Areca palm (Areca catechu L.; family Arecaceae) is an important tropical medicinal crop and is also used for masticatory and religious purposes in Asia. Improvements to areca properties made by traditional breeding tools have been very slow, and further advances in its cultivation and practical use require genomic information, which is still unavailable. Here, we present a chromosome-scale reference genome assembly for areca by combining Illumina and PacBio data with Hi-C mapping technologies, covering the predicted A. catechu genome length (2.59 Gb, variety “Reyan#1”) to an estimated 240× read depth. The assembly was 2.51 Gb in length with a scaffold N50 of 1.7Mb. The scaffolds were then further assembled into 16 pseudochromosomes, with an N50 of 172 Mb. Transposable elements comprised 80.37% of the areca genome, and 68.68% of them were long-terminal repeat retrotransposon elements. The areca palm genome was predicted to harbour 31,571 protein-coding genes and overall, 92.92% of genes were functionally annotated, including enriched and expanded families of genes responsible for biosynthesis of flavonoid, anthocyanin, monoterpenoid and their derivatives. Comparative analyses indicated that A. catechu probably diverged from its close relatives Elaeis guineensis and Cocos nucifera approximately 50.3 million years ago (Ma). Two whole genome duplication events in areca palm were found to be shared by palms and monocots, respectively. This genome assembly and associated resources represents an important addition to the palm genomics community and will be a valuable resource that will facilitate areca palm breeding and improve our understanding of areca palm biology and evolution.

中文翻译：

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槟榔（槟榔）的染色体规模基因组组装

槟榔（槟榔属槟榔科）是一种重要的热带药用作物，在亚洲也用于咀嚼和宗教用途。传统育种工具对槟榔特性的改进非常缓慢，其栽培和实际应用的进一步发展需要基因组信息，而这些信息仍然不可用。在这里，我们通过将 Illumina 和 PacBio 数据与 Hi-C 映射技术相结合，为槟榔提供了染色体规模的参考基因组组装，涵盖了预测的A. catechu基因组长度（2.59 Gb，品种“Reyan#1”）到估计的 240 倍读取深度。该组件长 2.51 Gb，支架 N50 为 1.7Mb。然后将支架进一步组装成 16 个假染色体，N50 为 172 Mb。转座元件占槟榔基因组的 80.37%，其中 68.68% 是长末端重复反转录转座子元件。预计槟榔基因组包含 31,571 个蛋白质编码基因，总体而言，92.92% 的基因被功能注释，包括负责黄酮类化合物、花青素、单萜类化合物及其衍生物生物合成的富集和扩展基因家族。比较分析表明，A. catechu可能与其近亲Elaeis guineensis和Cocos nucifera 不同大约 5030 万年前（Ma）。发现槟榔中的两个全基因组重复事件分别由棕榈和单子叶植物共享。这种基因组组装和相关资源代表了棕榈基因组学社区的重要补充，并将成为促进槟榔育种和提高我们对槟榔生物学和进化理解的宝贵资源。