Developing methods for long-read marine viral metagenomics

GSTDTAP

项目编号	NE/P008534/1
	Developing methods for long-read marine viral metagenomics
	[unavailable]
主持机构	University of Exeter
项目开始年	2017
	2017
项目结束日期	2018-12-31
资助机构	UK-NERC
项目类别	Research Grant
国家	英国
语种	英语
英文摘要	Everybody knows how important terrestrial plants are to the global climate, fixing atmospheric carbon and providing the oxygen that sustains life. What is less known is that marine microbes are responsible for around half of total global primary production. Seawater is teeming with microbes, with around 5 million in every teaspoon in surface water. These can be categorised as the phototrophs that fix atmospheric carbon, the heterotrophs that convert this carbon back to atmospheric CO2 and the vast number of viruses that interact with these two groups. At any given time, around 30% of marine microbes are infected by their associated viruses. Viral lysis kills 20% of bacterial standing stocks every day, releasing a soup of dissolved organic carbon that is the largest pool of available carbon on Earth. Heterotrophs rapidly convert this back into CO2, preventing it from sinking to the deep where it is locked away. Viruses can also act as agents of gene transfer, and can reconfigure host metabolism during infection, changing their metabolic inputs and outputs. Such changes then resonate throughout the community, ultimately shaping its function and composition. Traditionally, our understanding of viruses was limited to those for which we had successfully cultured the host. As >99% of microbes are uncultivated, this provided a very narrow representation of viral diversity. Recent advances in sequencing viruses directly from the environment, by preparing viral metagenomes (viromes) have revolutionised our understanding of the importance, abundance and impact of viruses on global biogeochemical cycles. However, such approaches rely on successfully assembling viral genomes from short read data, similar to reconstructing an enormous genomic jigsaw with billions of pieces. The high rates of evolution and extraordinary diversity of viruses makes this a challenge. Currently <1% of viral sequences from a metagenome can be assigned to a known viral group. This project will establish new methods to sequence viral metagenomes using the latest long-read sequencing technology. PacBio and Nanopore sequencers generate reads that are several thousand basepairs long, in some cases, sufficiently long to span an entire viral genome. This increased length makes assembly and analysis of viral genomes trivial. To date, application of long-read sequencing to viral metagenomics has been limited by a need for DNA input requirements that were orders of magnitude higher than that which can be reasonably extracted from an environmental viral sample. However, recent updates to library preparation for Nanopore and advances in DNA amplification for PacBio make it an opportune time to re-evaluate their use in viral metagenomics. As a result of long-read sequencing, extracting full length viral genomes from environmental samples will provide a step-change in the resolution with which we can perform viral ecology.
来源学科分类	Natural Environment Research
文献类型	项目
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/86518
专题	环境与发展全球科技态势
推荐引用方式 GB/T 7714	[unavailable].Developing methods for long-read marine viral metagenomics.2017.