Gene family innovation, conservation and loss on the animal stem lineage

• Published in: eLife Vol. 7
• Main Authors: Richter, Daniel J, Fozouni, Parinaz, Eisen, Michael B, King, Nicole
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 31.05.2018; eLife Sciences Publication; eLife Sciences Publications, Ltd
• Subjects: Amino Acid Sequence; Amino Acids, Essential - metabolism; ancestral gene content; Animals; Biochemistry, Molecular Biology; Biology; Cell adhesion & migration; Choanoflagellata - classification; Choanoflagellata - genetics; choanoflagellates; Datasets; Evolution, Molecular; Evolutionary Biology; Extinction, Biological; Gene families; Genes; Genetic Variation; Genomes; Genomics; innate immunity; Kinases; Life Sciences; Molecular Sequence Annotation; Multigene Family; Phylogeny; Poly A - metabolism; Probability; Protein Domains; Proteins; Receptors, Notch - chemistry; Receptors, Notch - metabolism; Signal Transduction; Species Specificity; Toll-like receptors; transcriptome; Transforming Growth Factor beta - metabolism; Urmetazoan; United States > US; San Francisco California; California; evolutionary biology; innate immunity; transcriptome; Urmetazoan; choanoflagellates; ancestral gene content
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.34226

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals.