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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 tRNA-Leu and nad1 genes. Dotted line indicates hypothetical amino acid translation of nucleotide sequence that codes for tRNA-Leu. Bold letters indicate the amino acids of the putative start codons that were previously proposed. The box indicates our proposed start codons, which shows that the TTG start codon (leucine) is more common than previously thought.
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fig5: An alignment of the tRNA-Leu and nad1 genes. Dotted line indicates hypothetical amino acid translation of nucleotide sequence that codes for tRNA-Leu. Bold letters indicate the amino acids of the putative start codons that were previously proposed. The box indicates our proposed start codons, which shows that the TTG start codon (leucine) is more common than previously thought.

Mentions: In insects, most protein-coding genes except cox1 use typical ATN (methionine or isoleucine) start codons, and we found the same pattern in all six beetle species (table 4). However, there were some genes that varied: nad1 of Trachypachus, Sphaerius, Chaetosoma, and Priasilpha and nad2 of Sphaerius. For these genes, there is no upstream possibility of ATN start codon due to in-frame stop codons, and downstream possibilities all create a considerable intergenic gap. In this study, we propose TTG (leucine) as a start codon for these genes (Okimoto et al. 1990). TTG has been proposed as a start codon for nad1 in several insects, including Anopheles quadrimaculatus (Mitchell et al. 1993), Tricholepidion gertschi (Nardi et al. 2003), and Pyrocoelia rufa (Bae et al. 2004). In justifying the use of this start codon, Bae et al. (2004) argued from the evolutionary economic perspective that it would minimize intergenic space and avoid overlap with the abutting tRNA. Even more importantly, TTG as a start codon of nad1 is positionally well conserved as inferred from an alignment of all published beetle mtgenomes (fig. 5). Although some of the previously published mtgenomes (Crioceris, Tribolium, and Anoplophora) annotated nad1 with a typical ATN start codon which created overlap with tRNA-Leu or a considerable intergenic gap, we suggest that TTG is a more conserved possibility (fig. 5). Additionally, with the revised start codons, the C-terminal end of the peptide is quite conserved with an acidic polar amino acid (D or E) at position 5, and neutral, nonpolar amino acids (I, L, M, V, or F) at positions 1–4 and 6–11 (fig. 5). The evolution of the TTG start codon does not appear to be lineage specific, however. Of the seven polyphagan species, two had the typical ATN (methionine) start codon, whereas the other five had the TTG (leucine) start codon (fig. 5). Different start codons were used in two lineages (Pyrocoelia and Rhagophthalmus) within the same superfamily (Elateroidea), suggesting that the TTG start codon has evolved multiple times within Coleoptera without much lineage-specific conservation.


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 tRNA-Leu and nad1 genes. Dotted line indicates hypothetical amino acid translation of nucleotide sequence that codes for tRNA-Leu. Bold letters indicate the amino acids of the putative start codons that were previously proposed. The box indicates our proposed start codons, which shows that the TTG start codon (leucine) is more common than previously thought.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: An alignment of the tRNA-Leu and nad1 genes. Dotted line indicates hypothetical amino acid translation of nucleotide sequence that codes for tRNA-Leu. Bold letters indicate the amino acids of the putative start codons that were previously proposed. The box indicates our proposed start codons, which shows that the TTG start codon (leucine) is more common than previously thought.
Mentions: In insects, most protein-coding genes except cox1 use typical ATN (methionine or isoleucine) start codons, and we found the same pattern in all six beetle species (table 4). However, there were some genes that varied: nad1 of Trachypachus, Sphaerius, Chaetosoma, and Priasilpha and nad2 of Sphaerius. For these genes, there is no upstream possibility of ATN start codon due to in-frame stop codons, and downstream possibilities all create a considerable intergenic gap. In this study, we propose TTG (leucine) as a start codon for these genes (Okimoto et al. 1990). TTG has been proposed as a start codon for nad1 in several insects, including Anopheles quadrimaculatus (Mitchell et al. 1993), Tricholepidion gertschi (Nardi et al. 2003), and Pyrocoelia rufa (Bae et al. 2004). In justifying the use of this start codon, Bae et al. (2004) argued from the evolutionary economic perspective that it would minimize intergenic space and avoid overlap with the abutting tRNA. Even more importantly, TTG as a start codon of nad1 is positionally well conserved as inferred from an alignment of all published beetle mtgenomes (fig. 5). Although some of the previously published mtgenomes (Crioceris, Tribolium, and Anoplophora) annotated nad1 with a typical ATN start codon which created overlap with tRNA-Leu or a considerable intergenic gap, we suggest that TTG is a more conserved possibility (fig. 5). Additionally, with the revised start codons, the C-terminal end of the peptide is quite conserved with an acidic polar amino acid (D or E) at position 5, and neutral, nonpolar amino acids (I, L, M, V, or F) at positions 1–4 and 6–11 (fig. 5). The evolution of the TTG start codon does not appear to be lineage specific, however. Of the seven polyphagan species, two had the typical ATN (methionine) start codon, whereas the other five had the TTG (leucine) start codon (fig. 5). Different start codons were used in two lineages (Pyrocoelia and Rhagophthalmus) within the same superfamily (Elateroidea), suggesting that the TTG start codon has evolved multiple times within Coleoptera without much lineage-specific conservation.

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