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A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

Sheffield NC, Song H, Cameron SL, Whiting MF - Mol. Biol. Evol. (2008)

Bottom Line: We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency.All six species of beetle have the same gene order as the ancestral insect.We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Brigham Young University, USA. ncs@byu.net

ABSTRACT
Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

Show MeSH
An alignment of tRNA-Ser(UCN) anticodon loops (and 3 paired stem nucleotides). Among beetles, Adephaga, Archostemata, and Myxophaga have the common GCU anticodon; all polyphagan species reported to date have the uncommon UCU anticodon, which suggests that this particular anticodon might be a possible molecular synapomorphy for Polyphaga.
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fig7: An alignment of tRNA-Ser(UCN) anticodon loops (and 3 paired stem nucleotides). Among beetles, Adephaga, Archostemata, and Myxophaga have the common GCU anticodon; all polyphagan species reported to date have the uncommon UCU anticodon, which suggests that this particular anticodon might be a possible molecular synapomorphy for Polyphaga.

Mentions: Although most arthropods use a GCU anticodon in tRNA-Ser(AGN), all beetle mtgenomes published so far have the UCU anticodon for this tRNA, suggesting that this anticodon may be a molecular synapomorphy for Coleoptera. Outside of Coleoptera, there are a few arthropods that reportedly use a UCU anticodon in tRNA-Ser(AGN), including the sea firefly Vargula hilgendorfii (Ogoh and Ohmiya 2004), the hermit crab Pagurus longicarpus (Hickerson and Cunningham 2000), and all species of lice studied to date (Cameron, Johnson, and Whiting 2007). With an expanded taxon sampling including all four coleopteran suborders, we found that while all the species belonging to the Polyphaga had the UCU anticodon, Trachypachus, Sphaerius, and Tetraphalerus, representing the smaller suborders Adephaga, Myxophaga, and Archostemata, respectively, had the common GCU anticodon instead (fig. 7). Except for the single base difference, the sequences for anticodon and anticodon loop, as well as the distal three paired bases, were identical across all beetles. Given that most arthropods have the GCU anticodon in the tRNA-Ser(AGN), it is possible to speculate that the ancestral anticodon for Coleoptera was GCU, which mutated to UCU in the common ancestor of Polyphaga, thus serving as a molecular synapomorphy for this suborder.


A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

Sheffield NC, Song H, Cameron SL, Whiting MF - Mol. Biol. Evol. (2008)

An alignment of tRNA-Ser(UCN) anticodon loops (and 3 paired stem nucleotides). Among beetles, Adephaga, Archostemata, and Myxophaga have the common GCU anticodon; all polyphagan species reported to date have the uncommon UCU anticodon, which suggests that this particular anticodon might be a possible molecular synapomorphy for Polyphaga.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2568038&req=5

fig7: An alignment of tRNA-Ser(UCN) anticodon loops (and 3 paired stem nucleotides). Among beetles, Adephaga, Archostemata, and Myxophaga have the common GCU anticodon; all polyphagan species reported to date have the uncommon UCU anticodon, which suggests that this particular anticodon might be a possible molecular synapomorphy for Polyphaga.
Mentions: Although most arthropods use a GCU anticodon in tRNA-Ser(AGN), all beetle mtgenomes published so far have the UCU anticodon for this tRNA, suggesting that this anticodon may be a molecular synapomorphy for Coleoptera. Outside of Coleoptera, there are a few arthropods that reportedly use a UCU anticodon in tRNA-Ser(AGN), including the sea firefly Vargula hilgendorfii (Ogoh and Ohmiya 2004), the hermit crab Pagurus longicarpus (Hickerson and Cunningham 2000), and all species of lice studied to date (Cameron, Johnson, and Whiting 2007). With an expanded taxon sampling including all four coleopteran suborders, we found that while all the species belonging to the Polyphaga had the UCU anticodon, Trachypachus, Sphaerius, and Tetraphalerus, representing the smaller suborders Adephaga, Myxophaga, and Archostemata, respectively, had the common GCU anticodon instead (fig. 7). Except for the single base difference, the sequences for anticodon and anticodon loop, as well as the distal three paired bases, were identical across all beetles. Given that most arthropods have the GCU anticodon in the tRNA-Ser(AGN), it is possible to speculate that the ancestral anticodon for Coleoptera was GCU, which mutated to UCU in the common ancestor of Polyphaga, thus serving as a molecular synapomorphy for this suborder.

Bottom Line: We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency.All six species of beetle have the same gene order as the ancestral insect.We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Brigham Young University, USA. ncs@byu.net

ABSTRACT
Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

Show MeSH