Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes  

作　　者：Upuli Nakandala Ardashir Kharabian Masouleh Malcolm WSmith Agnelo Furtado Patrick Mason Lena Constantin Robert J.Henry 

机构地区：[1]Queensland Alliance for Agriculture and Food Innovation,University of Queensland,Brisbane 4072,Australia [2]ARC Centre of Excellence for Plant Success in Nature and Agriculture,University of Queensland,Brisbane 4072,Australia [3]Department of Agriculture and Fisheries,Bundaberg Research Station,Bundaberg,Queensland 4670,Australia

出　　处：《Horticulture Research》2023年第5期193-206,共14页园艺研究（英文）

摘　　要：Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus.Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased,with the available genomes of varying accuracy and completeness.We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species;Citrus australis(round lime)using highly accurate PacBio HiFi long reads,complemented with Hi-C scaffolding.Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C.australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness(BUSCO).Repeat analysis showed that more than 50% of the genome contained interspersed repeats.Among them,LTR elements were the predominant type(21.0%),of which LTR Gypsy(9.8%)and LTR copia(7.7%)elements were the most abundant repeats.A total of 29464 genes and 32009 transcripts were identified in the genome.Of these,28222 CDS(25753 genes)had BLAST hits and 21401 CDS(75.8%)were annotated with at least one GO term.Citrus specific genes for antimicrobial peptides,defense,volatile compounds and acidity regulation were identified.The synteny analysis showed conserved regions between the two haplotypes with some structural variations in Chromosomes 2,4,7 and 8.This chromosome scale,and haplotype resolved C.australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.

关 键 词：CITRUS CITRUS breeding 

分 类 号：S666[农业科学—果树学]