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

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Nakandala, U., Masouleh, A. K., Smith, M. W., Furtado, A., Mason, P., Constantin, L. and Henry, R. J. (2023) Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes. Horticulture Research, 10 (5). ISSN 2052-7276


Article Link: https://doi.org/10.1093/hr/uhad058


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.

Item Type:Article
Corporate Creators:Department of Agriculture and Fisheries, Queensland
Business groups:Horticulture and Forestry Science
Subjects:Science > Botany > Genetics
Plant culture > Fruit and fruit culture
Plant pests and diseases
Live Archive:29 Aug 2023 23:54
Last Modified:29 Aug 2023 23:54

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