A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation

文献类型： 外文期刊

第一作者： Wang, Le

作者： Wang, Le;Lee, May;Wan, Zi Yi;Bai, Bin;Ye, Baoqing;Song, Zhuojun;Yue, Gen Hua;Bai, Bin;Alfiko, Yuzer;Purwantomo, Sigit;Suwanto, Antonius;Rahmadsyah, Rahmadsyah;Yue, Gen Hua

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关键词： Oil palm; Genome; Evolution; VIRESCENS; Molecular breeding

期刊名称：GENOMICS PROTEOMICS & BIOINFORMATICS （ 影响因子：9.5； 五年影响因子：10.1 ）

ISSN： 1672-0229

年卷期： 2023 年 21 卷 3 期

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收录情况： SCI

摘要： The palm family (Arecaceae), consisting of similar to 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, Dura, assembled by integrating long reads with similar to 150x genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

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