The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola)

Department of Evolutionary Biology, University of Siena, Via A, Moro 2, 53100 Siena, Italy.
BMC Genomics (Impact Factor: 3.99). 08/2008; 9(1):315. DOI: 10.1186/1471-2164-9-315
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ABSTRACT Mitogenomics data, i.e. complete mitochondrial genome sequences, are popular molecular markers used for phylogenetic, phylogeographic and ecological studies in different animal lineages. Their comparative analysis has been used to shed light on the evolutionary history of given taxa and on the molecular processes that regulate the evolution of the mitochondrial genome. A considerable literature is available in the fields of invertebrate biochemical and ecophysiological adaptation to extreme environmental conditions, exemplified by those of the Antarctic. Nevertheless, limited molecular data are available from terrestrial Antarctic species, and this study represents the first attempt towards the description of a mitochondrial genome from one of the most widespread and common collembolan species of Antarctica.
In this study we describe the mitochondrial genome of the Antarctic collembolan Cryptopygus antarcticus Willem, 1901. The genome contains the standard set of 37 genes usually present in animal mtDNAs and a large non-coding fragment putatively corresponding to the region (A+T-rich) responsible for the control of replication and transcription. All genes are arranged in the gene order typical of Pancrustacea. Three additional short non-coding regions are present at gene junctions. Two of these are located in positions of abrupt shift of the coding polarity of genes oriented on opposite strands suggesting a role in the attenuation of the polycistronic mRNA transcription(s). In addition, remnants of an additional copy of trnL(uag) are present between trnS(uga) and nad1. Nucleotide composition is biased towards a high A% and T% (A+T = 70.9%), as typically found in hexapod mtDNAs. There is also a significant strand asymmetry, with the J-strand being more abundant in A and C. Within the A+T-rich region, some short sequence fragments appear to be similar (in position and primary sequence) to those involved in the origin of the N-strand replication of the Drosophila mtDNA.
The mitochondrial genome of C. antarcticus shares several features with other pancrustacean genomes, although the presence of unusual non-coding regions is also suggestive of molecular rearrangements that probably occurred before the differentiation of major collembolan families. Closer examination of gene boundaries also confirms previous observations on the presence of unusual start and stop codons, and suggests a role for tRNA secondary structures as potential cleavage signals involved in the maturation of the primary transcript. Sequences potentially involved in the regulation of replication/transcription are present both in the A+T-rich region and in other areas of the genome. Their position is similar to that observed in a limited number of insect species, suggesting unique replication/transcription mechanisms for basal and derived hexapod lineages. This initial description and characterization of the mitochondrial genome of C. antarcticus will constitute the essential foundation prerequisite for investigations of the evolutionary history of one of the most speciose collembolan genera present in Antarctica and other localities of the Southern Hemisphere.

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Available from: Antonio Carapelli, Sep 25, 2015
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    • "Raw sequence data were compiled using SEQUENCHER v. 5.0 (Gene Codes Corporation, Ann Arbor, MI, USA) and complete COI sequences were aligned manually to published Collembola mtDNA genomes (Nardi et al., 2001; Cook et al., 2005; Carapelli et al., 2007; 2008; Torricelli et al., 2010). Nucleotide sequences were translated in MacClade v. 4.05 (Maddison & Maddison, 2000) to confirm the absence of stop codons and errors. "
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    ABSTRACT: Evaluating species boundaries remains a significant challenge in rare, difficult to collect, and/or understudied groups because of a lack of available data. Uninformative morphology, unknown ecologies and/or geographical distributions, inadequate comparative sequence data, and limited sample sizes present substantial challenges when applying commonly used methods for species delimitation. Here we present an approach that overcomes the challenges previously mentioned by integrating phylogeny, genetic distances, and a fixed diagnostic character (i.e. colour pattern) into the species delimitation process. The genus Entomobrya (Collembola) includes many species marked by complex and variable colour patterns. Many Entomobrya species have been named based exclusively on colour pattern, but the value of this character as a species-level diagnostic marker has been challenged. To test the hypothesis that colour forms in Entomobrya represent independent evolutionary lineages, i.e. distinct species, we used phylogenetic methods to evaluate the association between colour pattern and molecular variation in the cytochrome c oxidase I gene (COI) in 11 species of North American Entomobrya. The comparative analysis focused on 13 colour forms distributed amongst the species Entomobrya assuta, Entomobrya clitellaria, Entomobrya ligata, and Entomobrya quadrilineata. Phylogenetic analysis and genetic divergences sorted the 13 colour forms into seven independent evolutionary lineages, including three morphologically cryptic lineages diagnosable by colour pattern. However, genetic divergence did not always correlate with colour pattern variation, indicating that the diagnostic utility of colour pattern is species dependent and requires individual evaluation for each species. We propose that incorporation of the explicit species delimitation criteria developed for this study will result in a substantial advance in the identification and description of species in understudied taxa.
    Zoological Journal of the Linnean Society 02/2015; 173(4). DOI:10.1111/zoj.12220 · 2.72 Impact Factor
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    • "Mitochondrial genomes were amplified from 50 ng genomic DNA using Herculase™ II Fusion DNA polymerase (Agilent, Santa Clara, CA, USA) following manufacturer’s recommendations, except for DNA fragments comprising the AT-rich region that only amplified using an extension temperature of 60°C. The mitochondrial sequence of three species was obtained using standard protocols [12, 45]. The mitochondrial sequences of the remaining species were obtained by next generation sequencing using Roche FLX/454 or GS Junior technology. "
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    ABSTRACT: Background Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012). Results We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure. Conclusions Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.
    BMC Genomics 07/2014; 15(1):566. DOI:10.1186/1471-2164-15-566 · 3.99 Impact Factor
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    • "Asymmetry in the nucleotide composition between J-strand and N-strand is a common phenomenon in the metazoan mt-genome (Perna & Kocher 1995) and the trend is also present in A. heissi. Like most insect mtgenomes , A% and C% are higher than T% and G% on the J-strand, whereas the reverse is observed in the N-strand (Carapelli et al. 2008). On the J-strand of PCGs of A. heissi, cytosines were more frequent than guanines, generating a negative GC-skew (-0.13). "
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    ABSTRACT: Abstract The mitochondrial genome of a flat bug, Brachyrhynchus hsiaoi (Blöte), is a typical circular DNA molecule of 15,250 bp with 37 genes and 70.4% A + T content. The gene order is different from that of the putative ancestral arrangement of insects with a tRNA gene rearrangement, trnQ-trnI. This rearrangement has been found in other sequenced flat bugs and is likely synapomorphic for the Aradidae or some subgroup within this family. Ten protein-coding genes start with ATN codon and others use TTG. All the 22 tRNAs, ranging from 61 to 70 bp, have the clover-leaf structure except for the dihydrouridine (DHU) arm of trnS1 forms a simple loop. The sizes of the large and small ribosomal RNA genes are 1245 and 808 bp, respectively. The control region is located between rrnS and trnQ with 703 bp in length and 69.8% A + T content.
    Mitochondrial DNA 01/2014; 2014. DOI:10.3109/19401736.2013.867437 · 1.21 Impact Factor
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