Sequencing a Juglans regia×J.microcarpa hybrid yields high-quality genome assemblies of parental species
作者机构：Department of Plant SciencesUniversity of CaliforniaDavisCA 95616USA Ottawa Research and Development CentreAgriculture and Agri-Food CanadaOttawaON K1A 0C6Canada Genome CenterUniversity of CaliforniaDavisCA 95616USA Crops Pathology and Genetics Research UnitUSDA-ARSDavisCA 95616USA National Clonal Germplasm RepositoryUSDA-ARSDavisCA 95616USA
出 版 物：《Horticulture Research》 (园艺研究（英文）)
年 卷 期：2019年第6卷第1期
页 面：1271-1286页
核心收录：
学科分类：0710[理学-生物学] 0831[工学-生物医学工程（可授工学、理学、医学学位）] 1002[医学-临床医学] 1001[医学-基础医学(可授医学、理学学位)] 100214[医学-肿瘤学] 0901[农学-作物学] 0703[理学-化学] 0836[工学-生物工程] 0902[农学-园艺学] 10[医学] 0834[工学-风景园林学（可授工学、农学学位）]
基 金：supported by USDA/NIFA/SCRI under grant number 59-5306-2-333 and by the California Walnut Board.
摘 要：Members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.
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