161 research outputs found

    Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

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    The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest

    Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

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    The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae

    Complete mitochondrial genome of Carijoa riisei (Duchassaing & Michelotti, 1860) (Octocorallia: Alcyonacea: Stolonifera: Clavulariidae)

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    We report the first complete Stolonifera mitochondrial genome. Carijoa riisei (Duchassaing & Michelotti, 1860) isolate CLP2_A03 was collected by scuba at 32 m on the USTS Texas Clipper (27° 53.7827′N, 93° 36.2702′W). The complete mitogenome has the ancestral octocoral gene order for its 14 protein-coding genes, two rRNA genes, and one tRNA gene. It is 18,714 bp (30.7% A, 15.8% C, 18.8% G, and 34.7% T). Of the Alcyonacea mitogenomes published to date, it is most genetically similar (94% uncorrected) to Sinularia ceramensis Verseveldt, 1977 (NC_044122)

    Duplication and Remolding of tRNA Genes in the Mitochondrial Genome of \u3cem\u3eReduvius tenebrosus\u3c/em\u3e (Hemiptera: Reduviidae)

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    Most assassin bugs are predators that act as important natural enemies of insect pests. Mitochondrial (mt) genomes of these insects are double-strand circular DNAs that encode 37 genes. In the present study, we explore the duplication and rearrangement of tRNA genes in the mt genome of Reduvius tenebrosus, the first mt genome from the subfamily Reduviinae. The gene order rearranges from CR (control region)-trnI-trnQ-trnM-ND2 to CR-trnQ-trnI2-trnI1-trnM-ND2. We identified 23 tRNA genes, including 22 tRNAs commonly found in insects and an additional trnI (trnI2), which has high sequence similarity to trnM. We found several pseudo genes, such as pseudo-trnI, pseudo-CR, and pseudo-ND2, in the hotspot region of gene rearrangement (between the control region and ND2). These features provided evidence that this novel gene order could be explained by the tandem duplication/random loss (TDRL) model. The tRNA duplication/anticodon mutation mechanism further explains the presence of trnI2, which is remolded from a duplicated trnM in the TDRL process (through an anticodon mutation of CAT to GAT). Our study also raises new questions as to whether the two events proceed simultaneously and if the remolded tRNA gene is fully functional. Significantly, the duplicated tRNA gene in the mitochondrial genome has evolved independently at least two times within assassin bugs

    Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects

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    <p>Abstract</p> <p>Background</p> <p>Animal mitochondrial genomes are potential models for molecular evolution and markers for phylogenetic and population studies. Previous research has shown interesting features in hymenopteran mitochondrial genomes. Here, we conducted a comparative study of mitochondrial genomes of the family Braconidae, one of the largest families of Hymenoptera, and assessed the utility of mitochondrial genomic data for phylogenetic inference at three different hierarchical levels, i.e., Braconidae, Hymenoptera, and Holometabola.</p> <p>Results</p> <p>Seven mitochondrial genomes from seven subfamilies of Braconidae were sequenced. Three of the four sequenced A+T-rich regions are shown to be inverted. Furthermore, all species showed reversal of strand asymmetry, suggesting that inversion of the A+T-rich region might be a synapomorphy of the Braconidae. Gene rearrangement events occurred in all braconid species, but gene rearrangement rates were not taxonomically correlated. Most rearranged genes were tRNAs, except those of <it>Cotesia vestalis</it>, in which 13 protein-coding genes and 14 tRNA genes changed positions or/and directions through three kinds of gene rearrangement events. Remote inversion is posited to be the result of two independent recombination events. Evolutionary rates were lower in species of the cyclostome group than those of noncyclostomes. Phylogenetic analyses based on complete mitochondrial genomes and secondary structure of <it>rrnS </it>supported a sister-group relationship between Aphidiinae and cyclostomes. Many well accepted relationships within Hymenoptera, such as paraphyly of Symphyta and Evaniomorpha, a sister-group relationship between Orussoidea and Apocrita, and monophyly of Proctotrupomorpha, Ichneumonoidea and Aculeata were robustly confirmed. New hypotheses, such as a sister-group relationship between Evanioidea and Aculeata, were generated. Among holometabolous insects, Hymenoptera was shown to be the sister to all other orders. Mecoptera was recovered as the sister-group of Diptera. Neuropterida (Neuroptera + Megaloptera), and a sister-group relationship with (Diptera + Mecoptera) were supported across all analyses.</p> <p>Conclusions</p> <p>Our comparative studies indicate that mitochondrial genomes are a useful phylogenetic tool at the ordinal level within Holometabola, at the superfamily within Hymenoptera and at the subfamily level within Braconidae. Variation at all of these hierarchical levels suggests that the utility of mitochondrial genomes is likely to be a valuable tool for systematics in other groups of arthropods.</p

    First complete mitochondrial genome of the South American annual fish Austrolebias charrua (Cyprinodontiformes: Rivulidae): peculiar features among cyprinodontiforms mitogenomes

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    Selected nucleotide substitution models after the third codon positions were removed from the codon alignments. (PDF 7 kb

    Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

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    Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge

    Speciation, evolution and phylogeny of some shallow-water octocorals (Cnidaria: Anthozoa)

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    Shallow-water octocorals are among the most abundant macro-benthic organisms inhabiting tropical subtropical and temperate communities. In spite of being worldwide distributed and highly diverse, the systematics of many octocorals remains controversial and the understanding of the processes who led to their diversification is largely unexplored. This study includes five chapters, each dealing with different aspects of the systematics, phylogeny and evolution of six soft coral genera such as Lobophytum, Sarcophyton, Paramuricea, Leptogorgia, Muricea and Pacifigorgia. One of the main goals of the study was to explore, through the use of molecular methods, the genetic variation within species notoriously difficult to identify. Besides the use of standard molecular methods for phylogenetic reconstruction and species delimitation, the effectiveness of Next Generation Sequencing (NGS) technologies was tested for mitogenomic and genotyping analyses. In the first chapter the use of single-locus markers (e.g. COI, mtMutS and 28S rDNA) was investigated and different automated species delimitation methods (e.g. ABGD, bPTP) were employed to assess species richness among soft coral genera from Western Australia. The methods used appeared suitable for preliminary and rapid diversity assessments especially in the presence of species-rich genera such as Lobophytum and Sarcophyton where morphological identification is particularly difficult and time consuming. In the second chapter, along with the sequencing of complete mitogenomes of Mediterranean Paramuricea species (P. clavata and P. macrospina), the biogeography of the genus was investigated. The results revealed nucleotide and genome size polymorphisms, while the biogeographic predictions suggested that the Mediterranean species have resulted from independent speciation events, explaining in part the high phylogenetic divergence detected. In the third chapter, the sequencing of complete mitogenomes of five Leptogorgia species from different geographic areas (eastern Pacific, eastern Atlantic and Mediterranean) was followed by phylogenetic reconstructions based on an extended mtMutS dataset. The phylogenetic tree recovered Leptogorgia polyphyletic with a clear segregation between the eastern Pacific and eastern Atlantic forms. A time calibrated phylogeny provided insights into the evolution of the genus. In chapter four, using NGS approaches, the complete mitochondrial genome of two eastern Pacific Muricea species (M. crassa and M. purpurea) has been sequenced. The recovery of complete mitogenomes allowed to evaluate the presence of variable and informative regions and to infer a more robust phylogeny. Overall, the results showed high nucleotide diversity in the intergenic spacers, making these regions new potential molecular markers for species-level identifications. In the last chapter a genome-wide Single Nucleotide Polymorphisms (SNPs) and a Bayes Factor Delimitation method were used to infer the genetic relationships within species of the genus Pacifigorgia. The data obtained showed incongruence between molecular and morphological investigations suggesting the possibility of alternative taxonomic assignments for these species. This study provides information on the evolution and speciation of ecologically important soft corals, which distribution range from the littoral and sublittoral zones of the Mediterranean to the tropical and subtropical reefs of Western Australia (WA) and eastern Pacific (EP). The use of mitochondrial markers such as MutS allowed to shed some light on the biogeography and evolutionary history of widespread gorgonians with special emphasis on the Mediterranean endemics and the Atlantic species. Concerning the Western Australia, the obtained results will support the management and conservation of under-investigated marine biodiversity hotspots and potentially species-rich localities such as the Kimberley. In terms of species delimitation, the application of genome-wide SNPs and the use of NGS technologies showed a higher resolution when compared with the traditional methods based on DNA barcoding and single-locus phylogenies. The data generated have been used to clarify the systematics of the species investigated and will be considered as a baseline for future studies on population genetics with a closer look on the adaptive processes

    Mitochondrial genomic landscape: A portrait of the mitochondrial genome 40 years after the first complete sequence

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    open3noNotwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.openFormaggioni A.; Luchetti A.; Plazzi F.Formaggioni A.; Luchetti A.; Plazzi F
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