Analysis Of Cocos nucifera var. Catigan Green Dwarf (CATD) Draft Genome

The Philippines is one of the largest producers of coconut and possesses one of the largest collections of coconut accessions in the world. Here, we report our analyses on the draft genome of Cocos nucifera var Catigan Green Dwarf. We generated paired-end and mate-pair libraries using Illumina HiSeq with varying insert sizes (400 bp, 2 kbp, 5 kbp, and 10 kbp). After quality filtering and contaminant removal, the high quality reads were assembled using Platanus with default parameters. Based on QUAST, the genome assembly spans 2.04 Gbp with scaffold N50 of 121,027 bp and contains 65,637 scaffolds. On the basis of our estimated genome size of 2.9 Gbp using k-mer statistics and flow cytometry, the assembly captures ~95.6% of the genome. To evaluate gene space completeness, we used BUSCO pipeline, EST and transcript mapping. BUSCO analysis identified 867 (90%) complete USCOs out of 956 groups searched. Using BLAT, 97.5% of the Cocos nucifera ESTs downloaded from NCBI and 95% of the transcripts from our coconut transcriptome data are aligned to the genome assembly. An initial genome-wide identification of SSRs was also performed using MISA. A total of 582,585 simple sequence repeats (SSRs) were detected in Cocos nucifera var CATD genome sequences. The data presented here constitutes a resource for coconut varietal improvement through marker-assisted breeding and for comparison with other sequenced crops.