Data from: Here and there, but not everywhere: repeated loss of uncoupling protein 1 in amniotes

• Main Authors: McGaugh, Suzanne, Schwartz, Tonia S.
• Format: Dataset
• Language: unknown
• Published: 2016
• Subjects: Gavia stellata; Canis familiaris; Haliaeetus albicilla; Balaenoptera acutorostrata; Anolis carolinensis; Picoides pubescens; Cuculus canorus; Pteropus vampyrus; Merops nubicus; Cavia porcellus; Struthio camelus australis; Pseudopodoces humilis; Aquila chrysaetos canadensis; Meleagris gallopavo; Serinus canaria; Procavia capensis; Sarcophilus harrisii; Tupaia belangeri; Zonotrichia albicollis; Buceros rhinoceros silvestris; Homo Sapiens; Dipodomys ordii; Papio anubis; Candoia aspera; Melopsittacus undulatus; Pan troglogdytes; Myotis lucifugus; Thamnophis couchii; Corvus cornix cornix; Sus scrofa; Sceloporus undulatus; Charadrius vociferus; Rattus norvegicus; Crocodylus porosusæ; Alligator sinensis; Tauraco erythrolophus; Erinaceus europaeus; Microcebus murinus; Nipponia nippon; Xenopeltis unicolor; Ophiophagus hannah; Choloepus hoffmanni; Myotis brandtii; Dasypus novemcinctus; Tinamus guttatus; Pygoscelis adeliae; Orcinus orca; Tursiops truncatus; Phaethon lepturus; Phalacrocorax carbo; Hannah; Orca; Aquila chrysaetos
• Online Access: https://zenodo.org/record/4955459; https://doi.org/10.5061/dryad.934fg

Endothermy is an evolutionary innovation in eutherian mammals and birds. In eutherian mammals, UCP1 is a key protein in adaptive nonshivering thermogenesis (NST). Although ucp1 arose early in the vertebrate lineage, the loss of ucp1 was previously documented in several reptile species (including birds). Here we determine that ucp1 was lost at the base of the reptile lineage, as we fail to find ucp1 in every major reptile lineage. Furthermore, though UCP1 plays a key role in mammalian NST, we confirm that pig has lost several exons from ucp1 and conclude that pig is not a sole outlier as the only eutherian mammal lineage to do so. Through similarity searches and synteny analysis, we show that ucp1 has also been lost/pseudogenized in Delphinidae (dolphin, orca) and potentially Xenarthra (sloth, armadillo) and Afrotheria (hyrax). These lineages provide models for investigating alternate mechanisms of thermoregulation and energy metabolism in the absence of functional UCP1. Further, the repeated losses of a functional UCP1 suggest the pervasiveness of NST via UCP1 across the mammalian lineage needs re-evaluation. Supplemental_File1_Methods_Results_FiguresDetailed description of methods and results including figures S1 and S2.Supplemental_File2_TablesThis is a summary of results for each species analyzed in our study, including presence of ucp1 annotation, synteny analysis, and blasting of raw reads. This table also includes the ftp links to the sequence data used for each species. Species highlighted in purple had no evidence of ucp1 in Ensembl and were investigated further through synteny analysis and BLAST search of their raw data.Supplemental_File3_BlastQUERY_SyntenyThe exon sequences for ucp1 and six flanking genes used in the BLASTn for synteny analysis.Supplemental_File4_Protein_UCP1_Query_for_TBLASTNThe UCP1 protein sequences used for tBLASTn against the genomes.Supplemental_File5_BlastQUERY_for_raw_reads_mammalsThe ucp1 gene sequences used for BLASTn against the raw sequence data for ...