The animal kingdom shows an astonishing diversity, the product of over 550 million years of animal evolution. The current wealth of genome sequence data offers an opportunity to better understand the genomic basis of this diversity. Here we analyse a sampling of 102 whole genomes including >2.6 million protein sequences. We infer major genomic patterns associated with the variety of animal forms from the superphylum to phylum level. We show that a remarkable amount of gene loss occurred during the evolution of two major groups of bilaterian animals, Ecdysozoa and Deuterostomia, and further loss in several deuterostome lineages. Deuterostomes and protostomes also show large genome novelties. At the phylum level, flatworms, nematodes and tardigrades show the largest reduction of gene complement, alongside gene novelty. These findings paint a picture of evolution in the animal kingdom in which reductive evolution at the protein-coding level played a major role in shaping genome composition.
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Publicly available genomes are listed in Supplementary Table 1.
All the scripts used in this study can be found at https://github.com/CristiGuijarro/ComparativeGenomics.
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We thank I. Maeso for comments on the manuscript. C.G.-C. and J.P. received funding from the School of Biological Sciences (University of Essex).
The authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figs. 1–15 and Tables 1–3.
HG assignment for each genome, and how many proteins each genome has assigned to each cluster for core novel, core lost, novel and lost HGs for each phylum. Files are named by clade position in the phylogeny followed by the assigned clade name.
List of protein sequence headers or IDs assigned to each novel and lost HG for each phylum.
GO and model protein assignment for each of the core HGs analysed in the pipeline. There is a file for each of the core lost and core novel HGs for each clade analysed. GOs were mined from InterProScan.
GO and model protein assignment for each of the HGs analysed in the pipeline. There is a file for each of the lost and novel HGs for each clade analysed.
BLAST checks of the novel HGs (all the proteins in each HG) for each phylum with the RefSeq database. Thresholds include 1 × 10−6 e-value and >50% identity matches.
Available as an xlsx sorted document. The number of protein class Panther hits and other GOs for each node. The numbers between nodes cannot be compared due to the varying model organisms used and protein class annotations; however, each node should be compared internally within the same model organisms. Model organism for protein class used is the same as written in Supplementary Data 3 and 4. Orphan HGs were excluded from the analysis. Urochordate, cephalochordate, hemichordate, platyhelminth and tardigrade novelties were also excluded from these data due to the lack of protein classes in the Panther analysis for specific model organisms. GOs and protein IDs are available in Supplementary Data 3 and 4.
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Guijarro-Clarke, C., Holland, P.W.H. & Paps, J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat Ecol Evol (2020). https://doi.org/10.1038/s41559-020-1129-2