Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance

Abstract

Coconut (Cocos nucifera L.), an important source of vegetable oil, nutraceuticals, functional foods, and housing materials, provides raw materials for a repertoire of industries engaged in the manufacture of cosmetics, soaps, detergents, paints, varnishes, and emulsifiers, among other products. The palm plays a vital role in maintaining and promoting the sustainability of farming systems of the fragile ecosystems of islands and coastal regions of the tropics. In this study, we present the genome of a dwarf coconut variety ''Chowghat Green Dwarf'' (CGD) from India, possessing enhanced resistance to root (wilt) disease. Utilizing short reads from the Illumina HiSeq 4000 platform and long reads from the Pacific Biosciences RSII platform, we have assembled the draft genome assembly of 1.93 Gb. The genome is distributed over 26,855 scaffolds, with *81.56% of the assembled genome present in scaffolds of lengths longer than 50 kb. About 77.29% of the genome was composed of transposable elements and repeats. Gene prediction yielded 51,953 genes, which upon stringent filtering, based on Annotation Edit Distance, resulted in 13,707 genes, which coded for 11,181 proteins. Among these, we gathered transcript level evidence for a total of 6828 predicted genes based on the RNA-Seq data from different coconut tissues, since they presented assembled transcripts within the genome annotation coordinates. A total of 112 nucleotide-binding and leucine-rich repeat loci, belonging to six classes, were detected. We have also undertaken the assembly and annotation of the CGD chloroplast and mitochondrial genomes. The availability of the dwarf coconut genome shall prove invaluable for deducing the origin of dwarf coconut cultivars, dissection of genes controlling plant habit and fruit color, and accelerated breeding for improved agronomic traits.

An efficient repeat masking library for the genomic data of coconut and related trees

“…Compared to their results, our analysis showed 82.19 % overall masking, with 64.93 % LTR elements, which shows the better efficiency of the repeat library designed. The genome assembly of 'Chowghat Green Dwarf' (Muliyar et al, 2020) had reported 77.29 % repeat masking, of which 58.85 % were LTRs. These results are comparable to the present results of 66.18 % overall masking, comprising 46.89 % LTRs.…”

Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut

“…The genome was filtered through to uncover 112 nucleotide-binding-site and leucinerich repeat (NBS-LRR) loci, representing six types of resistance genes. The CGD genome contains sequence variance associated with disease resistance, making it a helpful tool for developing genomics-assisted breeding in coconuts [95].…”

Genome-wide diversity analysis to infer population structure and linkage disequilibrium among Colombian coconut germplasm

“…Coconut palms are monoic, having both male and female flowers on the same inflorescence, perennial diploids (2n = 32) and the sole species of the genus Cocos . Draft genomes have been published suggesting a genome size of about 1.93 Gb (dwarf coconut) to 2.4 Gb (tall Hainan coconut) and a complex genome structure composed of 50–70% of repetitive sequences, chromosome fractionation and duplication followed by rearrangements 2 , 4 , 8 , 9 . Many studies have been conducted to characterize the genetic diversity of coconut collections, and to understand coconut cultivation history 1 , 10 , 11 .…”