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. 2024 Apr 10;24(1):260.
doi: 10.1186/s12870-024-04988-8.

The genome of Citrus australasica reveals disease resistance and other species specific genes

Upuli Nakandala  1   2 , Agnelo Furtado  1   2 , Ardashir Kharabian Masouleh  1   2 , Malcolm W Smith  3 , Darren C Williams  4 , Robert J Henry  5   6
Affiliations

The genome of Citrus australasica reveals disease resistance and other species specific genes

Upuli Nakandala et al. BMC Plant Biol. .

Abstract

Background: The finger lime (Citrus australasica), one of six Australian endemic citrus species shows a high natural phenotypic diversity and novel characteristics. The wide variation and unique horticultural features have made this lime an attractive candidate for domestication. Currently no haplotype resolved genome is available for this species. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing.

Results: Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome.

Conclusions: The genome of C. australasica present in this study is of high quality and contiguity. This genome helps deepen our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.

Keywords: C. australasica specific genes; Chromosome scale genome; Colour related genes; Disease resistance; Genetic improvement; Haplotype-resolved.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The orthologous gene clusters in C. australasica and C. australis genomes identified using Orthovenn3. (a) The orthologous gene clusters present in C. australis and C. australasica. 19,980 orthologous clusters (48,185 genes) were shared between the two species and 666 gene clusters (4,191 genes) and 870 gene clusters (12,748 genes) were unique to C. australis and C. australasica respectively. (b) Orthologous gene clusters among C. australasica collapsed genome and the two haplotype genomes. 21,061 gene clusters (76,167 genes) were shared by three genomes and 709 clusters (3,307 genes), 445 clusters (1,676 genes), and 476 clusters (1,696 genes) were specific to the collapsed, hap1 and hap2 assemblies
Fig. 2
Fig. 2
Structural genomic differences between C. australasica and C. australis genomes and C. australasica haplotypes. Syntenic regions are indicated in grey color and unaligned regions are shown in white color. Different types of rearranged regions are shown with respective color codes. The analysis was done using Synteny and Rearrangement Identifier (SyRI) (a) The structural comparison between C. australasica and C. australis collapsed assemblies (b) The structural differences between C. australasica haplotypes
Fig. 3
Fig. 3
The Circos plot indicating the chromosomal locations of defense related genes in the C. australasica genome. Purple indicates the genes encoding leucine rich repeat proteins (LRR), red indicates the genes encoding pathogenesis related (PR) proteins, blue indicates the genes encoding guanine-nucleotide binding proteins and green indicate the genes encoding antimicrobial proteins (stress-responsive A/B barrel domain containing proteins, defensins, thionins, non-specific lipid transfer proteins, snakins, hevein-like proteins, knottin-type proteins). The innermost links indicate the collinear genes within the genome identified by whole genome self-homology and gene location information. Different colors for the links indicate the chromosome of origin of the links. Some collinear genes were identified within the same chromosome while others were identified between chromosomes. Collinear genes represent homologous genes in conserved orders on corresponding chromosomes. Circos plot was generated using shinyCircos-V2.0 and TBtools
Fig. 4
Fig. 4
Anthocyanin biosynthetic pathway of C. australasica reproduced with permission of Kanehisa Laboratories [48]. The main components in anthocyanin pathway are shown with red asterisks. Phenylalanine undergoes catalysis via a series of steps producing Cinnamic acid, Coumaric acid, 4-Coumaroyl-CoA, Naringenin chalcone, Naringenin, Dihydrokaempferol, Dihydroquercetin, Dihydromyricetin, Leucoanthocyanidins, Anthocyanidins, and Anthocyanins. The major types of anthocyanins identified from the annotation of C. australasica by KEGG analysis were pelargonidin, pelargonidin-3-sambubioside, cyanidin, cyanidin 3-glucoside, cyanidin 5-glucoside, cyanidin 3,5-diglucoside, cyanidin-3-sambubioside, delphinidin, delphidin-3-sambubioside, delphinidin 3-glucoside. The pathways were retrieved from KEGG pathway analysis
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