 , JiuMeng Min3 , ChunYan Xu3 , SongBo Wang3 , Guan-Zheng Qu1 , Andrew H. Paterson10 , David Sankoff5 , Hairong Wei4 and Guifeng Liu1, , Chuanping Yang,1,
1State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China 2BGI-Qingdao, BGI-Shenzhen, Qingdao, China 3BGITech, BGI-Shenzhen, Shenzhen, China 4College of Forest Resources and Environmental Science, Institute of Computing and Cybersystems, Michigan Technological University, Houghton, MI, USA 5Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada 6Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China 7School of Plant Sciences, University of Arizona, Tucson, AZ, USA 8Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, USA 9Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, P.R. China 10Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 11US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA 12Department of Biological Sciences, Eastern Illinois University, Charleston, IL, USA 13College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, P. R. China *Corresponding author. E-mail: liuguifeng@nefu.edu.cn,yangcp@nefu.edu.cn
Received: 20 Jul 2020 Revised: 08 Nov 2020 Accepted: 13 Dec 2020 Published online: 11 Feb 2021
Abstract
Betula L. (birch) is a pioneer hardwood tree species with ecological, economic, and evolutionary importance in the Northern Hemisphere. We sequenced the Betula platyphylla genome and assembled the sequences into 14 chromosomes. The Betula genome lacks evidence of recent whole-genome duplication and has the same paleoploidy level as Vitis vinifera and Prunus mume. Phylogenetic analysis of lignin pathway genes coupled with tissue-specific expression patterns provided clues for understanding the formation of higher ratios of syringyl to guaiacyl lignin observed in Betula species. Our transcriptome analysis of leaf tissues under a time-series cold stress experiment revealed the presence of the MEKK1–MKK2–MPK4 cascade and six additional mitogen-activated protein kinases that can be linked to a gene regulatory network involving many transcription factors and cold tolerance genes. Our genomic and transcriptome analyses provide insight into the structures, features, and evolution of the B. platyphylla genome. The chromosome-level genome and gene resources of B. platyphylla obtained in this study will facilitate the identification of important and essential genes governing important traits of trees and genetic improvement of B. platyphylla.
, Chuanping Yang,1 ,
