Computational protocol: Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes

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Protocol publication

[…] Sequenced fragments were assembled to create complete mitochondrial genomes using CodonCode Aligner v3 and BioEdit v7 []. During the processing of large fragments and walking sequences, regular manual examinations were made to ensure reliable assembly of the genome sequence. Annotation and boundary determination of protein-coding and ribosomal RNA genes were performed using NCBI-BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Transfer RNA genes and their secondary structures were identified using tRNAscan-SE 1.21 [], setting the cut-off values to 1 when necessary. The gene maps of each of the four flatfish mitogenomes were generated using CGView []. Mitogenomes of eight other Pleuronectoidea fishes were retrieved from GenBank (Additional file : Table S2), including one Scophthalmidae specimen, Scophthalmus maxima (S. max); one Paralichthyidae fish, Paralichthys olivaceus (P. oli); and the other six Pleuronectidae fishes: Kareius bicoloratus, Verasper variegatus (V. var), Verasper moseri (V. mos), Hippoglossus hippoglossus (H. hip), Hippoglossus stenolepis (H. ste), and Reinhardtius hippoglossoides (R. hip). […]

Pipeline specifications

Software tools CodonCode Aligner, BioEdit, BLASTN, tRNAscan-SE, CGView
Applications Genome annotation, Genome data visualization
Organisms Crossorhombus azureus, Pleuronichthys cornutus, Platichthys stellatus