RRAP: RPKM Recruitment Analysis Pipeline

Kojima, Conner Y.; Getz, Eric W.; Thrash, J. Cameron

doi:10.1128/mra.00644-22

Cited by 10 publications

(9 citation statements)

References 19 publications

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“…Metagenomic samples were compiled from the following datasets: TARA Oceans, BIOGEOTRACES, MALASPINA, the Bermuda Atlantic Time Series (BATS), the Chesapeake, Delaware, and San Francisco Bays, the Hawaiian Ocean Time series (HOT), the Columbia River and Yaquina Bay, the Baltic Sea, Pearl River, Sapelo Island, Southern California Bight, and the northern Gulf of Mexico(61)(62)(63)(64)(65)(66)(67)(68)(69). We recruited reads from all datasets to the AEGEAN-169 genomes via RRAP(70)(71)(72). Post-recruitment, we assessed subclade distribution by summing all Reads Per Kilobases of genome per Million bases of metagenome sequence (RPKM) values for the genomes within each subclade and plotting them by depth, temperature, and salinity.…”

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confidence: 99%

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

Getz

Lanclos

Kojima

et al. 2023

Preprint

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Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning Order level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to thePelagibacteralesis highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to thePelagibacterales. We used a new isolate genome, recently released single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with recruitment of metagenomes spanning open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade, and support the contention that this group represents a taxonomic Family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa.

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confidence: 99%

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

Getz

Lanclos

Kojima

et al. 2023

Preprint

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“…To determine genome, gene and transcript abundances MG and MT reads were mapped to DWH MAGs and non-DWH genomes using Bowtie 2 (ver. 2.3.4.1) (Langmead & Salzberg, 2012) following the script provided at https://merenlab.org/data/tara-oceans-mags/ and used in Thrash et al (2017) and more recently as the RRAP pipeline (Kojima et al, 2022). Before mapping cDNA reads ribosomal RNA was subtracted using riboPicker (ver 0.4.3) with the default settings (Schmieder et al 2012).…”

Section: Methodsmentioning

confidence: 99%

“…1.7-2) (Li et al, 2009) command idxstats with default settings. Subsequently, genome, gene and transcript abundances were normalized by calculating reads per kilobase per million mapped (RPKM) values according to Mortazavi et al (2008), and detailed in Thrash et al (2017) and Kojima et al (2022). RPKM values are reported as MG RPKM maximum/MT RPKM maximum in the results.…”

Section: Metagenomic Sequencing Assembly Annotation and Read Mappingmentioning

confidence: 99%

Novel, active, and uncultured hydrocarbon degrading microbes in the ocean

Howe,

Zaugg,

Mason

2024

Preprint

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Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon degrading microbes with clade specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Further, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume members in the SAR324 and UBA11654 coded for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provided missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.

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“…To examine the distribution of genomes in aquatic systems, we selected 1,059 metagenomes for read recruitment from the following regions: Baltic Sea, Chesapeake Bay, Columbia River, Black Sea, Gulf of Mexico, Pearl River, Sappelo Island, San Francisco Bay, BioGeoTraces, Tara Oceans, and HOT (accession numbers available in Table S1 ). We conducted read mapping and calculation of normalized abundances via Reads Per Kilobase (of genome) per Million (of recruited read base pairs) (RPKM) using RRAP(38).…”

Section: Methodsmentioning

confidence: 99%

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

Lanclos

Rasmussen

Kojima

et al. 2022

Preprint

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The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 466 high-quality publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided the first IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

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RRAP: RPKM Recruitment Analysis Pipeline

Cited by 10 publications

References 19 publications

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

Novel, active, and uncultured hydrocarbon degrading microbes in the ocean

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

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