Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura - PubMed (original) (raw)

Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura

Jeffrey L Boore. BMC Genomics. 2004.

Abstract

Background: Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although hundreds of these genome sequences have been reported, the taxonomic sampling is highly biased toward vertebrates and arthropods, with many whole phyla remaining unstudied. This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo.

Results: This mtDNA is 15,113 nts in length and 62% A+T. It contains the 37 genes that are typical for animal mtDNAs in an arrangement somewhat similar to that of annelid worms. All genes are encoded by the same DNA strand which is rich in A and C relative to the opposite strand. Codons ending with the dinucleotide GG are more frequent than would be expected from apparent mutational biases. The largest non-coding region is only 282 nts long, is 71% A+T, and has potential for secondary structures.

Conclusions: Urechis caupo mtDNA shares many features with those of the few studied annelids, including the common usage of ATG start codons, unusual among animal mtDNAs, as well as gene arrangements, tRNA structures, and codon usage biases.

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Figures

Figure 1

Figure 1

Mitochondrial gene map of the echiuran Urechis caupo. All genes are transcribed from the same DNA strand. Scaling is only approximate. Genes are designated by standard nomenclature except for tRNAs, which are identified only by the one-letter code for the corresponding amino acid, with the two serine and two leucine tRNAs differentiated by numeral as identified in Fig. 3. "nc" indicates the largest non-coding regions; it may be that transcription initiates here, but this is not known.

Figure 2

Figure 2

A greatly abbreviated schematic of the sequence of Urechis caupo mtDNA. In the interest of brevity, the middle portion of each large gene is omitted and replaced by a numeral indicating the number of nucleotides removed. Since all mitochondrial proteins are thought to initiate with formyl-methionine, an M is placed in parentheses at the first codon position of cox1 (GTG) and nad3 (ATC) to indicate nonconformity to the genetic code. Asterisks indicate inferred stop codons whether complete or abbreviated and plus symbols mark nucleotides that would form the first in frame, complete stop codon if genes instead overlap.

Figure 3

Figure 3

The 22 inferred tRNA genes folded into the typical cloverleafstructures. Nomenclature for tRNA substructures is indicated on tRNA(V).

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