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

Abstract

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.

Acknowledgements

This project was funded by the Hort Frontiers Advanced Production Systems Fund as part of the Hort Frontiers strategic partnership initiative developed by Hort Innovation, with co-investment from The University of Queensland, and contributions from the Australian Government and Bioplatforms Australia. UN was supported by a graduate scholarship from The University of Queensland. The authors acknowledge The University of Queensland Research Computing Centre (UQ-RCC) for providing all the computing resources for the study and the Flow Cytometry Facility at the Queensland Brain Institute.

Author contributions

RH, AF, AKM supervised, managed the project, advised and supported data analysis, and data interpretation. AF advised on experiments and AKM supported the genome assembly work. UN and PM performed DNA extractions. UN conducted RNA extractions, data analysis and data interpretation. LC contributed flow cytometry analysis. The manuscript was organized and written by UN. LC contributed to the manuscript with data interpretation of flow cytometry analysis. All authors approved the submitted version.

Data availability

Raw sequence data generated in this study have been deposited in NCBI Sequence Read Archive (SRA) under BioProject PRJNA910964 and BioSample SAMN32155198 with an accession ID of SRR22742835 for RNA-seq and SRR22793114 for whole genome short read data. The whole genome sequence data reported in this paper have been deposited in the Genome Warehouse in National Genomics Data Center [59, 60], Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation, under accession number GWHBQDX00000000, BioProject [PRJCA013889], and Biosample [SAMC1020632] that is publicly accessible at https://ngdc.cncb.ac.cn/gwh. The whole genome and annotation data of Citrus australis have also been submitted to Citrus genome database (https://www.citrusgenomedb.org/).

Conflict of interests statement

None declared.

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