I have been working with researchers at the University of Queensland’s QAAFI (Queensland Alliance for Agriculture and Food Innovation), offering technical assistance and co-authoring a couple of new papers. Both are open access so please have a read if this interests you.

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

https://www.researchsquare.com/article/rs-3479935/v1

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. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing.

Results

Hiasm 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 ve C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identied in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome.

Conclusions

This high quality, haplotype resolved genome contributes to our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.

Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes

https://www.maxapress.com/article/doi/10.48130/TP-2023-0021

Abstract

Citrus is widely consumed across the world as a fruit crop. Despite many citrus species being extensively studied around the world, phylogenetic relationships among Australian native species remain unresolved. Here we present the phylogenetic relationships among six Australian native species, two domesticated citrus cultivars of commercial importance in Australia, and another 13 accessions cultivated internationally based on complete, de novo assembled chloroplast genomes and 86 single copy nuclear genes. The chloroplast and nuclear phylogenies were topologically different. The Australian species formed a monophyletic clade based on their nuclear genes. The nuclear phylogeny revealed a close relationship between Citrus inodora and Citrus australasica. These two species were distinct from the other four Australian limes that were more closely related to each other. Citrus australasica had a unique chloroplast which was distinct from all other Australian limes. Among the other Australian limes, Citrus glauca was the most distinct species based on nuclear genes, however, it had a similar chloroplast sequence to C. australis. The undetermined Citrus sp. was more closely related to Citrus garrawayi, indicating that it is a distinct form of Citrus garrawayi. Citrus medica, had a chloroplast similar to Australian species. However, the nuclear gene phylogeny analysis revealed that C. medica was more closely related to Asian citrus species. This study improves our understanding of phylogenetic relationships among Australian citrus species and confirms their unique status within the genus since it formed a monophyletic clade which was clearly separated from the other non-Australian species.