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. 2021 Oct;21(7):2504-2519.
doi: 10.1111/1755-0998.13446. Epub 2021 Jun 29.

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

Yaodong Yang  1 , Liyun Huang  1 , Chunyan Xu  2 , Lan Qi  1 , Zhangyan Wu  2 , Jia Li  1 , Haixin Chen  2 , Yi Wu  1 , Tao Fu  2 , Hui Zhu  1 , Mumtaz Ali Saand  1 , Jing Li  1 , Liyun Liu  1 , Haikou Fan  1 , Huanqi Zhou  1 , Weiquan Qin  1
Affiliations

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

Yaodong Yang et al. Mol Ecol Resour. 2021 Oct.

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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References

REFERENCES

    1. Al-Dous, E. K., George, B., Al-Mahmoud, M. E., Al-Jaber, M. Y., Wang, H., Salameh, Y. M., Al-Azwani, E. K., Chaluvadi, S., Pontaroli, A. C., DeBarry, J., Arondel, V., Ohlrogge, J., Saie, I. J., Suliman-Elmeer, K. M., Bennetzen, J. L., Kruegger, R. R., & Malek, J. A. (2011). De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology, 29, 521-527.
    1. Al-Mssallem, I. S., Hu, S., Zhang, X., Lin, Q., Liu, W., Tan, J., Yu, X., Liu, J., Pan, L., Zhang, T., Yin, Y., Xin, C., Wu, H., Zhang, G., Ba Abdullah, M. M., Huang, D., Fang, Y., Alnakhli, Y. O., Jia, S., … Yu, J. (2013). Genome sequence of the date palm Phoenix dactylifera L. Nature Communications, 4, 2274.
    1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
    1. Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815. Retrieved from http://www.nature.com/nature/journal/v408/n6814/suppinfo/408796a0_S1.html
    1. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinki, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nature Genetics, 25, 25-29.

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