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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) Image reproduced on Xenbase with permission of the publisher and the copyright holder. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View |