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.

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity

“…This is a possible reflection of high fecundity and large population size, expected in most freshwater fish species (Karjalainen et al, 2016; Röpke et al, 2021). The detection of genetic diversity in highly heterozygous species can be compromised by either un-phased genome-assembly approaches or haplotype-merged assemblies, which would ultimately lead to a significant underestimation of true genetic diversity (Nakandala et al, 2023; Takeuchi et al, 2022). Collapsed reference genomes restrict assembly accuracy and exploration of heterozygous regions of the genome, missing out on potentially interesting intra-individual variation (Low et al, 2020).…”

The genomes of theMacadamiagenus

“…These variations in gene counts may be attributed species-specific genomic features. Haploid-resolved assemblies are essential in genomics research, as they facilitate accurate gene phasing, improved annotation, and enhanced insights into genetic diversity (Nakandala et al, 2023;Zhang et al, 2021;Cheng et al, 2021). Heterozygosity between the haplotypes in diploids can complicate the genome assemblies.…”

A flow cytometry protocol for accurate and precise measurement of plant genome size using frozen material

“…It is becoming more common to use flow cytometry to estimate genome size prior to sequencing plant genomes (Doležel et al ., 2007; Nakandala et al ., 2023). In instances where plant materials are sourced from remote and geographically distant locations, the challenge arises in maintaining the freshness of the specimens over extended periods.…”