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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.

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An alignment of the gap region between tRNA-Ser(UCN) and nad1 in all coleopteran genomes. The box indicates a conserved pentanucleotide region (TACTA) across all beetles. The dotted line indicates the location of nad1 in Rhagophthalmus if the current annotation is correct.
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fig3: An alignment of the gap region between tRNA-Ser(UCN) and nad1 in all coleopteran genomes. The box indicates a conserved pentanucleotide region (TACTA) across all beetles. The dotted line indicates the location of nad1 in Rhagophthalmus if the current annotation is correct.

Mentions: Although most spacers appeared to be unique to individual species (see below), a small intergenic region between the tRNA-Ser(UCN) and nad1 genes, ranging between 17 and 22 bp in length, was found in all six species. An intergenic spacer of this size at this location has been reported in other insects (e.g., Kim et al. 2006) and arthropods (e.g., Lavrov et al. 2000). Four of the six previously published beetle mtgenomes also have this intergenic spacer, which ranges between 16 and 20 bp in size, and only the two species of genus Rhagophthalmus lack it (Li et al. 2007). These latter two species have only about 4 bp in this region. However, we can attribute this disparity to insertions and deletions near the end of nad1 that may be the result of sequencing errors or correction by posttranslational modification. The Anoplophora sequence is also one nucleotide off, shifting the reading frame to avoid the conserved stop codon the other beetles use. In this case, the authors annotated the gene with a partial stop codon (T) to preserve the conserved spacer. According to Taanman (1999), this intergenic spacer region may correspond to the binding site of mtTERM, a transcription attenuation factor, as this position signifies the end of the major-strand coding region. Cameron and Whiting (2008) presented an alignment of several insect orders, highlighting a 7-bp motif (ATACTAA) conserved across Lepidoptera. When we aligned this region across all coleopteran mtgenomes, we found 5 bp (TACTA or its reverse complement TAGTA) to be conserved, and this region matches well the corresponding motif in Lepidoptera (Cameron and Whiting 2008; fig. 3).


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 the gap region between tRNA-Ser(UCN) and nad1 in all coleopteran genomes. The box indicates a conserved pentanucleotide region (TACTA) across all beetles. The dotted line indicates the location of nad1 in Rhagophthalmus if the current annotation is correct.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: An alignment of the gap region between tRNA-Ser(UCN) and nad1 in all coleopteran genomes. The box indicates a conserved pentanucleotide region (TACTA) across all beetles. The dotted line indicates the location of nad1 in Rhagophthalmus if the current annotation is correct.
Mentions: Although most spacers appeared to be unique to individual species (see below), a small intergenic region between the tRNA-Ser(UCN) and nad1 genes, ranging between 17 and 22 bp in length, was found in all six species. An intergenic spacer of this size at this location has been reported in other insects (e.g., Kim et al. 2006) and arthropods (e.g., Lavrov et al. 2000). Four of the six previously published beetle mtgenomes also have this intergenic spacer, which ranges between 16 and 20 bp in size, and only the two species of genus Rhagophthalmus lack it (Li et al. 2007). These latter two species have only about 4 bp in this region. However, we can attribute this disparity to insertions and deletions near the end of nad1 that may be the result of sequencing errors or correction by posttranslational modification. The Anoplophora sequence is also one nucleotide off, shifting the reading frame to avoid the conserved stop codon the other beetles use. In this case, the authors annotated the gene with a partial stop codon (T) to preserve the conserved spacer. According to Taanman (1999), this intergenic spacer region may correspond to the binding site of mtTERM, a transcription attenuation factor, as this position signifies the end of the major-strand coding region. Cameron and Whiting (2008) presented an alignment of several insect orders, highlighting a 7-bp motif (ATACTAA) conserved across Lepidoptera. When we aligned this region across all coleopteran mtgenomes, we found 5 bp (TACTA or its reverse complement TAGTA) to be conserved, and this region matches well the corresponding motif in Lepidoptera (Cameron and Whiting 2008; fig. 3).

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