2020 Volume 89 Issue 1 Pages 1_001-1_007
We have developed an application to select Bombyx mori orthologs from assembled RNA sequencing (RNA-seq) data in species of interest. The application, BmTOP (Bombyx mori tool for ortholog picking) is composed of 6 steps, 1) tblastx analysis using B. mori gene models 2017, 2) alignment of the first hit and assignment of the B. mori gene data, 3) elimination of multi-copy genes in species of interest, 4) elimination of data by less than a score and/or more than an expect value (e-value), 5) elimination of data when value of first hit divided by second hit is not less than a threshold, and 6) comparison with B. mori single-copy gene list to exclude B. mori multi-copy genes. As default, e-value not more than 1e−10 is set at Step 1, score 100 and e-value 1e−80 at Step 4, and result of calculation 1e−80 at Step 5. We subjected the newly read Colias erate RNA-seq data that carry 64,764 contigs with an N50 of 1,357 bp to BmTOP analysis. BmTOP selected 1,978 C. erate contigs as B. mori single-copy gene orthologs. The in-silico mapping of the orthologs covers all 28 B. mori chromosomes. The results are promising for successful primer design to select bacterial artificial chromosomes containing orthologs for gene-based comparative mapping using fluorescence in situ hybridization.
