文献类型：期刊文献

英文题名：Genome assembly and comparative analysis reveal the imbalanced subgenomes divergence and evolutionary history of Juglans cathayensis

作者：Xu, Haodong[1] Wang, Nian[1] Xiang, Yingxi[1] Sheng, Qilei[1] Xu, Yongjie[2] Pei, Dong[3] Wang, Hua[1]

第一作者：Xu, Haodong

通信作者：Wang, H[1];Pei, D[2]

机构：[1]Huazhong Agr Univ, Coll Hort & Forestry Sci, Wuhan 430070, Hubei, Peoples R China;[2]Hubei Acad Forestry Sci, Woody Grain & Oil Forest Engn Technol Res Ctr Hube, Wuhan 430075, Hubei, Peoples R China;[3]Chinese Acad Forestry, Res Inst Forestry, State Key Lab Tree Genet & Breeding, Key Lab Tree Breeding & Cultivat State Forestry &, Beijing 100091, Peoples R China

年份：2025

卷号：122

期号：5

外文期刊名：PLANT JOURNAL

收录：;EI(收录号：20252418575187);Scopus(收录号：2-s2.0-105007535632);WOS:【SCI-EXPANDED(收录号:WOS:001508964000006)】；

基金：The work was supported by the National Key Research and Development Plan of China (2023YFD2200303) and the National Natural Science Foundation of China (Key Program, 32330069). The work was also supported by the National Key Research and Development Plan of China (2018YFD10006004).

语种：英文

外文关键词：Juglans cathayensis; genome assembly; subgenome divergence; flavonoids; SOC1

摘要：Chinese walnut (Juglans cathayensis), a wild relative of Persian walnut (Juglans regia), is distinguished by its early maturation and higher resilience to abiotic stress. As a paleopolyploid species, J. cathayensis has undergone at least two whole genome duplications (WGD) and subgenome divergence, which may profoundly affect its phenotype. This study assembled a chromosome-level genome of about 553.7 Mb for J. cathayensis, with the 16 pseudochromosomes categorized into two subgenomes based on their phylogenetic relationship with potential ancestor Myrica rubra hypothesized by cytogenetics. We found that unbalanced burst insertion of long terminal repeat retrotransposons (LTR-RTs) resulted in genome expansion and subgenomic divergence. Most homoeologous gene pairings suggested subgenome-biased expression genes (SBEGs) in three organs; however, no dominant subgenome expression model was identified. The resequencing analysis of J. cathayensis and J. regia samples, along with transcriptome and metabolome results, revealed that the species-specific characteristics of J. cathayensis are directly linked to the accumulation of flavonoid metabolism. Moreover, a distinctive deletion (non-frameshift mutation) in the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) gene of J. cathayensis probably regulates the early maturation differences between J. cathayensis and other Juglans species. Our study elucidates the genetic mechanisms promoting subgenome divergence and accelerating the utilization of genetic resources in J. cathayensis.