Pipeline publication

[…] eadable. To address this issue, several primers based on the possible sequence deduced by the indefinite sequencing results of primers Dp21-F and Dp22-R were used. Fortunately, primer Dp23-F and its reverse complement primer Dp24-R, paired with Dp21-F and Dp22-R, respectively, were suitable for amplification and sequencing which allowed us to cover the remaining gaps., The partial mitogenome of Prioninae sp. (Coleoptera: Cerambycidae) is available in GenBank, so we used it as the reference sequence for mapping the amplified fragments of Do. paradoxus. The overlapping sequences were manually checked and assembled into a complete mitogenome via the alignment of neighboring fragments using the Clustal X program (Thompson et al. 1997). Protein-coding genes (PCGs) were identified by comparison with sequences from other Cerambycidae species. The 5ʹ ends of PCGs were assumed to be at the first legitimate in-frame start codon ATN in an open reading frame (ORF) that was not located within an upstream gene encoded on the same strand. A truncated stop codon (T or TA) adjacent to the beginning of the downstream gene was designated the termination codon (Wolstenholme 1992). The transfer RNA (tRNA) genes and their secondary structures were identified using the MITOS web server (Bernt et al. 2013). The large rRNA (lrRNA) gene was annotated to extend to the boundaries of the flanking tRNALeu(CUN) and tRNAVal. The 3ʹ end of the small rRNA (srRNA) gene was annotated to be adjacent to the start of tRNAVal, whereas the 5ʹ end was determined by comparing orthologous sequences of other known mitogenomes. The entire A+T-rich region was subjected to a search for the tandem repeats using Tandem Repeats Finder program (Benson 1999). Composition skew was used to describe the base composition of nucleotide sequences, with the relative number of As to Ts (AT skew = [A – T]/[A + T]) and Gs to Cs (GC skew = [G – C]/[G + C]) (Perna and Kocher 1995). Overlapping regions and intergenic spacers between genes were counted manually. Circular genome maps were generated by OrganellarGenomeDRAW (Lohse et al. 2013) and revised by hand. The sequence data were deposited in GenBank under accession MG460483., To reconstruct the phylogenetic relationships among Chrysomeloidae species, a total of 17 available Cerambycidea mitogenomes, including 13 Cerambycinae and 4 Chrysomelidae, were used (Table 1). The mitogenome of Spiniphilus spinicornis (Lin & Bi, 2011) (Coleoptera: Vesperidae), which belongs to Philinae of Vesperidae, was also included due to its association with Prioninae of Chrysomeloidae in their adult morphology (Nie et al. 2017). One neuropteran species, Polytoechotes punctatus (Fabricius) (Neuroptera: Polystoechotidae) (Beckenbach and Stewart 2009), served as an outgroup […]

Pipeline specifications

Software tools Clustal W, MITOS, TRF, Genome Maps, OGDRAW