EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol

Institute of Zoology and Zoological Museum, University of Hamburg, D-20146 Hamburg, Germany.
Molecular Phylogenetics and Evolution (Impact Factor: 3.92). 01/2008; 45(3):942-51. DOI: 10.1016/j.ympev.2007.09.002
Source: PubMed


Onychophora (velvet worms) represent a small animal taxon considered to be related to Euarthropoda. We have obtained 1873 5' cDNA sequences (expressed sequence tags, ESTs) from the velvet worm Epiperipatus sp., which were assembled into 833 contigs. BLAST similarity searches revealed that 51.9% of the contigs had matches in the protein databases with expectation values lower than 10(-4). Most ESTs had the best hit with proteins from either Chordata or Arthropoda (approximately 40% respectively). The ESTs included sequences of 27 ribosomal proteins. The orthologous sequences from 28 other species of a broad range of phyla were obtained from the databases, including other EST projects. A concatenated amino acid alignment comprising 5021 positions was constructed, which covers 4259 positions when problematic regions were removed. Bayesian and maximum likelihood methods place Epiperipatus within the monophyletic Ecdysozoa (Onychophora, Arthropoda, Tardigrada and Nematoda), but its exact relation to the Euarthropoda remained unresolved. The "Articulata" concept was not supported. Tardigrada and Nematoda formed a well-supported monophylum, suggesting that Tardigrada are actually Cycloneuralia. In agreement with previous studies, we have demonstrated that random sequencing of cDNAs results in sequence information suitable for phylogenomic approaches to resolve metazoan relationships.

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Available from: Hilke Ruhberg, Jun 12, 2015
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    • "For example, tardigrades have been traditionally considered to be allied with Arthropoda (Westheide and Rieger, 1996; Brusca and Brusca, 2003), a topology that is tentatively supported by a shared microRNA (Campbell et al., 2011), shared structures of the nervous system (Mayer et al., 2013) and engrailed expression patterns (Gabriel and Goldstein, 2007). Molecular studies using large-scale sequence alignments suggested that tardigrades may be more closely related to Nematoda (Giribet, 2003; Roeding et al., 2007; Lartillot and Philippe, 2008; Meusemann et al., 2010), although this topology may also be attributed to longbranch attraction (Rota-Stabelli et al., 2011). The worm-like ecdysozoan phyla (i.e., Nematoda, Nematomorpha, Priapulida, Kinorhyncha and Loricifera) have been referred to as ''Cycloneuralia'' (Schmidt-Rhaesa, 2013). "
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    ABSTRACT: The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns.
    Molecular Phylogenetics and Evolution 08/2014; 80(1). DOI:10.1016/j.ympev.2014.08.001 · 3.92 Impact Factor
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    • "Положение Tardigrada наболее противоречии вое. Одни данные свидетельствуют в пользу близз кого родства Tardigrada и Cycloneuralia (в частноо сти, Nematoda) (Roeding et al., 2007), тогда как, "
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    ABSTRACT: A review of more than hundred papers on the bilaterian phylogeny presenting the results of studies conducted in the last twenty years is analyzed. The review discusses the most significant results that were obtained using different materials (genes, proteins, and so on) and processed by different statistic models. A comparison of these results is possible with due regard for a special methodological approach; it is not considered in this paper. The review presents hypotheses developed in different time periods; it allows realizing how concepts of phylogeny of some animal groups change with time. This paper includes the data on the phylogeny of all bilaterian phyla belonging to three main stems (Lophotrochozoa, Ecdysozoa, and Deuterostomia). In addition, the data on the groups, the position of which on the bilaterian phylogenetic tree is still uncertain, are also presented. The review contains a list of references, which includes not only the works with summary results on phylogeny of Bilateria or some large groups, but also on phylogeny of taxa of the species rank.
    Zoologicheskiĭ zhurnal 03/2014; 93(3):318-341. DOI:10.7868/S0044513414030155 · 0.14 Impact Factor
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    • "Transcriptome sequencing using massively parallel sequencing technologies provides an attractive approach to obtaining large-scale sequence data for non-model organisms necessary for comparative genomic analysis [24,48]. Phylogenetic utility of transcriptome sequence data yields well-resolved and highly supported tree topologies for many groups of animals [49-51]; however, few such studies have been conducted with plant taxa [27]. Phylogenetic analysis of the genus Pinus has been limited mostly to plastid genome (cpDNA and mtDNA) sequences [21-23]. "
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    ABSTRACT: Background The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of P. tabuliformis genomic information. Results The increasing amount of transcriptome data on Pinus provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first P. tabuliformis transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the Pinus lineage. Conclusions A large collection of high-quality ESTs was obtained, de novo assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of P. tabuliformis and which will gradually be applied in breeding programs of P. tabuliformis. Furthermore, these data will facilitate future studies of the comparative genomics of P. tabuliformis and other related species.
    BMC Genomics 04/2013; 14(1):263. DOI:10.1186/1471-2164-14-263 · 3.99 Impact Factor
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