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全球分布的中心硅藻——骨条藻属的基因组序列草图。

The draft genome sequences of the cosmopolitan centric diatom, the genus Skeletonema.

作者信息

Nagai Satoshi, Minei Ryuhei, Takemura Ikuyo, Tabata Hiromasa, Töpel Mats, Pinder Matthew, Kourtchenko Olga, Lee-Kuo Kang, Van Nguyen Nguyen, Sildever Sirje, Ogura Atsushi, Gojobori Takashi

机构信息

Japan Fisheries Research and Education Agency, Yokohama Branch, Yokohama, Kanagawa, 236-8648, Japan.

Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga, 526-0829, Japan.

出版信息

Sci Data. 2025 Aug 5;12(1):1358. doi: 10.1038/s41597-025-05432-8.

DOI:10.1038/s41597-025-05432-8
PMID:40764321
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12325754/
Abstract

The genus Skeletonema stands out as one of the most prevalent and globally distributed diatoms within coastal marine ecosystems. Additionally, it holds significance as a pivotal organism across diverse research domains, encompassing biochemistry, ecophysiology, molecular biology, ecology, oceanography, and aquaculture. This study presents the draft genome assemblies and annotations of 11 strains in 9 Skeletonema species. We generated approximately 13.2-45.4 Gbp (DNA) and 6.0-15.4 Gbp (RNA) of sequencing data and produced draft haploid genomes with total lengths of 40.3-69.3 Mbp and N50 scaffold sizes of 0.35-1.09 Mbp containing 90-98% of orthologs conserved in Stramenopiles. We also identified 5.1-28.4 Mbp (11.0-41.1% of the draft genomes) of repetitive genome sequences and a total number of 15,275-21,376 protein-coding genes. The draft genomes of Skeletonema will facilitate further study, such as population dynamics, phylogeography, the process of speciation, and the evolution of gene function, and help to provide deep insight into the cosmopolitanism of this most successfully prosperous genus.

摘要

骨条藻属是沿海海洋生态系统中最常见且分布最广的硅藻之一。此外，它作为一种关键生物在多个研究领域具有重要意义，包括生物化学、生态生理学、分子生物学、生态学、海洋学和水产养殖。本研究展示了9种骨条藻属物种中11个菌株的基因组草图组装和注释。我们生成了约13.2 - 45.4 Gbp（DNA）和6.0 - 15.4 Gbp（RNA）的测序数据，并产生了单倍体基因组草图，其总长度为40.3 - 69.3 Mbp，N50支架大小为0.35 - 1.09 Mbp，包含90 - 98%在不等鞭毛类中保守的直系同源基因。我们还鉴定出5.1 - 28.4 Mbp（占基因组草图的11.0 - 41.1%）的重复基因组序列以及总共15,275 - 21,376个蛋白质编码基因。骨条藻属的基因组草图将有助于进一步的研究，如种群动态、系统地理学、物种形成过程以及基因功能的进化，并有助于深入了解这个最成功繁荣的属的世界性分布。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/c3c442b23475/41597_2025_5432_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/afccd82d5588/41597_2025_5432_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/ac6fc4cd4698/41597_2025_5432_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/fa5cb843066a/41597_2025_5432_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/35355041906b/41597_2025_5432_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/98670078ee45/41597_2025_5432_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/c403c46ba859/41597_2025_5432_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/67f4c02723fb/41597_2025_5432_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/c3c442b23475/41597_2025_5432_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/afccd82d5588/41597_2025_5432_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/ac6fc4cd4698/41597_2025_5432_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/fa5cb843066a/41597_2025_5432_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/35355041906b/41597_2025_5432_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/98670078ee45/41597_2025_5432_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/c403c46ba859/41597_2025_5432_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/67f4c02723fb/41597_2025_5432_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/10ae/12325754/c3c442b23475/41597_2025_5432_Fig8_HTML.jpg

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