Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.

IF 2.1 3区生物学 Q3 GENETICS & HEREDITY

G3: Genes|Genomes|Genetics Pub Date : 2024-09-04 DOI:10.1093/g3journal/jkae135

Eng-Ti Leslie Low, Kuang-Lim Chan, Noorhariza Mohd Zaki, Elizaveta Taranenko, Jared M Ordway, Corey Wischmeyer, Jaap Buntjer, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Jayanthi Nagappan, Rozana Rosli, Eugeniya Bondar, Nadzirah Amiruddin, Norashikin Sarpan, Ngoot-Chin Ting, Pek-Lan Chan, Meilina Ong-Abdullah, Marhalil Marjuni, Suzana Mustaffa, Norziha Abdullah, Norazah Azizi, Blaire Bacher, Nathan Lakey, Tatiana V Tatarinova, Mohamad Arif Abd Manaf, Ravigadevi Sambanthamurti, Rajinder Singh

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引用次数: 0

Abstract

Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.

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染色体尺度的 Elaeis guineensis 和 E. oleifera 组合：油棕科和其他油棕科植物的比较基因组学。

Elaeis guineensis 和 E. oleifera 是两种油棕榈树。E. guineensis 是最广泛种植的商业品种，从 E. oleifera 引种的理想性状正在进行中。我们报告了改进后的 E. guineensis 基因组组装，其连续性和完整性得到了大幅提高，同时还报告了首个染色体规模的 E. oleifera 基因组组装。每个基因组都是通过整合长线程测序、近距离连接测序、光学图谱和遗传图谱获得的。在这两个物种之间观察到了高度的种间基因组保护。该研究提供了迄今为止最广泛的基因注释，包括 46,697 个 E. guineensis 和 38,658 个 E. oleifera 基因预测。对重复元件家族的分析进一步确定了两个基因组的 DNA 重复结构。比较基因组分析确定了经实验验证的油棕榈树物种间的小结构变异，并解析了染色体融合机制，该机制是导致染色体非整倍性从 18 条进化到 16 条的原因。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

G3: Genes|Genomes|Genetics GENETICS & HEREDITY-

CiteScore

5.10

自引率

3.80%

发文量

305

审稿时长

3-8 weeks

期刊介绍： G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.