文献类型： 外文期刊

作者： Shi, Tian-Le ¹ ; Jia, Kai-Hua ¹ ; Bao, Yu-Tao ¹ ; Nie, Shuai ³ ; Tian, Xue-Chan ¹ ; Yan, Xue-Mei ¹ ; Chen, Zhao-Yang ¹ ; Li, Zhi-Chao ¹ ; Zhao, Shi-Wei ¹ ; Ma, Hai-Yao ¹ ; Zhao, Ye ¹ ; Li, Xiang ⁶ ; Zhang, Ren-Gang ⁷ ; Guo, Jing ⁸ ; Zhao, Wei ⁹ ; El-Kassaby, Yousry Aly ¹⁰ ; Mueller, Niels ¹¹ ; van de Peer, Yves ¹² ; Wang, Xiao-Ru ⁹ ; Street, Nathaniel Robert ¹⁶ ; Porth, Ilga ¹⁷ ; An, Xinmin ¹ ; Mao, Jian-Feng ¹ ;

作者机构： 1.Beijing Forestry Univ, Coll Biol Sci & Technol, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Natl Engn Lab Tree Breeding,Minist Educ,Natl Engn, Beijing 100083, Peoples R China

2.Shandong Acad Agr Sci, Inst Crop Germplasm Resources, Key Lab Crop Genet Improvement & Ecol & Physiol, Jinan 250100, Peoples R China

3.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou 510640, Peoples R China

4.Minist Agr & Rural Affairs, Coconstruct Minist & Prov, Key Lab Genet & Breeding High Qual Rice Southern C, Guangzhou 510640, Peoples R China

5.Guangdong Key Lab New Technol Rice Breeding, Guangzhou 510640, Peoples R China

6.Ningxia Univ, Sch Agr, Yinchuan 750021, Peoples R China

7.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species Ex, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China

8.Shandong Agr Univ, Coll Forestry, Tai An 271000, Peoples R China

9.Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden

10.Univ British Columbia, Fac Forestry, Dept Forest & Conservat Sci, Vancouver, BC V6T 1Z4, Canada

11.Thunen Inst Forest Genet, D-22927 Grosshansdorf, Germany

12.Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

13.VIB Ctr Plant Syst Biol, B-9052 Ghent, Belgium

14.Univ Pretoria, Ctr Microbial Ecol & Genom, Dept Biochem Genet & Microbiol, ZA-0028 Pretoria, South Africa

15.Nanjing Agr Univ, Acad Adv Interdisciplinary Studies, Coll Hort, Nanjing 210095, Peoples R China

16.Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, SE-90187 Umea, Sweden

17.Univ Laval, Fac Foresterie Geog & Geomatique, Dept Sci Bois & Foret, Quebec City, PQ G1V 0A6, Canada

期刊名称：PLANT PHYSIOLOGY （ 影响因子：7.4； 五年影响因子：8.7 ）

ISSN： 0032-0889

年卷期： 2024 年

页码：

收录情况： SCI

摘要： Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba x Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.