1 Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 75005 Paris, France; dorrell@bio.ens.psl.eu guillaume.blanc@mio.osupytheas.fr.
2 Aix Marseille University, Universite de Toulon, CNRS, Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France.
3 Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université Paris Sciences et Lettres, 75005 Paris, France.
4 Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, École Pratique des Hautes Études (EPHE), Université des Antilles (UA), 75005 Paris, France.
5 Department of Biology, Concordia University, H3G 1M8 QC, Montreal, H3G 1M8 QC, Canada.
6 Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Université Evry, Université Paris-Saclay, 91000 Evry, France.
7 FR 2424 CNRS, Analysis and Bioinformatics for Marine Science, Station Biologique de Roscoff, Université Pierre et Marie Curie Paris 06, 75005 Paris, France.
8 Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans Global Ocean Systems Ecology and Evolution, 75016 Paris, France.
9 Aix Marseille University, Universite de Toulon, CNRS, Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO) UM 110, 13288 Marseille, France; dorrell@bio.ens.psl.eu guillaume.blanc@mio.osupytheas.fr.

Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.

Proc Natl Acad Sci U S A. 2021 Jan 26; 118(4):

Authors: Dorrell RG, Villain A, Perez-Lamarque B, Audren de Kerdrel G, McCallum G, Watson AK, Ait-Mohamed O, Alberti A, Corre E, Frischkorn KR, Pierella Karlusich JJ, Pelletier E, Morlon H, Bowler C, Blanc G

Abstract

Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.

PMID: 33419955 [PubMed - as supplied by publisher]