DNA Barcoding; Foraminifera; Next Generation Sequencing; Eukaryotes; Ancient DNA; Diversity; Phylogeny; Evolution; Metabarcoding
Dufresne Yoann, Lejzerowicz Franck, Perret-Gentil Laure Apotheloz, Pawlowski Jan, Cordier Tristan (2019), SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data, in BMC Bioinformatics
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Gooday Andrew J., Holzmann Maria, Goineau Aurélie, Kamenskaya Olga, Melnik Vyacheslav F., Pearce Richard B., Weber Alexandra A.-T., Pawlowski Jan (2018), Xenophyophores (Rhizaria, Foraminifera) from the Eastern Clarion-Clipperton Zone (equatorial Pacific): the Genus Psammina, in Protist
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Gooday Andrew J, Holzmann Maria, Goineau Aurélie, Pearce Richard B, Voltski Ivan, Weber Alexandra A-T, Pawlowski Jan (2018), Five new species and two new genera of xenophyophores (Foraminifera: Rhizaria) from part of the abyssal equatorial Pacific licensed for polymetallic nodule exploration, in Zoological Journal of the Linnean Society
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Hozmann Maria, Sylvain Rigaud, Amini Shahrouz, Voltski Ivan, Pawlowski Jan (2018), Cyrea szymborska Gen. Et Sp. Nov., a New Textulariid Foraminifer from the Mediterranean Sea, in Journal of Foraminiferal Research
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Gschwend Florian, Majda Aneta, Majewski Wojciech, Pawlowski Jan (2016), Psammophaga fuegia sp. nov., a new monothalamid foraminifera from the Beagle Channel, South America, in Acta Protozoologica
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Over the last few years the research on molecular evolution and ecology of protists have greatly benefited from the development of high-throughput next-generation sequencing (NGS) technologies. The deluge of sequence data allowed refining the phylogenomic tree of eukaryotes and revealed a new dimension of eukaryotic diversity based on in-depth environmental surveys. However, this progress of phylogenomic and metagenomic studies driven by the new sequencing technologies did not contribute equally to the knowledge of all groups of protists.The present project focuses on the genetically most undersampled super-group of eukaryotes: the Rhizaria and its flagship taxon, the Foraminifera. The project is a continuation of the long-term research on molecular evolution of foraminifera and other protists conducted by the applicant since several years. In our previous studies we have pioneered the use of NGS tools to explore protist evolutionary history and diversity, raising several important questions concerning the origin of foraminifera, their spectacular diversification, widespread occurrence, and ecological role. In this project we will further address these questions from genomic and metagenomic perspectives.The project is divided into three parts, including (1) phylogenomic analyses, (2) genetic variability, and (3) environmental diversity assessment. In the first part, we will use NGS to fuel genomic and transcriptomic databases focusing on the foraminiferal mitochondrial genome and the genes involved in process of skeletonization and biomineralization. In the second part, we will develop the NGS-based single-cell barcoding approach in order to tackle the issue of ribosomal RNA genes variability and its possible origins. The third part will comprise the development of mathematical and computational tools for NGS diversity data analyses and their various applications, notably for the establishment of biotic indices of present and past environmental changes. Our project will contribute substantially to the knowledge of foraminifera. It will promote the revision of their classification, prompt their use as ecological indicators, and introduce non-fossilized taxa as paleoceanographic proxies. Importantly, the project will also have a broader impact on the study of other protists. On the one hand, it will contribute to the development of innovative approaches such as the single-cell multiplexed NGS barcoding as well as algorithms for rapid, accurate and robust analysis of NGS diversity data. On the other hand, it will open new avenues for the investigation of important biological processes such as hybridization that have not yet been deeply explored in protists. Moreover, by surveying the environmental diversity of the whole eukaryotic domain, this project is bound to discover numerous groups of protists likely to become the future gold standards for environmental biomonitoring.