A haplotype-resolved genome provides insight into allele-specific expression in wild walnut (Juglans regia L.)

文献类型： 外文期刊

第一作者： Han, Liqun

作者： Han, Liqun;Zhao, Yu;Li, Ning;Xu, Yuhui;Ma, Kai;Luo, Xiang

作者机构： Xinjiang Acad Agr Sci, Inst Hort Crops, State Key Lab Genet Improvement & Germplasm Innova, Key Lab Genome Res & Genet Improvement Xinjiang Ch, Urumqi, Peoples R China;Henan Agr Univ, Coll Agron, Zhengzhou, Peoples R China

期刊名称：SCIENTIFIC DATA （ 2022影响因子：9.8； 五年影响因子：10.8 ）

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年卷期： 2024 年 11 卷 1 期

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收录情况： SCI

摘要： Wild germplasm resources are crucial for gene mining and molecular breeding because of their special trait performance. Haplotype-resolved genome is an ideal solution for fully understanding the biology of subgenomes in highly heterozygous species. Here, we surveyed the genome of a wild walnut tree from Gongliu County, Xinjiang, China, and generated a haplotype-resolved reference genome of 562.99 Mb (contig N50 = 34.10 Mb) for one haplotype (hap1) and 561.07 Mb (contig N50 = 33.91 Mb) for another haplotype (hap2) using PacBio high-fidelity (HiFi) reads and Hi-C technology. Approximately 527.20 Mb (93.64%) of hap1 and 526.40 Mb (93.82%) of hap2 were assigned to 16 pseudochromosomes. A total of 41039 and 39744 protein-coding gene models were predicted for hap1 and hap2, respectively. Moreover, 123 structural variations (SVs) were identified between the two haplotype genomes. Allele-specific expression genes (ASEGs) that respond to cold stress were ultimately identified. These datasets can be used to study subgenome evolution, for functional elite gene mining and to discover the transcriptional basis of specific traits related to environmental adaptation in wild walnut.

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