Chromosome-scale and haplotype-resolved genome assembly of Populus trichocarpa

被引:1
作者
Gao, Wentao [1 ]
Wang, Sui [2 ,3 ]
Jiang, Tao [4 ]
Hu, Heng [1 ]
Gao, Runtian [1 ]
Zhou, Murong [1 ]
Wang, Guohua [5 ,6 ]
机构
[1] Northeast Forestry Univ, Coll Life Sci, Harbin 150040, Heilongjiang, Peoples R China
[2] Northeast Agr Univ, Natl Key Lab Smart Farm Technol & Syst, Harbin 150038, Heilongjiang, Peoples R China
[3] Northeast Agr Univ, Key Lab Soybean Biol Chinese, Educ Minist, Harbin 150038, Heilongjiang, Peoples R China
[4] Harbin Inst Technol, Sch Comp Sci & Technol, Harbin 150001, Heilongjiang, Peoples R China
[5] Northeast Forestry Univ, Coll Comp & Control Engn, Harbin 150040, Heilongjiang, Peoples R China
[6] Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Heilongjiang, Peoples R China
基金
中国国家自然科学基金;
关键词
PROTEIN; ALIGNMENTS; ANNOTATION; COTTONWOOD; EVOLUTION; DATABASE; PROGRAM; TREE; TOOL; RNA;
D O I
10.1093/hr/uhaf012
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Populus trichocarpa, a pivotal model organism for woody transgenic research, not only garners substantial scientific interest but plays an integral role in forestry economics. Previous genomic assemblies of P. trichocarpa predominantly treated its heterozygous genome as homozygous, thereby neglecting crucial haplotypic diversity. Leveraging the high-fidelity (HiFi) sequencing capabilities of PacBio sequencing and the chromosome conformation capture insights provided by Illumina's Hi-C technique, this study is the first to achieve a near telomere-to-telomere assembly of both paternal and maternal haplotypes in P. trichocarpa. Comparative genomic analysis between these haplotypes has uncovered several allelic variants and pathways critical for trait determination through allele-specific expression. Furthermore, utilizing RNA-seq data from multiple tissues, this investigation has detailed the tissue-specific expression patterns of the leucine-rich repeat gene family, which are essential in mediating plant signal transduction and developmental regulation. Our results not only illuminate the functional genomics landscape of P. trichocarpa but also provide invaluable theoretical underpinnings for the genetic improvement of woody plants and a robust framework for exploring genetic variability and allelic expression disparities in arboreal species.
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页数:14
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