The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae).
Mitochondrial genes and genomes have long been applied in phylogenetics. Current protocols to sequence mitochondrial genomes rely almost exclusively on long range PCR or on the direct sequencing. While long range PCR includes unnecessary biases, the purification of mtDNA for direct sequencing is not straightforward. We used total RNA extracted from liver and Illumina HiSeq technology to sequence mitochondrial transcripts from three fish (Ancistrus spp.) and assemble their mitogenomes. Based on the mtDNA sequence of a close related species, we estimate to have sequenced 92%, 95% and 99% of the mitogenomes. Taken the sequences together, we sequenced all the 13 protein-coding genes, two ribosomal RNAs, 22 tRNAs and the D-loop known in vertebrate mitogenomes. The use of transcriptomic data allowed the observation of the punctuation pattern of mtRNA maturation, to analyze the transcriptional profile, and to detect heteroplasmic sites. The assembly of mtDNA from transcriptomic data is complementary to other approaches and overcomes some limitations of traditional strategies for sequencing mitogenomes. Moreover, this approach is faster than traditional methods and allows a clear identification of genes, in particular for tRNAs and rRNAs.
Laboratório de Toxicologia Ambiental, DCB, Escola Nacional de Saúde Pública - ENSP, Fundação Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brasil.
Daniel A
DA
Moreira
Divisão de Genética, Instituto Nacional do Cancer - INCA, Rio de Janeiro, Brasil.
Carolina
C
Furtado
Laboratório de Toxicologia Ambiental, DCB, Escola Nacional de Saúde Pública - ENSP, Fundação Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brasil. Electronic address: parente@ensp.fiocruz.br.
Thiago E
TE
Parente
D000818:Animals; D005399:Fishes / Q000235:genetics*; D054629:Genome, Mitochondrial; D017421:Sequence Analysis / Q000379:methods*; D059467:Transcriptome
Biodiversity; Illumina; Mitochondrial transcripts; Mitogenome; RNA; Siluriformes; Transcriptome