Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes

Patin, N. V.; Goodwin, K. D.

doi:10.1128/msystems.00595-22

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Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes

2022
By Patin, N. V. ; Goodwin, K. D.
Source: MSystems, 7(6)

[PDF-2.19 MB]

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Details:

Journal Title:

mSystems
Personal Author:

Patin, N. V. ; Goodwin, K. D.

Patin, N. V. ; Goodwin, K. D. Less -
NOAA Program & Office:

CIMAS (Cooperative Institute for Marine and Atmospheric Studies) ; OAR (Oceanic and Atmospheric Research) ; AOML (Atlantic Oceanographic and Meteorological Laboratory) ; NMFS (National Marine Fisheries Service) ; SWFSC (Southwest Fisheries Science Center)

CIMAS (Cooperative Institute for Marine and Atmospheric Studies) ; OAR (Oceanic and Atmospheric Research) ; AOML (Atlantic Oceanographic and Meteorological Laboratory) ; NMFS (National Marine Fisheries Service) ; SWFSC (Southwest Fisheries Science Center) Less -
Description:

Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing. We applied Pacific Biosciences (PacBio) CCS (circular consensus sequencing) HiFi shotgun sequencing to 14 marine water column samples and compared the results with those for short-read metagenomes from the corresponding environmental DNA samples. We found that long-read metagenomes varied widely in quality and biological information. The community compositions of the corresponding long- and short-read metagenomes were frequently dissimilar, suggesting higher stochasticity and/or bias associated with PacBio sequencing. Long reads provided few improvements to the assembly qualities, gene annotations, and prokaryotic metagenome-assembled genome (MAG) binning results. However, only long reads produced high-quality eukaryotic MAGs and contigs containing complete zooplankton marker gene sequences. These results suggest that high-quality long-read metagenomes can improve marine community composition analyses and provide important insight into eukaryotic phyto- and zooplankton genetics, but the benefits may be outweighed by the inconsistent data quality.
Keywords:

[+]

Biotic Communities DNA Metagenomics Biochemistry Computer Science Applications Ecology, Evolution, Behavior And Systematics EDNA Genetics Long-read Sequencing Marine Microbiomes Metagenomics Microbiology Modeling And Simulation Molecular Biology Physiology
Source:

MSystems, 7(6)
DOI:

https://doi.org/10.1128/msystems.00595-22
Document Type:

Journal Article
Funding:

Grant no. NA20OAR4320472
License:

https://creativecommons.org/publicdomain/zero/1.0/
Rights Information:

CC0 Public Domain
Compliance:

Submitted
Main Document Checksum:

[+]

urn:sha256:b247a418cd766b495aa59e6e627af2a8c0ab5cb3dc5a9e9492bbfd03a9cf43bb
Download URL:

https://repository.library.noaa.gov/view/noaa/48145/noaa_48145_DS1.pdf
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Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes

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