Decoding the Citrus australis genome: Insights into HLB resistance and breeding potentials in Australian limes

Citrus is a globally valued fruit crop, of which Australia is native to six species of citrus, all of which are limes. However, Huanlongbing (HLB) or greening disease caused by vector-transmitted bacteria (Candidatus Liberibacter) has caused severe economic losses to citrus industries around the world. C. australis and other Australian native tilia species and their derived hybrids exhibit varying degrees of resistance to HLB, providing a valuable genetic resource for breeding HLB-resistant cultivars. Although several citrus species have been sequenced and assembled, the reference genome of Australian limes has not been reported, so resolving its genome assembly and gene annotation will provide a valuable resource for improving citrus through genome-assisted breeding approaches.

In April 2023, Horticulture Research published a research paper entitled by “Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes ”.

This study investigates the phased high-quality chromosome level genome assembly of the Australian native citrus species Citrus australis (round lime) by using highly accurate PacBio HiFi long reads and Hi-C scaffolding. The genome assembly size of the nuclear DNA content of the collapsed genome was first estimated to be 331.1 Mb using kmergenie and genomescope methods. Subsequently, genome assembly using Hifiasm was conducted with three distinct methodologies (primary and alternate mode, default option, and Hi-C). Based on the assembly statistics, it is clear that Hifiasm with the Hi-C partition option assembled the best phased haplotypes. Further scaffolding using hi-C data led to the production of nine main pseudomolecules with an N50 of 36.3 Mb .Additionally repeat sequences and genes were annotated for nine pseudochromosomes in the collapsed assembly. Repeat analysis showed that more than 50% of the genome contained interspersed repeats. Of these, LTR elements were the predominant type (21.0%), while LTR Gypsy (9.8%) and LTR copia (7.7%) elements were the most abundant repeat sequences. A synteny block analysis found most genes conserved across the two haplotypes' nine chromosomes, though some showed signs of translocations. For non-coding genes, the Barrnap tool identified ribosomal blocks and genes in various chromosomes. A total of 29,464 genes and 32,009 transcripts were identified in the genome. Of these, 28,222 CDSs (25,753 genes) had BLAST hits and 21,401 CDSs (75.8%) were annotated with at least one GO term. Exploration of important genes in citrus revealed the presence of genes specific to antimicrobial peptides, defense, volatile compounds, and acidity regulation in the C. australis genome. This includes genes related to HLB resistance and genes controlling terpenoid synthesis, thus revealing the genetic basis of citrus volatile compounds.

In conlusion, researchers have achieved a high-quality chromosome level genome assembly for the Australian native citrus species, Citrus australis (round lime). This advanced genome assembly paves the way for enhanced citrus breeding efforts, offering insights into evolutionary relationships between wild and domesticated citrus species, and will be instrumental for genomic-assisted breeding approaches.

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References

Authors

Upuli Nakandala^1,2, Ardashir Kharabian Masouleh^1,2, Malcolm W. Smith³, Agnelo Furtado^1,2, Patrick Mason^1,2, Lena Constantin^1,2 and Robert J. Henry^1,2,*

Affiliations

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

About Robert J. Henry

He is currently Professor of Agriculture Innovation at the University of Queensland. Professor Henry's speciality research area is the study of agricultural crops using molecular tools. He is particularly interested in Australian flora and plants of economic and social importance, and has led genome sequencing research to obtain novel genetic resources to diversify food crops and provide improved food products.