Taxon-rich transcriptomics supports higher-level phylogeny and major evolutionary trends in Foraminifera.

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Publisher: Elsevier B.V.
Document Type: Report
Length: 436 words

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Keywords Foraminifera; Monothalamids; Globothalamea; Tubothalamea; Xenophyophores; Phylogenomics Highlights * Transcriptomics of Foraminifera. * Phylogenomics of Foraminifera based on 199-protein coding genes. * Monothalamids are a single-chambered paraphyletic group. * Monothalamids give rise to the multi-chambered Tubothalamea and Globothalamea. * First transcriptomes of the deep-sea xenophyophore giants. Abstract Foraminifera, classified in the supergroup Rhizaria, are a common and highly diverse group of mainly marine protists. Despite their evolutionary and ecological importance, only limited genomic data (one partial genome and nine transcriptomic datasets) have been published for this group. Foraminiferal molecular phylogeny is largely based on 18S rRNA gene sequence analysis. However, due to highly variable evolutionary rates of substitution in ribosomal genes plus the existence of intragenomic variation at this locus, the relationships between and within foraminiferal classes remain uncertain. We analyze transcriptomic data from 28 species, adding 19 new species to the previously published dataset, including members of the strongly under-represented class Monothalamea. A phylogenomic reconstruction of Rhizaria, rooted with alveolates and stramenopiles, based on 199 genes and 68 species supports the monophyly of Foraminifera and their sister relationship to Polycystinea. The phylogenomic tree of Foraminifera is very similar to the 18S rRNA tree, with the paraphyletic single-chambered monothalamids giving rise to the multi-chambered Tubothalamea and Globothalamea. Within the Monothalamea, our analyses confirm the monophyly of the giant, deep-sea xenophyophores that branch within clade C and indicate the basal position of monothalamous clades D and E. The multi-chambered Globothalamea are monophyletic and comprise the paraphyletic Textulariida and monophyletic Rotaliida. Our phylogenomic analyses support major evolutionary trends of Foraminifera revealed by ribosomal phylogenies and reinforce their current higher-level classification. Author Affiliation: (a) Department of Genetics and Evolution, University of Geneva, 1211 Geneva, Switzerland (b) National Oceanography Centre, European Way, Southampton SO14 3ZH, UK (c) Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK (d) Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA (e) Department of Biological Sciences, Smith College, Northampton, MA 01063, USA (f) University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, USA (g) Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland (h) NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Jahnebakken 5, 5007 Bergen, Norway (i) ID-Gene Ecodiagnostics, Chemin du Pont-du-Centenaire 109, CH-1228 Plan-les-Ouates, Switzerland * Corresponding author. Article History: Received 10 November 2021; Revised 10 May 2022; Accepted 18 May 2022 Byline: Roberto Sierra [Roberto.Sierra@me.com] (a,*), Florian Mauffrey (a), Joana Cruz (a), Maria Holzmann (a), Andrew J. Gooday (b,c), Xyrus Maurer-Alcalá (d), Rabindra Thakur (e,f), Mattia Greco (e,g), Agnes K.M. Weiner (e,h), Laura A. Katz (e,f), Jan Pawlowski (a,g,i)

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Gale Document Number: GALE|A708782310