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Comparative genomics reveals new functional insights in uncultured MAST species

AuthorsLabarre, Aurélie ; López-Escardó, David ; Latorre, Fran ; Leonard, Guy; Bucchini, François; Obiol, Aleix ; Cruaud, Corinne; Sieracki, Michael E.; Jaillon, Olivier; Wincker, Patrick; Vandepoele, Klaas; Logares, Ramiro ; Massana, Ramon
Issue DateJan-2021
PublisherInternational Society for Microbial Ecology
CitationISME Journal - International Society for Microbial Ecology 15: 1767-1781 (2021)
AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles
Description15 pages, 7 figures, 1 table, supplementary information https://doi.org/10.1038/s41396-020-00885-8.-- Data availability: Sequencing reads have been deposited at the GenBank Database under Project numbers PRJEB6603 for Tara SAGs and PRJEB41235 for BMMO SAGs. Additional data have been deposited in Figshare under the project number 10.6084/m9.figshare.c.5008046, including genome coassemblies, CDS predictions, alignments and phylogenetic trees, and used scripts. Individual SAGs, coassembled contigs, predicted genes, and proteins can also be explored through an in-house developed web repository (sag.icm.csic.es)
Publisher version (URL)https://doi.org/10.1038/s41396-020-00885-8
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