S7 Fig. Phylogenetic and syntenic analyses of the Nemp family. A. Phylogenetic analysis. A phylogenetic tree was constructed by the Maximum Likelihood (ML) method using Treefinder with the protein matrix LG after amino acid sequences of the DUF2215 domain in various organisms were aligned using the ClustalW alignment tool with the Gonnet series protein weight matrix (see S4 Fig) and trimmed using trimAl. Values beside nodes show the number of times that a node was supported in 1000 bootstrap pseudoreplication. Arabidopsis Nemp homologs (At_Nemp-A, B, and C) serve as outgroups. Note that Nemp is evolutionary conserved from metazoans to choanoflagellates to plants, mainly in the terminal part of region A (see S4 Fig). In vertebrates, a Nemp1 homolog, named TMEM194B or Nemp2, is present in the genome databases of zebrafish, chick, mice, and humans. A de novo phylogenetic tree revealed that Nemp1 and Nemp2 form sister groups in vertebrates (not shown), indicating that Nemp2 is the vertebrate paralog of Nemp1. Abbreviations of species and common names are as follows: plant Arabidopsis thaliana (At), Florida lancelet Branchiostoma floridae (Bf), nematode Caenorhabditis elegans (Ce), ascidian Ciona intestinalis (Ci), Drosophila melanogaster (Dm), zebrafish Danio rerio (Dr), chick Gallus gallus (Gg), human Homo sapiens (Hs), choanoflagellate Monosiga brevicollis (Mb), mouse Mus musculus (Mm), sea anemone Nematostella vectensis (Nv), African clawed frog Xenopus laevis (Xl), and western clawed frog Xenopus tropicalis (Xt). Accession numbers of amino acid sequences: Hs_Nemp1, O14524; Mm_Nemp1, Q6ZQE4; Gg_Nemp1, XM_001232566; Xl_Nemp1a, NP_001090391; Xl_Nemp1b, NP_001091224; Xt_Nemp1, NP_001034832; Dr_Nemp1, XP_683418; Hs_Nemp2, A6NFY4; Mm_Nemp2, Q8CB65; Gg_Nemp2, Q5ZJY9; Dr_Nemp2, XP_693037; Bf_Nemp, XP_002585718; Ci_Nemp, AK116477; Sk_Nemp, XP_002741981; Sp_Nemp, XP_001196379; Dm_Nemp, NP_573142; Ce_Nemp, NP_497202; Nv_Nemp, XP_001640959; At_Nemp-A, NM_102639; At_Nemp-B, NM_001037091; At_Nemp-C, NM_114844; Mb_Nemp, XP_001742508. B. Conserved synteny of vertebrate nemp2 genes. A boat-shape object represents a gene with a direction, in which the tip of boat corresponds to the 3’ end of the gene. Genes indicated with a same color mean orthologous genes, in which white boats indicates unrelated genes. Black boats indicate nemp2. Black circles indicate the ends of chromosomes or scaffolds. These maps are drawn based on JGI Metazome data, with some manual editing and corrections. The corresponding synteny maps of X. laevis (ver. 7.1) and X. tropicalis (ver. 7.1) suggest that Xenopus species do not have nemp2 orthologs. In addition, EST databases for X. laevis and X. tropicalis do not contain nemp2-like sequences. C. Diagram of Arabidopsis Nemp-A,-B, and-C proteins. According to the Arabidopsis genome sequence, typical signal peptide (SP) sequences were not detected in At_Nemp-B and At_Nemp-C. At_Nemp-C is predicted to contain six TMs, but the last two TMs may be a single TM. Colored boxes: blue, signal peptides (SP); magenta, transmembrane domains (TMs); yellow, region B.
Image published in: Shibano T et al. (2015)
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