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.

中文翻译：

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具有增强抗病性的矮椰子（Chowghat 绿矮星）的核和细胞器基因组的组装和注释

椰子 ( Cocos nuciferaL.) 是植物油、营养保健品、功能性食品和住宅材料的重要来源，为化妆品、肥皂、洗涤剂、油漆、清漆和乳化剂等产品的制造行业提供原材料。棕榈树在维护和促进热带岛屿和沿海地区脆弱生态系统的农业系统的可持续性方面发挥着至关重要的作用。在这项研究中，我们展示了来自印度的矮椰子品种“Chowghat Green Dwarf”（CGD）的基因组，该品种对根（枯萎）病具有增强的抗性。利用来自 Illumina HiSeq 4000 平台的短读段和来自 Pacific Biosciences RSII 平台的长读段，我们组装了 1.93 Gb 的基因组组装草图。基因组分布在 26,855 个支架上，其中约 81 个。56% 的组装基因组存在于长度超过 50 kb 的支架中。大约 77.29% 的基因组由转座元件和重复序列组成。基因预测产生了 51,953 个基因，经过严格过滤，基于注释编辑距离，产生了 13,707 个基因，编码了 11,181 个蛋白质。其中，我们根据来自不同椰子组织的 RNA-Seq 数据收集了总共 6828 个预测基因的转录水平证据，因为它们在基因组注释坐标内呈现了组装的转录本。共检测到 112 个核苷酸结合和富含亮氨酸的重复基因座，属于六类。我们还进行了 CGD 叶绿体和线粒体基因组的组装和注释。