世界性硅藻 Skeletonema costatum 染色体级基因组组装为生态适应提供洞察力

IF 4.6 2区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Algal Research-Biomass Biofuels and Bioproducts Pub Date : 2024-10-20 DOI:10.1016/j.algal.2024.103761
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引用次数: 0

摘要

世界性硅藻物种 Skeletonema costatum 是一种具有重要生态意义的优势浮游植物,经常出现在沿海河口和海洋水域,并经常引起有害藻类的大量繁殖。尽管它在生态学上具有重要意义,但染色体组水平的基因组组装仍然缺乏,这阻碍了对其进化和环境适应性的深入了解。在此,我们报告了海洋硅藻 S. costatum 的染色体组水平基因组组装。组装的基因组大小为 136.49 Mb,等位基因 N50 为 302 Kb,95.30% 的读数锚定在 23 个假染色体上,支架 N50 为 6.19 Mb。共预测出 28,321 个编码蛋白质的基因,其中 86.03% 已进行功能注释。对基因组组装和基因组注释的 BUSCO 评估均超过 90%。系统进化分析表明,S. costatum与其近缘种S. marinoi在大约2260万年前从共同祖先分化而来,这符合预期的拓扑结构。S. costatum的基因组大小比其近缘硅藻大,主要是由于其含有较多的转座元件和较多的蛋白编码基因。共线性分析表明,S. costatum 与其他 Skeletonema 之间具有很强的共线性,大多数染色体显示出明显的一一对应关系。在 S. costatum 中发现了一个较大的隐色素基因家族,其中有 9 个拷贝具有蓝光光感受器的功能,这可能有助于其生态成功。S. costatum高质量染色体级基因组组装的获得是一个宝贵的资源,可促进比较基因组学揭示重要的生态线索和基因家族,以及未来对Skeletonema物种间的遗传学和环境研究。
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Chromosome-level genome assembly of the cosmopolitan diatom Skeletonema costatum provides insights into ecological adaptation
The cosmopolitan diatom species Skeletonema costatum is an ecologically important dominant phytoplankton frequently found in the coastal estuarine and marine waters, and often causes harmful algae blooms. Despite of its critical ecological importance, chromosome-level genome assemble is still unavailable, hindering in-depth understanding of their evolution and environmental adaption. Here, we report a chromosome-level genome assembly for the marine diatom species S. costatum. The assembled genome size was 136.49 Mb, with a contig N50 of 302 Kb and 95.30 % of the reads anchored into 23 pseudo-chromosomes with a scaffold N50 of 6.19 Mb. A total of 28,321 protein-coding genes were predicted, with 86.03 % being functional annotated. The BUSCO assessment of genome assembly and genome annotation were both above 90 %. Phylogenetic analysis showed the expected topology, with S. costatum and its closely related species S. marinoi diverged from their common ancestor around 22.6 million years ago. The genome size of S. costatum is comparatively larger than those of its closely related diatoms, due mostly to its higher transposable element contents and larger number of proteincoding genes. Collinearity analysis revealed strong collinearity between S. costatum and other Skeletonema with most chromosomes showing clear one-to-one correspondences. A larger family of nine copies of the cryptochrome genes that function as blue light photoreceptors were identified in S. costatum, which could contribute its ecological success. The availability of the high-quality chromosome-level genome assembly for S. costatum represents a valuable resource that may facilitate comparative genomics for revealing important ecological clues and gene families, and future genetics and environmental studies among Skeletonema species.
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来源期刊
Algal Research-Biomass Biofuels and Bioproducts
Algal Research-Biomass Biofuels and Bioproducts BIOTECHNOLOGY & APPLIED MICROBIOLOGY-
CiteScore
9.40
自引率
7.80%
发文量
332
期刊介绍: Algal Research is an international phycology journal covering all areas of emerging technologies in algae biology, biomass production, cultivation, harvesting, extraction, bioproducts, biorefinery, engineering, and econometrics. Algae is defined to include cyanobacteria, microalgae, and protists and symbionts of interest in biotechnology. The journal publishes original research and reviews for the following scope: algal biology, including but not exclusive to: phylogeny, biodiversity, molecular traits, metabolic regulation, and genetic engineering, algal cultivation, e.g. phototrophic systems, heterotrophic systems, and mixotrophic systems, algal harvesting and extraction systems, biotechnology to convert algal biomass and components into biofuels and bioproducts, e.g., nutraceuticals, pharmaceuticals, animal feed, plastics, etc. algal products and their economic assessment
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