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Oct, 2021;21 (7): 2504-2519.

Chromosome-scale genome assembly of areca palm (Areca catechu).

Yaodong Yang, Liyun Huang, Chunyan Xu, Lan Qi, Zhangyan Wu, Jia Li, Haixin Chen, Yi Wu, Tao Fu, Hui Zhu, Mumtaz Ali Saand, Jing Li, Liyun Liu, Haikou Fan, Huanqi Zhou, Weiquan Qin
Author Information
  1. Yaodong Yang: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  2. Liyun Huang: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  3. Chunyan Xu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  4. Lan Qi: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  5. Zhangyan Wu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  6. Jia Li: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  7. Haixin Chen: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  8. Yi Wu: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  9. Tao Fu: BGI Genomics, BGI-Shenzhen, Shenzhen, China.
  10. Hui Zhu: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  11. Mumtaz Ali Saand: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  12. Jing Li: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  13. Liyun Liu: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  14. Haikou Fan: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  15. Huanqi Zhou: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China.
  16. Weiquan Qin: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China. ORCID
PMID: 34133844 DOI: 10.1111/1755-0998.13446

Abstract

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.

Keywords

Arecaceae Arecoline evolution genome

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Grants

  1. 1630152017019/the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
  2. 16301520190011/the fundamental Scientific Research Funds for Chinese Academy of Tropical Agriculture Sciences
  3. 17CXTD-14/Central Public-interest Scientific Institution Basal Research Fund for Innovative Research Team Program of CATAS
  4. 17CXTD-28/Central Public-interest Scientific Institution Basal Research Fund for Innovative Research Team Program of CATAS
  5. ZDKJ201817-3/Hainan Major Research Fund of science and technology

MeSH Term

Areca
Chromosomes
Genome
Genomics
Phylogeny
Plant Breeding
Journal Article

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