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海洋硅藻菌株UHM3201（施瓦尔茨、斯坦切娃和斯图尔特，2022年）及其固氮内共生蓝细菌的基因组序列。

The genome sequences of the marine diatom strain UHM3201 (Schvarcz, Stancheva & Steward, 2022) and its nitrogen-fixing, endosymbiotic cyanobacterium.

作者信息

Schvarcz Christopher R, Stancheva Rosalina, Turk-Kubo Kendra A, Wilson Samuel T, Zehr Jonathan P, Edwards Kyle F, Steward Grieg F, Archibald John M, Oatley Graeme, Sinclair Elizabeth, Santos Camilla, Paulini Michael, Aunin Eerik, Gettle Noah, Niu Haoyu, McKenna Victoria, O'Brien Rebecca

机构信息

Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA.

Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA.

出版信息

Wellcome Open Res. 2024 Apr 29;9:232. doi: 10.12688/wellcomeopenres.21534.1. eCollection 2024.

DOI:10.12688/wellcomeopenres.21534.1
PMID:38867757
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11167328/
Abstract

We present the genome assembly of the pennate diatom strain UHM3201 (Ochrophyta; Bacillariophyceae; Rhopalodiales; Rhopalodiaceae) and that of its cyanobacterial endosymbiont (Chroococcales: Aphanothecaceae). The genome sequence of the diatom is 60.3 megabases in span, and the cyanobacterial genome has a length of 2.48 megabases. Most of the diatom nuclear genome assembly is scaffolded into 15 chromosomal pseudomolecules. The organelle genomes have also been assembled, with the mitochondrial genome 40.08 kilobases and the plastid genome 130.75 kilobases in length. A number of other prokaryote MAGs were also assembled.

摘要

我们展示了羽纹硅藻菌株UHM3201（褐藻门；硅藻纲；棒杆藻目；棒杆藻科）及其蓝藻内共生体（色球藻目：隐球藻科）的基因组组装情况。硅藻的基因组序列跨度为60.3兆碱基，蓝藻基因组长度为2.48兆碱基。硅藻核基因组组装的大部分被构建成15个染色体假分子。细胞器基因组也已组装完成，线粒体基因组长度为40.08千碱基，质体基因组长度为130.75千碱基。还组装了许多其他原核生物的宏基因组组装基因组（MAGs）。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/5a1af540c3e4/wellcomeopenres-9-23805-g0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/09415d0711c9/wellcomeopenres-9-23805-g0000.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/fa363d03a976/wellcomeopenres-9-23805-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/164f72c43b5b/wellcomeopenres-9-23805-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/f5ce947e6afd/wellcomeopenres-9-23805-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/a5b9c60dbacb/wellcomeopenres-9-23805-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/e0bfb298abc8/wellcomeopenres-9-23805-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/5a1af540c3e4/wellcomeopenres-9-23805-g0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/09415d0711c9/wellcomeopenres-9-23805-g0000.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/fa363d03a976/wellcomeopenres-9-23805-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/164f72c43b5b/wellcomeopenres-9-23805-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/f5ce947e6afd/wellcomeopenres-9-23805-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/a5b9c60dbacb/wellcomeopenres-9-23805-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/e0bfb298abc8/wellcomeopenres-9-23805-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aaf8/11167328/5a1af540c3e4/wellcomeopenres-9-23805-g0006.jpg

相似文献

[1]
The genome sequences of the marine diatom strain UHM3201 (Schvarcz, Stancheva & Steward, 2022) and its nitrogen-fixing, endosymbiotic cyanobacterium.

Wellcome Open Res. 2024-4-29

[2]
Overlooked and widespread pennate diatom-diazotroph symbioses in the sea.

Nat Commun. 2022-2-10

[3]
Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.

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[4]
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[5]
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[6]
Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.

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[7]
Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont.

ISME J. 2024-1-8

[8]
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[9]
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[10]
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引用本文的文献

[1]
Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis.

Proc Natl Acad Sci U S A. 2025-8-19

[2]
Protein import into bacterial endosymbionts and evolving organelles.

FEBS J. 2025-6

[3]
Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis.

bioRxiv. 2025-2-18

本文引用的文献

[1]
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.

BMC Bioinformatics. 2023-7-18

[2]
YaHS: yet another Hi-C scaffolding tool.

Bioinformatics. 2023-1-1

[3]
Overlooked and widespread pennate diatom-diazotroph symbioses in the sea.

Nat Commun. 2022-2-10

[4]
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.

Mol Biol Evol. 2021-9-27

[5]
Towards complete and error-free genome assemblies of all vertebrate species.

Nature. 2021-4

[6]
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.

Nat Methods. 2021-2

[7]
Significantly improving the quality of genome assemblies through curation.

Gigascience. 2021-1-9

[8]
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.

Genome Biol. 2020-9-14

[9]
MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics.

Mol Ecol Resour. 2020-7

[10]
BlobToolKit - Interactive Quality Assessment of Genome Assemblies.

G3 (Bethesda). 2020-4-9

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