Eukaryota/genetics; Evolution, Molecular; Genome; Phylogeny; Plants; Plastids/genetics; Algae; CASH; Contamination; Endosymbiotic gene transfer (EGT); Eukaryotic evolution; Horizontal or lateral gene transfer (HGT/LGT); Kleptoplasty; Organelles; Orthology; Phylogenomics; Proteomes
Abstract :
[en] OBJECTIVES: Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary. DATA DESCRIPTION: We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.
Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes
Language :
English
Title :
Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages.
Publication date :
2021
Journal title :
BMC Research Notes
eISSN :
1756-0500
Publisher :
BioMed Central, London, United Kingdom
Volume :
14
Issue :
1
Pages :
143
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture [BE] F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE] ULiège - Université de Liège [BE]
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Van Vlierberghe M, Philippe H, Baurain D. Supplementary file 1-Methods. 2021. Figshare. 10.6084/m9.figshare.13604102.v3.
Van Vlierberghe M, Philippe H, Baurain D. Data file 1-Taxonomic sampling. 2021. Figshare. 10.6084/m9.figshare.13603511.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data set 1-Proteome set description. 2021. Figshare. 10.6084/m9.figshare.13113893.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data set 2-Proteome set. 2021. Figshare. 10.6084/m9.figshare.13573424.v2.
Van Vlierberghe M, Philippe H, Baurain D. Data file 2-BUSCO report. 2021. Figshare. 10.6084/m9.figshare.13235045.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data set 3-Forty-two reports and configuration files. 2021. Figshare. 10.6084/m9.figshare.13235063.v3.
Van Vlierberghe M, Philippe H, Baurain D. Data file 3-Orthogroup properties. 2021. Figshare. 10.6084/m9.figshare.13312622.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data set 4-Orthogroups. 2021. Figshare. 10.6084/m9.figshare.13573658.v3.
Van Vlierberghe M, Philippe H, Baurain D. Data set 5-Clans. 2021. Figshare. 10.6084/m9.figshare.13573415.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data file 4-Organelle database. 2021. Figshare. 10.6084/m9.figshare.13246841.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data file 5-Plastid-targeted proteins. 2021. Figshare. 10.6084/m9.figshare.13246784.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data file 6-eggNOG OG annotations. 2021. Figshare. 10.6084/m9.figshare.13415048.v1.
Van Vlierberghe M, Philippe H, Baurain D. Data file 7-eggNOG clan annotations. 2021. Figshare. 10.6084/m9.figshare.13415060.v1.
