Assembly of highly heterozygous mango (Mangifera indica cv. Amrapali) genome using PacBio long sequence reads

Mango (Mangifera indica L.), a member of the family Anacardiaceae is an allotetraploid fruit tree with small genome size of 439 Mb (2n= 40). India is the largest producer of mango growing more than 1,000 varieties, where it is known as ‘king of fruits’ for its rich taste, flavor, color and diverse end-usage. To facilitate the assembly of highly heterozygous diploid genome of a popular mango variety ‘Amrapali’ we used PacBio-SMRT sequencing with long average read lengths and 70x genome coverage. De novo assembly using FALCON diploid assembler resulted in an assembly of 323 Mbp in 9,550 large contigs, with 73.2% genome coverage, largest contig size of 1.09 Mb and N50 of 98.3 Kb. Gene prediction using FGENESH revealed total 43,247 gene models with an average gene size of 894 bps in a range of 150 to12,102 bp. Comparison with the other published plant genomes showed highest similarity with Citrus sinensis. We identified 122,332 genomic SSR and developed 8,451 Type1 SSR and 835 HSSR markers with high level of detectable polymorphism. Further, we have identified 1.67 million high quality SNPs by ddRAD sequencing of 91 diverse mango varieties for which a database has been created and population structure of Indian mango varieties is determined. Using this data a single-copy gene based 50K SNP chip has been designed for genotyping using Affymetrix platform. These genomic resources will fast track the mango varietal improvement for higher productivity, disease resistance and superior end-use quality.