A Hybrid Approach for Improved Genome Assembly of Coconut (Cocos nucifera L.) to Aid Development of Breeding Tools

Coconut is the only reported species under the genus Cocos which is a member of the family Arecaceae and sub-family Arecoideae. It is a major agricultural crop in humid areas in the tropics with an estimated world annual production of 50–60 million tons. However, coconut production has been threatened by major challenges such as low productivity of cultivated varieties and presence of biotic and abiotic stresses. To achieve the optimum potential of this important crop, recent advancement in the field of genomics is exploited to develop outstanding and value-added coconut variety.

Catigan Green Dwarf (CATD) was selected for genome sequencing due to its simple genome and low heterozygosity. This is also the variety of coconut recommended by coconut breeders among their dwarf coconut collections. PacBio sequence was generated at 11X coverage and corrected with 40X Illumina paired-end MiSeq reads and assembled. The current assembly covers 70% (1.9 Gb) of the estimated genome size of 2.7 Gb and has an N50 of 114 Kb. An estimate of 73% of the genome is comprised of repeat sequences. Expression data has been used to define gene structures using ab initio predictors. The genome assembly is currently stored in a database prototype based on the Sol Genomics Network website’s backbone in order to facilitate maximum utility of the genome sequence data i.e. gene discovery, molecular marker development and routine marker-assisted breeding applications in coconut. This genome database will be integrated with phenotype data for phenotype-genome association studies aiding coconut breeders and scientists.