Complete mitochondrial DNA sequence of the ark shell Scapharca broughtonii: An ultra-large metazoan mitochondrial genome |
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| Authors: | Yun-Guo Liu Tadahide Kurokawa Masashi Sekino Toru Tanabe Kazuhito Watanabe |
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| Institution: | 1. Tohoku National Fisheries Research Institute, Fisheries Research Agency, 3-27-5 Shinhama, Shiogama, Miyagi, Japan;2. National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa, Japan;3. Miyagi Prefecture Fisheries Technology Institute, 97-6 Sodenohama, Watanoha, Ishinomaki, Miyagi, Japan;1. Graduate Program of Biotechnology and Environmental Monitoring, Campus of Sorocaba, Federal University of São Carlos (UFSCAR), Rodovia João Leme dos Santos, Km 110, Itinga, Sorocaba, SP, Brazil;2. Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCAR) São Carlos, SP, Brazil;3. Center of Nuclear Energy (CENA), ESALQ, University of São Paulo, Piracicaba, SP, Brazil;1. National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada;2. University of Manitoba, Department of Medical Microbiology and Infectious Diseases, Winnipeg, Manitoba R3E 0J9, Canada |
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| Abstract: | The complete mitochondrial (mt) genome of the ark shell Scapharca broughtonii was determined using long PCR and a genome walking sequencing strategy with genus-specific primers. The S. broughtonii mt genome (GenBank accession number AB729113) contained 12 protein-coding genes (the atp8 gene is missing, as in most bivalves), 2 ribosomal RNA genes, and 42 transfer tRNA genes, in a length of 46,985 nucleotides for the size of mtDNA with only one copy of the heteroplasmic tandem repeat (HTR) unit. Moreover the S. broughtonii mt genome shows size variation; these genomes ranged in size from about 47 kb to about 50 kb because of variation in the number of repeat sequences in the non-coding region. The mt-genome of S. broughtonii is, to date, the longest reported metazoan mtDNA sequence. Sequence duplication in non-coding region and the formation of HTR arrays were two of the factors responsible for the ultra-large size of this mt genome. All the tRNA genes were found within the S. broughtonii mt genome, unlike the other bivalves usually lacking one or more tRNA genes. Twelve additional specimens were used to analyze the patterns of tandem repeat arrays by PCR amplification and agarose electrophoresis. Each of the 12 specimens displayed extensive heteroplasmy and had 8–10 length variants. The motifs of the HTR arrays are about 353–362 bp and the number of repeats ranges from 1 to 11. |
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