Chromosome-scale haplotype genome assemblies for the Australian mango 'Kensington Pride' 1 and a wild relative, Mangifera laurina, provide insights into anthracnose-resistance and volatile 2 compound biosynthesis genes

Abstract Mango (Mangifera indica) is one of the most popular fruits cultivated in tropical and subtropical regions of the world. The availability of reference genomes helps to identify the genetic basis of important traits. Here we report assembled high-quality chromosome-level genomes for the Australian mango cultivar ‘Kensington Pride’, and M. laurina; a wild relative, which shows resistance to anthracnose disease. PacBio HiFi sequencing with higher genome coverage enabled the assembly of both genomes with 100% completeness. Genome sizes of ‘Kensington Pride’ and M. laurina were 367 Mb and 379 Mb, respectively, with all 20 chromosomes in both genomes having telomeres at both ends. K-mer analysis revealed that these genomes are highly heterozygous and significant structural variations were identified between ‘Kensington Pride’, M. laurina, and the recently published genome of the cultivar ‘Irwin’. Functional annotation identified key genes involved in carotenoid, anthocyanin, and terpenoid biosynthesis, responsible for fruit color and flavour in mango. Furthermore, the presence of a SNP in β-1,3-glucanase 2 gene associated with anthracnose resistance was analyzed. Whole genome duplication analysis confirmed that mangoes have undergone two polyploidization events during their evolution. Analysis revealed a conserved pattern of colinear genes, although many colinear blocks were also identified on non-homologous chromosomes. Practitioner Points PacBio HiFi sequencing and high coverage produced genomes for ‘Kensington Pride’ mango and M. laurina with 100% completeness, identifying all the telomeres in the assembled chromosomes. Significant structural variations were identified between ‘Kensington Pride’, M. laurina, and the published ‘Irwin’ genome. Genes linked in the biosynthesis of unique terpenoids were identified, and the structural differences in the annotated β-1,3-glucanase 2 genes associated with anthracnose resistance provide a resource for gene expression analysis in susceptible and resistant cultivars. Competing Interest Statement The authors declare no competing interest. Footnotes Email addresses of the authors: Upendra Kumari Wijesundara (w.wijesundara{at}uq.edu.au), Agnelo Furtado (a.furtado{at}uq.edu.au), Ardashir Kharabian Masouleh (a.kharabianmasouleh{at}uq.edu.au), Natalie L. Dillon (natalie.dillon{at}daf.qld.gov.au), Heather E Smyth (h.smyth{at}uq.edu.au)