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1.
BMC Evol Biol ; 8: 251, 2008 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-18798978

RESUMO

BACKGROUND: A recent study by Barthélémy et al. described a set of ribosomal protein (RP) genes extracted from a collection of expressed sequence tags (ESTs) of the chaetognath (arrow worm) Spadella cephaloptera. Three main conclusions were drawn in this paper. First, the authors stated that RP genes present paralogous copies, which have arisen through allopolyploidization. Second, they reported two alternate nucleotide stretches conserved within the 5' untranslated regions (UTR) of multiple ribosomal cDNAs and they suggested that these motifs are involved in the differential transcriptional regulation of paralogous RP genes. Third, they claimed that the phylogenetic position of chaetognaths could not be accurately inferred from a RP dataset because of the persistence of two problems: a long branch attraction (LBA) artefact and a compositional bias. RESULTS: We reconsider here the results described in Barthélémy et al. and question the evidence on which they are based. We find that their evidence for paralogous copies relies on faulty PCR experiments since they attempted to amplify DNA fragments absent from the genomic template. Our PCR experiments proved that the conserved motifs in 5'UTRs that they targeted in their amplifications are added post-transcriptionally by a trans-splicing mechanism. Then, we showed that the lack of phylogenetic resolution observed by these authors is due to limited taxon sampling and not to LBA or to compositional bias. A ribosomal protein dataset thus fully supports the position of chaetognaths as sister group of all other protostomes. This reinterpretation demonstrates that the statements of Barthélémy et al. should be taken with caution because they rely on inaccurate evidence. CONCLUSION: The genomic study of an unconventional model organism is a meaningful approach to understand the evolution of animals. However, the previous study came to incorrect conclusions on the basis of experiments that omitted validation procedures.


Assuntos
Evolução Molecular , Genoma , Invertebrados/classificação , Filogenia , Animais , Sequência de Bases , DNA Complementar/genética , Etiquetas de Sequências Expressas , Invertebrados/genética , Análise de Componente Principal , Proteínas Ribossômicas/genética , Alinhamento de Sequência , Trans-Splicing
2.
Genome Biol Evol ; 9(6): 1374-1384, 2017 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-28854623

RESUMO

The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.


Assuntos
Eucariotos/genética , Variação Genética , Genoma Mitocondrial , Animais , DNA Mitocondrial/genética , Eucariotos/classificação , Evolução Molecular , Mitocôndrias/genética , Filogenia
4.
Gene ; 340(2): 291-301, 2004 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-15475171

RESUMO

The Brachyury family of T-domain containing transcription factor has been recently the subject of a number of Evo-Devo studies, with expression data obtained from a wide sampling of eumetazans, pointing to a possible conserved role in the formation of the blastopore and the extremities of the digestive tract. Here we present a comparative analysis of Brachyury sequences at the metazoan scale, using published data and two new sponge Brachyury sequences. Alignment features, gene phylogeny, and the evolution of variable positions within the T-domain are discussed in the light of available data about functional constraints on the residues. Interestingly, the high sequence divergence observed in Brachyury T-domains from sponges appears to be mostly the consequence of autapomorphic changes within the sponge lineages, rather than the retention of primitive character states.


Assuntos
Filogenia , Poríferos/genética , Proteínas com Domínio T/genética , Sequência de Aminoácidos , Animais , Sítios de Ligação/genética , Evolução Molecular , Dados de Sequência Molecular , Poríferos/classificação , Homologia de Sequência de Aminoácidos
5.
Genome Biol Evol ; 2: 665-77, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20829282

RESUMO

Little is known about the relationships between genome polymorphism, mobile element dynamics, and population size among animal populations. The chaetognath species Spadella cephaloptera offers a unique perspective to examine this issue because they display a high level of genetic polymorphism at the population level. Here, we have investigated in detail the extent of nucleotide and structural polymorphism in a region harboring Hox1 and several coding genes and presumptive functional elements. Sequencing of several bacterial artificial chromosome inserts representative of this nuclear region uncovered a high level of structural heterogeneity, which is mainly caused by the polymorphic insertion of a diversity of genetic mobile elements. By anchoring this variation through individual genotyping, we demonstrated that sequence diversity could be attributed to the allelic pool of a single population, which was confirmed by detection of extensive recombination within the genomic region studied. The high average level of nucleotide heterozygosity provides clues of selection in both coding and noncoding domains. This pattern stresses how selective processes remarkably cope with intense sequence turnover due to substitutions, mobile element insertions, and recombination to preserve the integrity of functional landscape. These findings suggest that genome polymorphism could provide pivotal information for future functional annotation of genomes.


Assuntos
Elementos de DNA Transponíveis , Evolução Molecular , Genes Homeobox , Invertebrados/genética , Polimorfismo Genético , Animais , Cromossomos Artificiais Bacterianos/genética , Variação Genética , Genética Populacional , Genômica , Família Multigênica , Fases de Leitura Aberta , Recombinação Genética , Análise de Sequência de DNA
6.
Genome Biol ; 9(6): R94, 2008.
Artigo em Inglês | MEDLINE | ID: mdl-18533022

RESUMO

BACKGROUND: The chaetognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chaetognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chaetognaths prompted further investigation of their genomic features. RESULTS: Transcriptomic and genomic data were collected from the chaetognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chaetognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chaetognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chaetognath phylum and we further report that this processing is associated with operonic transcription. CONCLUSION: These findings reveal both shared ancestral and unique derived characteristics of the chaetognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chaetognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes.


Assuntos
Perfilação da Expressão Gênica , Invertebrados/genética , Animais , Evolução Molecular , Duplicação Gênica , Genoma , Invertebrados/classificação , Filogenia
7.
Mol Phylogenet Evol ; 38(3): 621-34, 2006 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-16434216

RESUMO

While the phylogenetic position of Chaetognatha has became central to the question of early bilaterian evolution, the internal systematics of the phylum are still not clear. The phylogenetic relationships of the chaetognaths were investigated using newly obtained small subunit ribosomal RNA nuclear 18S (SSU rRNA) sequences from 16 species together with 3 sequences available in GenBank. As previously shown with the large subunit ribosomal RNA 28S gene, two classes of Chaetognatha SSU rRNA gene can be identified, suggesting a duplication of the whole ribosomal cluster; allowing the rooting of one class of genes by another in phylogenetic analyses. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the molecular data, and statistical tests showed (1) that there are three main monophyletic groups: Sagittidae/Krohnittidae, Spadellidae/Pterosagittidae, and Eukrohniidae/Heterokrohniidae, (2) that the group of Aphragmophora without Pterosagittidae (Sagittidae/Krohnittidae) is monophyletic, (3) the Spadellidae/Pterosagittidae and Eukrohniidae/Heterokrohniidae families are very likely clustered, (4) the Krohnittidae and Pterosagittidae groups should no longer be considered as families as they are included in other groups designated as families, (5) suborder Ctenodontina is not monophyletic and the Flabellodontina should no longer be considered as a suborder, and (6) the Syngonata/Chorismogonata and the Monophragmophora/Biphragmophora hypotheses are rejected. Such conclusions are considered in the light of morphological characters, several of which are shown to be prone to homoplasy.


Assuntos
Anelídeos/classificação , DNA Ribossômico/genética , Filogenia , RNA Ribossômico 18S/genética , Animais , Anelídeos/genética , Sequência de Bases , Teorema de Bayes , Clonagem Molecular , Primers do DNA , Funções Verossimilhança
8.
Dev Genes Evol ; 215(7): 369-73, 2005 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-15789247

RESUMO

Hox genes encode a set of evolutionarily conserved transcription factors that regulate anterior-posterior patterning. Here we report the first developmental expression of a Hox gene from Chaetognatha. These metazoans have been shown recently to be part of the protostome group of bilaterians. We describe the analysis of the SceMed4 gene (a Spadella cephaloptera Median Hox gene) including its expression from late stages of egg development to 7 days after hatching. In all of these stages, SceMed4 is expressed in two lateral stripes in a restricted region of the developing ventral ganglion.


Assuntos
Sistema Nervoso Central/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Genes Homeobox , Invertebrados/embriologia , Invertebrados/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Sistema Nervoso Central/crescimento & desenvolvimento , Embrião não Mamífero , Gânglios Espinais/embriologia , Hibridização In Situ , Invertebrados/classificação , Dados de Sequência Molecular , Homologia de Sequência de Aminoácidos
9.
Mol Biol Evol ; 21(11): 2122-9, 2004 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-15306659

RESUMO

Determining the phylogenetic position of enigmatic phyla such as Chaetognatha is a longstanding challenge for biologists. Chaetognaths (or arrow worms) are small, bilaterally symmetrical metazoans. In the past decades, their relationships within the metazoans have been strongly debated because of embryological and morphological features shared with the two main branches of Bilateria: the deuterostomes and protostomes. Despite recent attempts based on molecular data, the Chaetognatha affinities have not yet been convincingly defined. To answer this fundamental question, we determined the complete mitochondrial DNA genome of Spadella cephaloptera. We report three unique features: it is the smallest metazoan mitochondrial genome known and lacks both atp8 and atp6 and all tRNA genes. Furthermore phylogenetic reconstructions show that Chaetognatha belongs to protostomes. This implies that some embryological characters observed in chaetognaths, such as a gut with a mouth not arising from blastopore (deuterostomy) and a mesoderm derived from archenteron (enterocoely), could be ancestral features (plesiomorphies) of bilaterians.


Assuntos
DNA Mitocondrial , Invertebrados/genética , RNA de Transferência/genética , Sequência de Aminoácidos , Animais , DNA Mitocondrial/genética , Genoma , Modelos Genéticos , Dados de Sequência Molecular , Filogenia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos
10.
Dev Genes Evol ; 213(3): 142-8, 2003 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-12690453

RESUMO

We present the isolation of six Hox genes in the chaetognath Spadella cephaloptera. We identified one member of the paralogy group 3, four median genes and a mosaic gene that shares features of both median and posterior classes ( SceMedPost). Several hypotheses may account for the presence of a mosaic Hox gene in this animal. Here we propose that SceMedPost may represent an ancestral gene, which has not diverged totally into a posterior or a median one. This hypothesis has interesting implications for the reconstruction of the evolutionary history of Hox genes and suggests that Chaetognatha lineage divergence could predate the deuterostome/protostome split. Such a phylogenetic position is considered in the light of their embryological and morphological characters.


Assuntos
Evolução Molecular , Genes Homeobox/genética , Invertebrados/genética , Família Multigênica/genética , Filogenia , Sequência de Aminoácidos , Animais , Primers do DNA , França , Modelos Genéticos , Dados de Sequência Molecular , Alinhamento de Sequência , Análise de Sequência de DNA
11.
Syst Biol ; 52(3): 311-33, 2003 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-12775522

RESUMO

Because calcareous sponges are triggering renewed interest with respect to basal metazoan evolution, a phylogenetic framework of their internal relationships is needed to clarify the evolutionary history of key morphological characters. Morphological variation was scored at the suprageneric level within Calcispongia, but little phylogenetic information could be retrieved from morphological characters. For the main subdivision of Calcispongia, the analysis of morphological data weakly supports a classification based upon cytological and embryological characters (Calcinea/Calcaronea) rather than the older classification scheme based upon the aquiferous system (Homocoela/Heterocoela). The 18S ribosomal RNA data were then analyzed, both alone and in combination with morphological characters. The monophyly of Calcispongia is highly supported, but the position of this group with respect to other sponge lineages and to eumetazoan taxa is not resolved. The monophyly of both Calcinea and Calcaronea is retrieved, and the data strongly rejected the competing Homocoela/Heterocoela hypothesis. The phylogeny implies that characters of the skeleton architecture are highly homoplastic, as are characters of the aquiferous system. However, axial symmetry seems to be primitive for all Calcispongia, a conclusion that has potentially far-reaching implications for hypotheses of early body plan evolution in Metazoa.


Assuntos
Filogenia , Poríferos/classificação , RNA Ribossômico 18S/genética , Animais , Sequência de Bases , Funções Verossimilhança , Dados de Sequência Molecular , Poríferos/anatomia & histologia , Alinhamento de Sequência
12.
Rouxs Arch Dev Biol ; 196(4): 243-247, 1987 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28305699

RESUMO

We report a direct examination of the expression of one collagen gene (DCg1) during Drosophila melanogaster metamorphosis, based on data from in situ hybridization. The transcripts of this gene, thought to encode a basement membrane type IV collagen, are mainly accumulated during ecdysis in wandering haemocytes. Our results demonstrate that haemocytes contribute to extracellular matrix deposition and seem to perform a fibroblastic function during Drosophila development.

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