Computational protocol: The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Similar protocols

Protocol publication

[…] We used a Pacific Biosciences RSII sequencer to sequence the mitogenomes of the three Callosobruchus species, employing the SMRT-analysis HGAP3 pipeline for assembly, and a Pacific Biosciences Sequel sequencer to sequence the mitogenome of A. obtectus, using the SMRT-analysis HGAP4 pipeline for assembly. The mitogenomes were annotated using DOGMA () and MITOS (). An Illumina HiSeq2500 platform (v4 sequencing chemistry) was used for the resequencing of the three C. maculatus populations which were assembled using MITObim V 1.8 () and MIRA V 4.0.2 (). The RNA sequencing involved standard RNA extraction and library preparation protocols followed by Illumina HiSeq2500 sequencing, described in detail in and ( online). […]

Pipeline specifications

Software tools HGAP, DOGMA, MITOS, MITObim
Applications Genome annotation, RNA-seq analysis
Chemicals Fatty Acids, NAD