The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
22 Oct 2024
22 Oct 2024
Historique:
received:
22
04
2024
accepted:
15
10
2024
medline:
23
10
2024
pubmed:
23
10
2024
entrez:
22
10
2024
Statut:
epublish
Résumé
Marine microbial eukaryotes (protists) perform essential metabolic functions in oceanic ecosystems. The diversity of protist functions remains poorly understood as few species have been isolated in laboratory settings. Metatranscriptomes provide an invaluable tool for exploring protist diversity and genetic capacities within their natural habitats. Here, we introduce the North Pacific Eukaryotic Gene Catalog, a compilation of metatranscriptome data derived from a total of 261 metatranscriptomes: 169 metatranscriptomes were derived from samples collected on three meridional surface transects along 158°W, each spanning ~20 degrees of latitude from the North Pacific Subtropical Gyre (NPSG) to the North Pacific Transition Zone (NPTZ); 92 metatranscriptomes were derived from two diel-resolved field studies, one in the NPSG at 157°W, 23°N, one in the NPTZ at 158°W, 41°N. The metatranscriptome sequences were de novo assembled into 175 assemblies and pooled into five datasets each containing between 22 M and 49 M contigs clustered at 99% protein identity. Assemblies were annotated by taxonomy and function, and enumerated by short read alignment. All data are available in the Zenodo repository, with underlying code available on github.
Identifiants
pubmed: 39438508
doi: 10.1038/s41597-024-04005-5
pii: 10.1038/s41597-024-04005-5
doi:
Types de publication
Dataset
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1161Subventions
Organisme : Simons Foundation
ID : #823165
Organisme : Simons Foundation
ID : #999392
Organisme : Simons Foundation
ID : #426570SP
Organisme : Simons Foundation
ID : #723795
Organisme : Simons Foundation
ID : #329108
Informations de copyright
© 2024. The Author(s).
Références
Worden, A. Z. et al. Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science 347, 1257594 (2015).
doi: 10.1126/science.1257594
pubmed: 25678667
Caron, D. A. et al. Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nat. Rev. Microbiol. 15, 6–20 (2017).
doi: 10.1038/nrmicro.2016.160
pubmed: 27867198
Sutherland, B. J. G. et al. Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment. Environ. DNA 5, 920–933 (2023).
doi: 10.1002/edn3.353
Zehnpfennig, J. R. et al. Diel Patterns in Marine Microbial Metatranscriptomes Reflect Differences in Community Metabolic Activity Over Depth on the Continental Shelf of the North Atlantic. Front. Mar. Sci. 9, 1–11 (2022).
doi: 10.3389/fmars.2022.798877
Lampe, R. H. et al. Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton. Nat. Commun. 14, 7215 (2023).
doi: 10.1038/s41467-023-42949-1
pubmed: 37940668
pmcid: 10632500
Carradec, Q. et al. A global ocean atlas of eukaryotic genes. Nat. Commun. 9, 373 (2018).
doi: 10.1038/s41467-017-02342-1
pubmed: 29371626
pmcid: 5785536
Karl, D. M. A Sea of Change: Biogeochemical Variability in the North Pacific Subtropical Gyre. Ecosystems 2, 181–214 (1999).
doi: 10.1007/s100219900068
Juranek, L. W. et al. The importance of the phytoplankton “middle class” to ocean net community productivity. Global Biogeochem. Cycles 34, (2020).
Graff van Creveld, S. et al. Divergent functions of two clades of flavodoxin in diatoms mitigate oxidative stress and iron limitation. eLife 12, e84392 (2023).
doi: 10.7554/eLife.84392
pubmed: 37278403
pmcid: 10287166
Lambert, B. et al. The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics. Proc. Natl. Acad. Sci. 119, e2100916119 (2022).
doi: 10.1073/pnas.2100916119
pubmed: 35145022
pmcid: 8851463
Park, J. et al. Siderophore production and utilization by marine bacteria in the North Pacific Ocean. Limnol. Oceanogr. 68, 1636–1653 (2023).
doi: 10.1002/lno.12373
Durham, B. P. et al. Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nat. Microbiol. 4, 1706–1715 (2019).
doi: 10.1038/s41564-019-0507-5
pubmed: 31332382
Coesel, S. N. et al. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proc. Natl. Acad. Sci. 118, e2011038118 (2021).
doi: 10.1073/pnas.2011038118
pubmed: 33547239
pmcid: 8017926
Groussman, R. D., Coesel, S. N., Durham, B. P. & Armbrust, E. V. Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre. Front. Microbiol. 12, 1–15 (2021).
doi: 10.3389/fmicb.2021.682651
Groussman, R. MarFERReT v1.1 + MARMICRODB v1.0 multi-kingdom marine reference protein sequence library. Zenodo https://doi.org/10.5281/zenodo.10586950 (2024).
Groussman, R. D., Blaskowski, S., Coesel, S. & Armbrust, E. V. MarFERReT: an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Zenodo https://doi.org/10.5281/zenodo.10170983 (2023).
Hogle, S. L. MARMICRODB database for taxonomic classification of (marine) metagenomes. Zenodo https://doi.org/10.5281/zenodo.3520509 (2019).
Mistry, J. et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 49, D412–D419 (2021).
doi: 10.1093/nar/gkaa913
pubmed: 33125078
Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).
doi: 10.1093/bioinformatics/btz859
pubmed: 31742321
Wilson, S. T. et al. Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera. Nat. Microbiol. 2, 17118 (2017).
doi: 10.1038/nmicrobiol.2017.118
pubmed: 28758990
Satinsky, B. M., Gifford, S. M., Crump, B. C. & Moran, M. A. Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis. in Methods in Enzymology 237–250, https://doi.org/10.1016/B978-0-12-407863-5.00012-5 (2013).
Groussman, R., Coesel, S. & Armbrust, E. V. The North Pacific Eukaryotic Gene Catalog: Raw assemblies from Gradients 1, 2 and 3. Zenodo https://doi.org/10.5281/zenodo.10699458 (2023).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
doi: 10.1038/nmeth.1923
pubmed: 22388286
pmcid: 3322381
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
doi: 10.1093/bioinformatics/btu170
pubmed: 24695404
pmcid: 4103590
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
doi: 10.1038/nbt.1883
pubmed: 21572440
pmcid: 3571712
Rice, P., Longden, I. & Bleasby, A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000).
doi: 10.1016/S0168-9525(00)02024-2
pubmed: 10827456
Steinegger, M. & Söding, J. Clustering huge protein sequence sets in linear time. Nat Commun 9, 2542 (2018).
doi: 10.1038/s41467-018-04964-5
pubmed: 29959318
pmcid: 6026198
Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34, 525–527 (2016).
doi: 10.1038/nbt.3519
pubmed: 27043002
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015).
doi: 10.1038/nmeth.3176
pubmed: 25402007
Groussman, R. D., Blaskowski, S., Coesel, S. N. & Armbrust, E. V. MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes. Sci Data 10, 926 (2023).
doi: 10.1038/s41597-023-02842-4
pubmed: 38129449
pmcid: 10739892
Federhen, S. The NCBI Taxonomy database. Nucleic Acids Res. 40, D136–D143 (2012).
doi: 10.1093/nar/gkr1178
pubmed: 22139910
Groussman, R., Blaskowski, S., Coesel, S. & Armbrust, E. V. The North Pacific Eukaryotic Gene Catalog: metatranscriptome assemblies with taxonomy, function and abundance annotations. Zenodo https://doi.org/10.5281/zenodo.12630398 (2024).
Eddy, S. R. Accelerated Profile HMM Searches. PLoS Comput. Biol. 7, e1002195 (2011).
doi: 10.1371/journal.pcbi.1002195
pubmed: 22039361
pmcid: 3197634
Paysan-Lafosse, T. et al. InterPro in 2022. Nucleic Acids Res. 51, D418–D427 (2023).
doi: 10.1093/nar/gkac993
pubmed: 36350672
Groussman, R., Coesel, S. & Armbrust, E. V. The North Pacific Eukaryotic Gene Catalog: KOfam protein function annotations. Zenodo https://doi.org/10.5281/zenodo.13743267 (2024).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP199207 (2024).
Coesel, S., Groussman, R. & Armbrust, E. V. TSA: seawater metagenome, transcriptome shotgun assembly. GenBank https://identifiers.org/ncbi/insdc:GKYU00000000 (2024).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP309146 (2024).
Coesel, S., Groussman, R. & Armbrust, E. V. TSA: seawater metagenome, transcriptome shotgun assembly. GenBank https://identifiers.org/ncbi/insdc:GKYT00000000 (2024).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP489541 (2024).
Coesel, S., Groussman, R. & Armbrust, E. V. TSA: seawater metagenome, transcriptome shotgun assembly. GenBank https://identifiers.org/ncbi/insdc:GKYS00000000 (2024).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP489879 (2024).
Coesel, S., Groussman, R. & Armbrust, E. V. TSA: seawater metagenome, transcriptome shotgun assembly. GenBank https://identifiers.org/ncbi/insdc:GKYV00000000 (2024).
NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP490084 (2024).
Coesel, S., Groussman, R. & Armbrust, E. V. TSA: seawater metagenome, transcriptome shotgun assembly. GenBank https://identifiers.org/ncbi/insdc:GKYW00000000 (2024).
Groussman, R., Blaskowski, S., Coesel, S. & Armbrust, E. V. The North Pacific Eukaryotic Gene Catalog: clustered nucleotide metatranscripts and read counts. Zenodo https://doi.org/10.5281/zenodo.13826820 (2024).
Groussman, R. Diel-regulated transcriptional cascades of microbial eukaryotes in the North Pacific Subtropical Gyre. Zenodo https://doi.org/10.5281/zenodo.5009803 (2021).
Cohen, N. R., Alexander, H., Krinos, A. I., Hu, S. K. & Lampe, R. H. Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications. Front. Mar. Sci. 9, 1–18 (2022).
doi: 10.3389/fmars.2022.867007
Graff van Creveld, S., Coesel, S. N., Schatz, M. J. & Armbrust, E. V. New eukaryotic phytoplankton isolates from the oligotrophic tropical Pacific Ocean. J. Phycol. 60, 598–603 (2024).
doi: 10.1111/jpy.13447
pubmed: 38625734
Ashkezari, M. D. et al. Simons Collaborative Marine Atlas Project (Simons CMAP): an open-source portal to share, visualize and analyze ocean data. Limnol. Oceanogr. Methods 19, 488–496 (2021).
doi: 10.1002/lom3.10439