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Article|03 Apr 2023|OPEN
Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes
Upuli Nakandala1,2 , Ardashir Kharabian Masouleh1,2 , Malcolm W. Smith3 , Agnelo Furtado1,2 , Patrick Mason1,2 , Lena Constantin1,2 , Robert J. Henry,1,2 ,
1Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
2ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane 4072, Australia
3Department of Agriculture and Fisheries, Bundaberg Research Station, Bundaberg, Queensland 4670, Australia
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad058 (2023)
Views: 192

Received: 20 Dec 2022
Accepted: 27 Mar 2023
Published online: 03 Apr 2023


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 29 464 genes and 32 009 transcripts were identified in the genome. Of these, 28 222 CDS (25 753 genes) had BLAST hits and 21 401 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.