The affected mango genes include those with potential economic importance such as 6945 genes for defense/resistance/immune response, 323 genes for fruit development, and 338 genes for anthocyanin production. The analysis of variant effects and functional annotation across the three mango species revealed 56,982 variants with high-impact effects mapped onto 37,746 genes, of which 25% were found to be novel. Approximately 50, 46, and 38% of the variants were unique in the three Philippine mango genomes. Using these two currently available mango genomes, most variants were observed in M. The high confidence variants were identified by successfully mapping 93–95% of the quality-filtered reads to the Alphonso and Tommy Atkins mango reference genomes. Here, we sequenced the whole genome of the three Philippine mango species, namely, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica “Carabao” variety using Illumina HiSeq 2500, to identify and analyze their genome-wide variants (SNPs and InDels). However, genomic studies of Philippine mangoes remain largely unexplored and lacking. The Philippines is among the top 10 major exporters of mango worldwide.
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