DOI: 10.5061/dryad.kwh70rz03
title: Phylogenetics identifies two eumetazoan TRPM clades and an eighth TRP family, TRP soromelastatin (TRPS)

description: Transient receptor potential melastatins (TRPMs) are most well known as
 cold and menthol sensors, but are in fact broadly critical for life, from
 ion homeostasis to reproduction. Yet, the evolutionary relationship
 between TRPM channels remains largely unresolved, particularly with
 respect to the placement of several highly divergent members. To
 characterize the evolution of TRPM and like channels, we performed a
 large-scale phylogenetic analysis of &gt;1,300 TRPM-like sequences
 from 14 phyla (Annelida, Arthropoda, Brachiopoda, Chordata, Cnidaria,
 Echinodermata, Hemichordata, Mollusca, Nematoda, Nemertea, Phoronida,
 Priapulida, Tardigrada, and Xenacoelomorpha), including sequences from a
 variety of recently sequenced genomes that fill what would otherwise be
 substantial taxonomic gaps. These findings suggest: 1) the previously
 recognized TRPM family is in fact two distinct families, including
 canonical TRPM channels and an eighth major previously undescribed family
 of animal TRP channel, TRP soromelastatin; 2) two TRPM clades predate the
 last bilaterian–cnidarian ancestor; and 3) the vertebrate–centric trend of
 categorizing TRPM channels as 1–8 is inappropriate for most phyla,
 including other chordates. 
description: Data Collection &
 Curation Starting with previously
 characterized TRPM sequences from human (NCBI CCDS), mouse (NCBI CCDS),
 <i>Drosophila melanogaster</i> (FlyBase), and
 <i>Caenorhabditis elegans</i> (WormBase), a TRPM-like protein
 sequence database was assembled by performing BLASTp against NCBI
 collections of non-redundant protein sequences, with <i>D.
 melanogaster</i> Trpm (isoform RE, FlyBase ID: FBtr0339077) serving
 as the bait sequence.  Only BLAST hits &gt;300 amino acids in length
 with an E-value less than 1E-30 were retained.  As we were interested in
 the origins of TRPM channels, and in less-studied taxa, only three
 tetrapod sequence-sets were included, from human, mouse, and
 chicken. In order to expand the taxa sampled,
 tBLASTn and BLASTp were used to search genomically-informed gene models
 for 11 cnidarians, 2 xenacoelomorphs, 1 hemichordate, 1 nemertean, 1
 phoronid, 2 agnathans, and 4 chondrichthyes (<b>Table
 S1</b>). We used several methods in order to
 validate and improve the quality of the initial database.  First, CD-HIT
 (threshold 90% similarity) was used to identify and remove duplicate
 sequences and predicted isoforms, retaining the longest isoform
 (<i>27-29</i>).  Phobius was then used to predict
 transmembrane topology (<i>30, 31</i>); sequences which did
 not have at least 6 predicted transmembrane (TM) segments were removed. 
 Sequences with more than the 6 predicted TM segments were analyzed via
 InterProScan (<i>32</i>), and those with more than 1
 ion-transport domain were removed.  More than 90% of the remaining
 sequences contained a highly conserved glycine residue in the predicted TM
 domain (corresponding to <i>D. melanogaster</i> G-1049); the
 vast majority of those missing this residue had large gaps in an initial
 alignment and were subsequently removed. Searches for
 TRPS (ced-11-like), TRPN, and TRPC sequences followed the same protocol. 
 For TRPS, sequences from <i>Caenorhabditis elegans</i>,
 <i>Strigamia maritima</i>, and <i>Octopus
 vulgaris</i> were used as bait.  For TRPN and TRPC datasets,
 <i>Drosophila melanogaster</i> nompC (isoform PA, FlyBase ID:
 FBpp0084879) and Trp (isoform PA, Flybase ID: FBpp0084879) served as bait
 sequences, respectively.