Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
Data files
Sep 20, 2023 version files 37.21 MB
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Extended_references_Table_1.pdf
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Output_files.tar.gz
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README.md
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Supplementary_Figures.pdf
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Abstract
Early metazoan evolution was characterized by the expansion of many gene families involved in novel multicellularity-related functions, like the Tudor family. In eukaryotes, Tudor genes are numerous and heterogeneous, mostly associated with gene expression regulation. However, the family underwent a lineage-specific expansion in animals, with novel elements almost exclusively involved in the germline-specific regulation of retrotransposons through piRNAs (as spatiotemporal regulators of the key-element Piwi, another previously supposedly animal-specific gene). In the present analysis, we used online-available proteomes for a total of 25 major taxonomic groups to characterize the Tudor gene family at a holozoan-wide level, and we confirmed the apomorphic expansion of piRNA-related Tudor genes in animals. However, we could also interestingly observe the presence of elements of the piRNA pathway, both Tudor and Piwi genes, in some Ichthyosporea species, suggesting that some elements of the pathway were already present in the last common ancestor of Holozoa. Moreover, we observed an outstanding variability (34-fold) of Tudor gene number both between and within metazoan phyla, that could be associated with convergent genomic and phenotypic evolutions. Expansions were usually sided by whole genome duplications and/or life history traits such as parthenogenesis, possibly leading to the expansion of retrotransposon silencing pathways. Reductions were instead mostly associated with overall phenotypic and genomic simplifications, like almost all endoparasites of our dataset. Lastly, we phylogenetically tested a previously proposed model for the evolution of the three possible secondary structures of the Tudor domains and we could mostly (but not completely) confirm the model.
https://doi.org/10.5061/dryad.j6q573nmc
Description of the data and file structure
The .png and files of supplementary figures are numbered as in the manuscript; the .xlsx file contain as separate sheets the supplementary tables as numbered in the manuscript.
The PDF files Supplementary_Tables and Supplementary_Figures collectively contain tables and figure of supplementary information, numbered following appearance in the text, and followed by captions.
The PDF file Extended_references_Table_1 contains the reference list for papers cited in Table 1 of the manuscript
The compressed directory Output_files.tar.gz contains output result files of the sequence analyses (each OG MAFFT-DASH alignment and HMM profile + all 10 ML replicate topologies; an explanatory README.md is present within the directory).
Sharing/Access information
For any other intermediate file or request, please contact the corresponding author: giovanni.piccinini5@unibo.it
- Piccinini, Giovanni; Valdrè, Umberto; Milani, Liliana (2025). The Early Evolution of Tudor Genes in Holozoa and How Their Distribution Was Influenced by Life History Traits in Metazoa. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evaf051
