Chromosome-Scale Haplotype Genome Assemblies for the Australian Mango ‘Kensington Pride’ and a Wild Relative, Mangifera laurina, Provide Insights Into Anthracnose-Resistance and Volatile Compound Biosynthesis Genes

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 presence/absence variations of key genes involved in carotenoid, anthocyanin, and terpenoid biosynthesis, responsible for fruit colour and flavour in mango. Furthermore, the presence of a SNP in β-1,3-glucanase 2 gene, previously reported to be associated with anthracnose resistance, was analysed. 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.