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Cnidarian milestones in metazoan evolution. Integr Comp Biol 2007;47:693–700
"... Synopsis Cnidarians display most of the characters considered as milestones of metazoan evolution. Whereas a tissue-level organization was probably already present in the multicellular common ancestor of all animals, the Urmetazoa, the emergence of important animal features such as bilateral symmetr ..."
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Synopsis Cnidarians display most of the characters considered as milestones of metazoan evolution. Whereas a tissue-level organization was probably already present in the multicellular common ancestor of all animals, the Urmetazoa, the emergence of important animal features such as bilateral symmetry, triploblasty, a polarized nervous system, sense organs (eyes, statocysts), and a (chitinous or calcium-based) continuous skeleton can be traced back before the divergence between cnidarians and bilaterians. Modularity and metamery might be also regarded as two faces of the same medal, likely involving conserved molecular mechanisms ruling animal body architectures through regional specification of iterated units. Available evidence indicates that the common ancestor of cnidarians and bilaterians, the UrEumetazoa, was a surprisingly complex animal with nerve cell differentiation. We suggest that paedomorphic events in descendants of this ancestor led to the array of diversity seen in the main extant animal phyla. The use of molecular analyses and identifying the genetic determinants of anatomical organizations can provide an integrative test of hypotheses of homologies and independent evidence of the evolutionary relationships among extant taxa.
854 The Hox gene complement of a pelagic chaetognath, Flaccisagitta enflata
"... Synopsis Chaetognaths are transparent marine animals that are ubiquitous and abundant members of oceanic zooplanktonic communities. Their phylogenetic position within the Metazoa, however, has remained obscure since their discovery. Morphology and embryology have traditionally allied chaetognaths wi ..."
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Synopsis Chaetognaths are transparent marine animals that are ubiquitous and abundant members of oceanic zooplanktonic communities. Their phylogenetic position within the Metazoa, however, has remained obscure since their discovery. Morphology and embryology have traditionally allied chaetognaths with deuterostomes, but molecular evidence suggests otherwise. Two recent multigene expressed sequence tag (EST) molecular phylogenomic studies suggest that chaetognaths are either sister to the Lophotrochozoa (Matus et al. 2006) or to all protostomes (Marlétaz et al. 2006). We have isolated eight Hox genes, one Parahox gene, and Mox, a related homeodomain gene, from the pelagic chaetognath, Flaccisagitta enflata. Although chaetognath central class Hox genes lack the Lox5 or ‘‘spiralian’ ’ parapeptide, a diagnostic amino-acid motif that has been utilized previously to assign lophotrochozoan affinity, they do possess a central class Hox gene that has a partial ‘‘Ubd-A peptide’ ’ found in both ecdysozoan and lophotrochozoan Ubx/Abd-A/ Lox2/Lox4 genes. Additionally, we report the presence of two distinct chaetognath posterior Hox genes that possess both ecdysozoan and lophotrochozoan signature amino-acid motifs. The phylogenetic position of chaetognaths, as well as the evolution of the Hox cluster, is discussed in light of these data.
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"... Synopsis In order to address this subject further and to assess progress in the examination of animal origins and transi-tions, an international group of scientists was convened at the Society for Comparative Biology meeting in January 2007. ‘‘That theory is worthless. It isn’t even wrong!’’ ..."
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Synopsis In order to address this subject further and to assess progress in the examination of animal origins and transi-tions, an international group of scientists was convened at the Society for Comparative Biology meeting in January 2007. ‘‘That theory is worthless. It isn’t even wrong!’’
Tree thinking for all biology: the problem with reading phylogenies as ladders of progress
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Nucleic Acids Research, 2009, 1–14 doi:10.1093/nar/gkn1084
, 2008
"... Non-coding RNA annotation of the genome ..."
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doi:10.1093/nar/gkn1084 Non-coding RNA annotation of the genome of Trichoplax adhaerens
, 2008
"... A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast iden ..."
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A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs—in particular rRNAs, tRNAs and some snRNAs—we developed a semiglobal dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as singlecopy genes or with very small copy numbers in the Trichoplax genome.
Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens
"... A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast iden ..."
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A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs — in particular rRNAs, tRNAs, and some snRNAs — we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome. Key words: Trichoplax adhaerens, non-coding RNA, genome annotation, homology search, spliceosomal RNAs, microRNAs
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"... Tree thinking for all biology: the problem with reading phylogenies as ladders of progress ..."
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Tree thinking for all biology: the problem with reading phylogenies as ladders of progress
