Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Article Title: Comparative analyses of the major royal jelly protein gene cluster in three Apis species with long amplicon sequencing
Figure Lengend Snippet: Graphical presentation of the data analysis pipeline. 2D raw reads (1) were size-selected (minimum read length of 6.5 kb) (2) and mapped against the three reference genomes, in order to assign the reads by species and genomic target (3). Only those reads that matched our quality filters (similarity fraction: 0.6 [0.5 for adAmp3, 6 and 7], length fraction: 0.7 [0.5 for adAmp3, 6 and 7]) were included in further analyses (4). Per amplicon sixteen reads (minimum number of reads that mapped to an amplicon—amAmp6) were selected and aligned to each other independent of a reference sequence to build the nanopore-derived consensus sequence (5). Finally, the consensus sequence and the reference sequence were aligned (6). In order to correct the genomic reference sequences of the mrjp gene cluster of A. mellifera , A. florea and A. dorsata , assembly gaps (N) and local mis-assemblies were identified based on this consensus/reference sequence alignment. Assembly gaps (N) in the reference sequence were replaced with the consensus sequence and mis-assemblies were either discarded (when only present in the reference but not in the consensus sequence) or included (when only present in the consensus but not in the reference sequence).
Article Snippet: Sequencing Long-amplicon sequencing was performed with MinION (Oxford Nanopore Technologies Ltd)—a nanopore-based sequencing technology capable of producing read length s of up to 200 kb , , facilitating continuous sequencing across the entire mrjp cluster region.
Techniques: Amplification, Sequencing, Derivative Assay