Laure Guillou . et al. -- 8 pages, 1 figure, 1 table ; The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists ; The European Union's Seventh Framework Programmes (FP7) BIOMARKS (2008-6530, ERA-net Biodiversa) and MicroB3 [287589] and the following ANR (France) projects: AQUAPARADOX, PARALEX and GIME. Funding for open access charge: ANR Paralex (French) and BIOMARKS (FP7) ; Peer reviewed
8 pages, 3 figures, 2 tables, supporting Information https://doi.org/10.1111/jeu.12825.-- This is the pre-peer reviewed version of the following article: Bradley A. Weiler, Elisabet L. Sà, Michael E. Sieracki, Ramon Massana, Javier del Campo. Mediocremonas mediterraneus, a New Member within the Developea. Journal of Eukaryotic Microbiology 68(1): e12825 (2021), which has been published in final form at https://doi.org/10.1111/jeu.12825. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions ; The stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile: Mediocremonas mediterraneus, a free‐swimming heterotrophic predator. M. mediterraneus cell bodies measure between 2.0–4.0 μm in length and 1.2–3.7 μm in width, possessing two flagella and an oval body morphology. The growth and grazing rate of M. mediterraneus in batch cultures ranges from 0.68 to 1.83 d−1 and 1.99 to 5.38 bacteria/h, respectively. M. mediterraneus was found to be 93.9% phylogenetically similar with Developayella elegans and 94.7% with Develorapax marinus, two members within the class Developea. The phylogenetic position of the Developea and the ability of M. mediterraneus to remain in culture make it a good candidate for further genomic studies that could help us to better understand phagotrophy in marine systems as well as the transition from heterotrophy to phototrophy within the stramenopiles ; This work was supported by two grants from the Spanish government, FLAME (CGL2010‐16304, MICINN) and ALLFLAGS (CTM2016‐75083‐R, MINECO), and by the National Science Foundation Award DEB‐1031049 to MES. BW was supported by the Natural Sciences and Engineering Research Council of Canada Postgraduate Scholarships‐Doctoral Program (NSERC PGS‐D). BW and JdC were supported by start‐up funds from the University of Miami, Rosenstiel School of Marine and Atmospheric Sciences ; Peer reviewed
Adl, Sina, M. . et al.-- 116 pages, 1 figure, 4 tables, 3 appendices ; This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users ; Research support was provided as follows: SMA by NSERC 249889‐2007; DB by NERC NE/H009426/1 and NE/H000887/1; MWB by NSF 1456054; FB by a Fellowship from Science for Life Laboratory and VR/2017‐04563; PC by EU‐Horizon 2020 research and innovation program through the SponGES project 679849 [.]; IC by CSF 18‐18699S; BE by RCN TaxMArc 268286/GMR; LG by ANR HAPAR (ANR‐14‐CE02‐0007); VH MK JL by ERDF; MEYS with ERC 771592 CZ 1.05/1.1.00/02.0109 BIOCEV; SK by RSF 16‐14‐10302; MK by CSF GA18‐28103S; CEL by NSF 1541510 and NIH‐AI124092; EL by CAM: 2017‐T1/AMB‐5210; and by grant 2017‐T1/AMB‐5210 from the program >Atracción de talentos> from the Consejería de Educación, Juventud y Deporte, Comunidad de Madrid; JL by ERC CZ LL1601 and OPVVV 16_019/0000759; MP by NSF DEB‐1455611; DJR by the Beatriu de Pinós postdoctoral programme of the Government of Catalonia's Secretariat for Universities and Research of the Ministry of Economy and Knowledge; CLS by the intramural research program of the National Library of Medicine, National Institutes of Health; AS by RSF 17‐14‐01391 and RFBR 16‐04‐01454 NY by NSF DEB 1557102; VZ by RFBR 16‐34‐60102 mol‐a‐dk; UniEuk and EukRef by the Gordon and Betty Moore Foundation ; Peer Reviewed
The work is part of the EU ERA-Net program BiodivERsA, under the project BioMarKs (Biodiversity of Marine euKaryotes).-- 14 pages, 8 figures, supplementary material https://doi.org/10.1038/s41598-018-27509-8 ; Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected ; This work was supported by an Institució Catalana de Recerca i Estudis Avançats contract, two grants (BFU-2011-23434 and BFU2014-57779-P) from the Ministerio de Economia y Competitividad (MINECO), one of which (BFU2014-57779-P) was co-funded by the European Regional Development Fund (FEDER), and a European Research Council Consolidator Grant (ERC-2012-Co -616960) to I.R.-T. We also acknowledge financial support from the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya (Project 2014 SGR 619). J.d.C. was supported by a Marie Curie International Outgoing Fellowship grant (FP7-PEOPLE-2012-IOF - 331450 CAARL). J.P. acknowledges support from the European Research Council under the European Union's Seventh Framework Program (FP7/2007–2013)/ERC grant [268513] ; Peer Reviewed
Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected. ; This work was supported by an Institució Catalana de Recerca i Estudis Avançats contract, two grants (BFU-2011-23434 and BFU2014-57779-P) from the Ministerio de Economia y Competitividad (MINECO), one of which (BFU2014-57779-P) was co-funded by the European Regional Development Fund (FEDER), and a European Research Council Consolidator Grant (ERC-2012-Co -616960) to I.R.-T. We also acknowledge financial support from the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya (Project 2014 SGR 619). J.d.C. was supported by a Marie Curie International Outgoing Fellowship grant (FP7-PEOPLE-2012-IOF - 331450 CAARL). J.P. acknowledges support from the European Research Council under the European Union's Seventh Framework Program (FP7/2007–2013)/ERC grant [268513]. The work is part of the EU ERA-Net program BiodivERsA, under the project BioMarKs (Biodiversity of Marine euKaryotes)
Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity. ; Funding was provided by Washington University in St. Louis, the Canada Research Chairs Program, and a National Sciences and Engineering Research Council of Canada Discovery Grant (to A.D.M.); the Alberta Children's Hospital Research Institute (A.D.M., J.D.O., and M.C.J.); the Beatriu de Pinós postdoctoral programme of the Government of Catalonia's Secretariat for Universities and Research of the Ministry of Economy and Knowledge 2017 BP 00265 (to J.D.O.); and the Japan Society for the Promotion of Science 15H02421 and 18H04005 (to S.K.). This work was partly funded by a Methuselah Foundation grant (to J.P.d.M.); and the Comisión Nacional de Investigación Científica y Tecnológica Chile through the doctoral studentship number 21170433 and the scholarship from the Higher Education Quality Improvement Program (MECESUP) AUS 2003 (to D.T.-M.). GenAge is funded by a Biotechnology and Biological Sciences Research Council Grant BB/R014949/1 (to J.P.d.M.). T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), "Unidad de Excelencia María de Maeztu", funded by the Agencia Estatal de Investigación (CEX2018-000792-M), Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). C.F. is supported by the "La Caixa" doctoral fellowship program. E.L. is supported by CGL2017-82654-P (MINECO/FEDER, UE). M.C.J. is supported by funding from the Natural Environment Research Council (NE/T000341/1). The funding bodies played no role in the design of the study, in the collection, analysis, and interpretation of data, or in writing the report.
