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

Carapelli A, Comandi S, Convey P, Nardi F, Frati F - BMC Genomics (2008)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Evolutionary Biology, University of Siena, Via A, Moro 2, 53100 Siena, Italy. carapelli@unisi.it

ABSTRACT

Background: 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.

Results: 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.

Conclusion: 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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Graphical representation of the percentage of As (red) and Ts (black) across the whole mtDNA segment calculated using the program MacVector® 7.2.3 (Accelrys). Y-axis values represent nucleotide %, calculated with a 100-bp sliding window; x-axis values represent the nucleotide positions corresponding to the linearized genome. Below the graphs, position and orientation of each gene.
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Figure 3: Graphical representation of the percentage of As (red) and Ts (black) across the whole mtDNA segment calculated using the program MacVector® 7.2.3 (Accelrys). Y-axis values represent nucleotide %, calculated with a 100-bp sliding window; x-axis values represent the nucleotide positions corresponding to the linearized genome. Below the graphs, position and orientation of each gene.

Mentions: In this respect, the frequency of adenines and thymines is approximately equal in the genes encoded on the J-strand, whereas a higher percentage of A vs T (counting on the J-strand) is observed in those oriented on the N-strand (Figure 3). If the strand displacement model of mtDNA replication described in mammals and Drosophila also holds for Collembola, we can speculate that the block of genes spanning from rrnS to trnF (all genes oriented on the N-strand except for trnT, nad6, cob and trnS(uga); Figures 1 and 3) is more prone to the deamination type C→U than the opposite strand (due to higher DSSH), and that transitions between C and T are more frequent than those between A and G. Perhaps this trend, observed only in the PCGs oriented on the N-strand, is dependent on a higher number of mutations occurring during transcription, rather than replication, and is consequently less etched in the PCGs encoded on the J-strand. In addition, it has been demonstrated that cytosine is the most unstable of the four bases and the number of C deaminations is more pronounced in single-strand DNAs [53].


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

Carapelli A, Comandi S, Convey P, Nardi F, Frati F - BMC Genomics (2008)

Graphical representation of the percentage of As (red) and Ts (black) across the whole mtDNA segment calculated using the program MacVector® 7.2.3 (Accelrys). Y-axis values represent nucleotide %, calculated with a 100-bp sliding window; x-axis values represent the nucleotide positions corresponding to the linearized genome. Below the graphs, position and orientation of each gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483729&req=5

Figure 3: Graphical representation of the percentage of As (red) and Ts (black) across the whole mtDNA segment calculated using the program MacVector® 7.2.3 (Accelrys). Y-axis values represent nucleotide %, calculated with a 100-bp sliding window; x-axis values represent the nucleotide positions corresponding to the linearized genome. Below the graphs, position and orientation of each gene.
Mentions: In this respect, the frequency of adenines and thymines is approximately equal in the genes encoded on the J-strand, whereas a higher percentage of A vs T (counting on the J-strand) is observed in those oriented on the N-strand (Figure 3). If the strand displacement model of mtDNA replication described in mammals and Drosophila also holds for Collembola, we can speculate that the block of genes spanning from rrnS to trnF (all genes oriented on the N-strand except for trnT, nad6, cob and trnS(uga); Figures 1 and 3) is more prone to the deamination type C→U than the opposite strand (due to higher DSSH), and that transitions between C and T are more frequent than those between A and G. Perhaps this trend, observed only in the PCGs oriented on the N-strand, is dependent on a higher number of mutations occurring during transcription, rather than replication, and is consequently less etched in the PCGs encoded on the J-strand. In addition, it has been demonstrated that cytosine is the most unstable of the four bases and the number of C deaminations is more pronounced in single-strand DNAs [53].

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Evolutionary Biology, University of Siena, Via A, Moro 2, 53100 Siena, Italy. carapelli@unisi.it

ABSTRACT

Background: 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.

Results: 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.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus