DOI: 10.5061/dryad.np5hqbzr0
title: Data from: Tek/Tie2 is not required for cardiovascular development in zebrafish

description: Angiopoietin/TIE signalling plays a major role in blood and lymphatic
 vessel development.  In mouse, Tek/Tie2 mutants die prenatally
 due to a severely underdeveloped cardiovascular system.  In
 contrast, in zebrafish, previous studies have reported that while embryos
 injected with tek morpholinos (MOs) exhibit severe vascular defects, tek
 mutants display no obvious vascular malformations.  To further
 investigate the function of zebrafish Tek, we generated a panel of
 loss-of-function tek mutants, including RNA-less alleles, an allele
 lacking the MO-binding site, an in-frame deletion allele, and a premature
 termination codon-containing allele.  Our data show that all
 these mutants survive to adulthood with no obvious cardiovascular
 defects.  MO injections into tek mutants lacking the MO-binding
 site or the entire tek locus cause similar vascular defects as those
 observed in MO-injected +/+ siblings, indicating off-target effects of the
 MOs.  Surprisingly, comprehensive phylogenetic profiling and
 synteny analyses reveal that Tek was lost in the largest teleost clade,
 suggesting a lineage-specific shift in the function of TEK during
 vertebrate evolution.  Altogether, these data show that Tek is
 dispensable for zebrafish development, and probably dispensable in most
 teleost species.
description: <b>Evolutionary
 analysis of TEK, TIE1 and Angiopoietins</b> We used HaMStR-OneSeq v1.8.0
 (Ebersberger et al., 2014) (https://github.com/BIONF/HaMStR) to determine
 the presence-absence pattern of orthologs to human TEK (UniprotID:
 Q02763), TIE1 (UniprotID: P35590), Angiopoietin-1 (UniprotID: Q15389) and
 Angiopoietin-2<i> </i>(UniprotID: O15123) across 255 species
 represented in the RefSeq partition of non-mammalian vertebrate genomes
 available at NCBI Genome (Februrary 2020)
 (https://ftp.ncbi.nlm.nih.gov/genomes/refseq/), complemented with the
 Quest For Orthologs reference proteomes
 (https://www.ebi.ac.uk/reference_proteomes/), and with the sea urchin
 (<i>Strongylocentrotus purpuratus</i>) proteome from NCBI
 Genome.  The full list of taxa is provided in Table
 S3. 
 Pairwise protein feature
 architecture similarities (Koestler et al., 2010) between the human seed
 proteins and their respective orthologs were assessed and scored with
 feature architecture similarity (https://github.com/BIONF/FAS).
  Phylogenetic profiles
 together with the protein feature architecture were visualized and
 analysed with PhyloProfile (Tran et al.,
 2018). 
 Representative orthologs from 5 Sarcopterygians, 76
 Actinopterygians, 5 Chondrichthyans, and additionally from 2 chordate
 outgroup species were aligned with Muscle v3.8.31 (Edgar, 2004), and
 alignment columns with more than 50% gaps were excluded prior to phylogeny
 reconstruction using a custom Perl script.  The processed alignment served
 as an input for a maximum likelihood tree reconstruction with RAxML
 v.8.2.11 (Stamatakis, 2014) choosing the option to automatically select
 the optimal model of sequence evolution (option PROTGAMMAAUTO).  Branch
 support was assessed with 100 non-parametric bootstrap replicates using
 the rapid bootstrapping algorithm implemented into RAxML (Stamatakis et
 al., 2008).  Tree display and editing were performed with iTOL (Letunic
 and Bork, 2019).
description: The files in this folder provide the necessary information to
 visualise and analyse the phylogenetic profiles of human Tek (Q02763),
 Tie1 (P35590), ANGP1 (Q15389), and ANGP2 (O15123) that were created
 with fDOG (https://github.com/BIONF/fDOG). The information can be viewed in any text editor, however, we suggest to use PhyloProfile (https://github.com/BIONF/PhyloProfile) for this purpose. Please find below a brief description of the files and their content.   tektie_angp.phyloprofile: This file contains the presence-absence pattern of orthologs to the four seed proteins across a selection of animal species focussing on vertebrates. The file format is a tab-delimited text with the following information: geneID - the name of the human seed protein ncbiID - is the NCBI taxonomy id of the species/strain the ortholog was identified in  orthoID - a compound identifier of the orthologous protein. The individual fields are separated by a ‘|’ (Examle: TIE1|DICTD@515635@3|B8E0P1|1) TIE1 - Seed name DICTD@515635@3 - Identifier of the species the ortholog was found in. Here, Dictiostelium discoideum (Ncbi Tax Id 515635) internal version 3 B8E0P1 - Sequence id of the ortholog (here Uniprot) 1 - flag indicating that the protein is the representative ortholog (either the only one found, or in the case that more than one co-ortholog was found, the one that is most similar to the seed protein. If the sequence is not the representative ortholog, the flag will be ‘0' FAS_F - The feature architecture similarity score between the seed protein and its ortholog (seed is reference). For details see (https://github.com/BIONF/FAS) FAS_B - The feature architecture similarity score between the ortholog and its seed protein (ortholog is reference). For details see (https://github.com/BIONF/fDOG)                         tektie_angp.extended.fa: This file holds the sequence information of the seed proteins and their orthologs in a multi-sequence FASTA format. There is a 1:1 relation between the entires in the tektie_angp.phyloprofile file and the sequences in the FASTA file, and the information in the ‘orthoID’ field is used as sequence identifier in the FASTA file   tektie_angp_forward.domains - This file holds the information from the feature architecture similarity analysis in a tab delimited text format. The human seed sequence serves as reference. Example: TEK#DICTD@515635@3|B8E0P1|1     HUMAN@9606@3|Q02763     1124    pfam_Ig_Tie2_1  24      118     0.2161  Y TEK#DICTD@515635@3|B8E0P1|1 - Seed name (TEK) and id of the ortholog HUMAN@9606@3|Q02763 - seed species and id information 1124 - length of the protein pfam_Ig_Tie2_1 - Feature name 24 - feature start in sequence 118 - feature end in sequence 0.2161 - Weight of the feature during similarity scoring (see https://github.com/BIONF/FAS) Y - Feature was used in the architecture comparison between the seed and the ortholog. ’N’ otherwise   tektie_angp_reverse.domains - Same as *_forward.domains but using the orthologous sequence serves as reference