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来自墨西哥湾北部“死亡区”的宏基因组组装和原核宏基因组组装基因组序列

Metagenomic Assembly and Prokaryotic Metagenome-Assembled Genome Sequences from the Northern Gulf of Mexico "Dead Zone".

作者信息

Thrash J Cameron, Baker Brett J, Seitz Kiley W, Temperton Ben, Campbell Lauren Gillies, Rabalais Nancy N, Henrissat Bernard, Mason Olivia U

机构信息

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.

Marine Science Institute, University of Texas, Austin, Port Aransas, Texas, USA.

出版信息

Microbiol Resour Announc. 2018 Sep 6;7(9). doi: 10.1128/MRA.01033-18. eCollection 2018 Sep.

DOI:10.1128/MRA.01033-18
PMID:30533941
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6256533/
Abstract

Coastal regions experiencing declining dissolved oxygen are increasing in number and severity around the world. However, despite the importance of microbial metabolism in coastal hypoxia, few metagenomic surveys exist. Our data set from within the second largest human-caused hypoxic region provides opportunities to more deeply explore the microbiology of these systems.

摘要

全球范围内,溶解氧下降的沿海地区数量在增加,且情况愈发严重。然而,尽管微生物代谢在沿海低氧环境中十分重要,但针对此的宏基因组学调查却很少。我们从第二大人为造成的低氧区域获取的数据集,为更深入探究这些系统的微生物学提供了契机。

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本文引用的文献

1
Declining oxygen in the global ocean and coastal waters.全球海洋和沿海水域的氧气减少。
Science. 2018 Jan 5;359(6371). doi: 10.1126/science.aam7240.
2
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico "Dead Zone".未培养细菌浮游生物谱系在墨西哥湾“死亡区”的代谢作用。
mBio. 2017 Sep 12;8(5):e01017-17. doi: 10.1128/mBio.01017-17.
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IMG/M: integrated genome and metagenome comparative data analysis system.IMG/M:综合基因组与宏基因组比较数据分析系统
Nucleic Acids Res. 2017 Jan 4;45(D1):D507-D516. doi: 10.1093/nar/gkw929. Epub 2016 Oct 13.
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.CheckM:评估从分离株、单细胞和宏基因组中获得的微生物基因组质量。
Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14.
5
Archaeal enrichment in the hypoxic zone in the northern Gulf of Mexico.墨西哥湾北部缺氧区的古菌富集。
Environ Microbiol. 2015 Oct;17(10):3847-56. doi: 10.1111/1462-2920.12853. Epub 2015 Apr 27.
6
Genomes of planktonic Acidimicrobiales: widening horizons for marine Actinobacteria by metagenomics.浮游嗜酸菌纲的基因组:通过宏基因组学拓展海洋放线菌的视野
mBio. 2015 Feb 10;6(1):e02083-14. doi: 10.1128/mBio.02083-14.
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Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria.宏基因组学揭示了一类新的低 GC 及超小型海洋放线菌。
Sci Rep. 2013;3:2471. doi: 10.1038/srep02471.
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IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.IDBA-UD:一个用于具有高度不均匀深度的单细胞和宏基因组测序数据的从头组装程序。
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The genomic standards consortium: bringing standards to life for microbial ecology.基因组标准协会:让微生物生态学标准落地生根。
ISME J. 2011 Oct;5(10):1565-7. doi: 10.1038/ismej.2011.39. Epub 2011 Apr 7.