A Reference Genome of Mango (Mangifera indica L. cv Amrapali)

Mango (Mangifera indica L.) is an evergreen fruit tree belonging to order Sapindales of the family Anacardiaceae. It has 20 pairs of chromosomes with an estimated genome size of 439 Mbp. It is known as the king of fruits due to its large production volume, huge variability of fruit appearance and taste and diverse end-usage, but mango breeding is challenging due to long juvenile phase, high heterozygosity and heavy fruit drops. A major limiting factor for mango improvement is the paucity of genomic resources. To fill the gap we generated 44.8 Gbp of genomic sequence (102x coverage) using PacBio platform. The genome was assembled and polished using FALCON and Quiver software, respectively. The resulting 9,500 contigs (401 Mbp) were arranged in to 4,312 scaffolds (403 Mpb), covering 91.8 % of the genome with largest scaffold of 2.1 Mbp and N50 of 282 kbp. Over 80% of the scaffolds were anchored to 20 mango chromosomes with 6,242 markers of a recently published high-density genetic map of total 6,594 markers (94.66% coverage). Total 53,018 genes were predicted, annotated and manually curated. Further, 168,484 SSRs were mined, including 30,821 Type 1 and 12,855 highly variable SSR. We also identified 5.2 million high quality SNPs in 19,656 single-copy genes by re-sequencing of 24 diverse mango cultivars and developed a 80K SNP chip. Mango showed highest similarity with Citrus sinensis among the published fruit genomes. The reference genome would fast track mango varietal improvement for stress tolerance, higher productivity and superior quality.