1,576 research outputs found

    Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution

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    The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments.publishedVersio

    Rearrangement and evolution of mitochondrial genomes in parrots

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    © 2015 Elsevier Inc. Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at fourfold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated

    The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria

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    <p>Abstract</p> <p>Background</p> <p>The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch <it>Rhabdopleura compacta </it>to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution.</p> <p>Results</p> <p>The mitochondrial DNA of <it>Rhabdopleura compacta </it>corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in <it>R. compacta </it>is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of <it>R. compacta</it>, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in <it>R. compacta </it>but possess an identical mutation in the anticodon sequence of the tRNA<sub>Lys</sub>.</p> <p>Conclusion</p> <p>A strong reversed asymmetrical mutational constraint in the mitochondrial genome of <it>Rhabdopleura compacta </it>may have arisen by an inversion of the replication direction and adaptation to this bias in the protein sequences leading to an enigmatic mitochondrial genome. Although, phylogenetic analyses of protein coding sequences are hampered, features of the tRNA system of <it>R. compacta </it>support the monophyly of Ambulacraria. The identical reassignment of AGG to Lysine in two distinct groups may have occurred by convergent evolution in the anticodon sequence of the tRNA<sub>Lys</sub>.</p

    Abandoning sex: multiple origins of asexuality in the ciliate Tetrahymena

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    Un nuevo género para Habrothrix angustidens y Akodon serrensis (RODENTIA, CRICETIDAE): de nuevo palentología y neontología se encuentran en el legado de Lund

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    We describe a new genus of sigmodontine rodent to allocate a fossil species from Lagoa Santa cave deposits, Habrothrix angustidens Winge, and a living species from southeastern Atlantic Forest described at the start of the past century, Akodon serrensis Thos. Tentatively, both forms are considered as synonyms pending a detailed revision of the genus. The new genus belongs to the Akodon Division of the diverse tribe Akodontini where, based on molecular evidence, it is sister to Thaptomys, another forest-dwelling akodontine. The new genus is characterized by a unique combination of morphological traits including tail shorter than head-and-body; manual and pedal digits with short claws; skull robust with pointed rostrum, broad and somewhat flat interorbital region with frontal borders divergent posteriorly, and enlarged braincase without crests; large incisive foramina with expanded palatal process of premaxillary; broad mesopterygoid fossa with anterior margin rounded; alisphenoid strut present; carotid arterial circulation pattern primitive; molars noticeably large in relation to the skull and moderately hypsodont; main molar cusps arranged in opposite pairs; first upper molar without anteromedian flexus; length of third lower molar subequal to those of second lower molar; mandible without distinct capsular process; gall bladder present; stomach unilocular and hemiglandular; 2n = 46 (FN = 46). The new genus is an Atlantic Forest endemic, indicating that the diversity of Akodontini has been overlooked outside of the Andes.Describimos un nuevo género de roedor sigmodontino para ubicar una especie fósil de los depósitos de Lagoa Santa, Habrothrix angustidens Winge y una especie viviente del sudeste de la Selva Atlántica descripta en los comienzos de la centuria pasada, Akodon serrensis Thos. Tentativamente, ambas formas son consideradas sinónimos a la espera de una revisión detallada de la diversidad del género. El nuevo género pertenece a la División Akodon de la diversa tribu Akodontini donde, sobre la base de evidencia molecular, resulta hermano de Thaptomys, otro akodontino especialista de selva. El nuevo género se caracteriza por una combinación única de rasgos morfológicos incluyendo una cola más corta que el largo cabeza-cuerpo, garras de los dedos de la mano y el pie cortas, cráneo robusto con rostro puntiagudo, región interorbitaria ancha y algo chata con los bordes frontales divergentes hacia atrás y caja craneana agrandada y sin crestas, forámenes incisivos expandidos con proceso palatal del premaxilar bien desarrollado, fosa mesopterigoidea ancha con el borde anterior redondeado, barra alisfenoidea presente, patrón de circulación carotídea primitivo, molares notablemente grandes en relación a las proporciones del cráneo y moderadamente hipsodontes, principales cúspides de los molares dispuestas en pares opuestos, primer molar superior carente de flexo anteromediano, largo del tercer molar inferior subigual al del segundo molar inferior, mandíbula sin proyección capsular evidente, vesícula biliar presente, estómago unilocular-hemiglandular, 2n = 46 (FN = 46). El nuevo género es endémico de la Selva Atlántica indicando una insospechada diversidad de los Akodontini en regiones extraandinas.Fil: Pardiñas, Ulises Francisco J.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Geise, Lena. Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier; BrasilFil: Ventura, Karen. Universidade Federal de Itajubá; BrasilFil: Lessa, Gissele. Universidade Federal de Viçosa; Brasi

    AQPX-cluster aquaporins and aquaglyceroporins are asymmetrically distributed in trypanosomes

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    Major Intrinsic Proteins (MIPs) are membrane channels that permeate water and other small solutes. Some trypanosomatid MIPs mediate the uptake of antiparasitic compounds, placing them as potential drug targets. However, a thorough study of the diversity of these channels is still missing. Here we place trypanosomatid channels in the sequence-function space of the large MIP superfamily through a sequence similarity network. This analysis exposes that trypanosomatid aquaporins integrate a distant cluster from the currently defined MIP families, here named aquaporin X (AQPX). Our phylogenetic analyses reveal that trypanosomatid MIPs distribute exclusively between aquaglyceroporin (GLP) and AQPX, being the AQPX family expanded in the Metakinetoplastina common ancestor before the origin of the parasitic order Trypanosomatida. Synteny analysis shows how African trypanosomes specifically lost AQPXs, whereas American trypanosomes specifically lost GLPs. AQPXs diverge from already described MIPs on crucial residues. Together, our results expose the diversity of trypanosomatid MIPs and will aid further functional, structural, and physiological research needed to face the potentiality of the AQPXs as gateways for trypanocidal drugs.Fil: Tesan, Fiorella Carla. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Lorenzo Lopez, Juan Ramiro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Alleva, Karina Edith. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Fox, Ana Romina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentin

    Computational Biology and High Performance Computing 2000

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    Tutorial to be presented at Supercomputing 2000, Dallas TX, 6-10 November 2000.This work was supported by the Director, Office of Science, Office of Advanced Scientific computing Research, Mathematical, Information, and Computational Sciences Division of the U.S. Department of Energy under Contract No. DE-AC03-76SF0009
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