Additional file 1 of Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish

Additional file 1: Table S1. Diversity of B chromosome in the Astyanax genus. 2n = diploid chromosome number. Bs = range of B chromosomes found in each population. a = acrocentric. m = metacentric. sm = submetacentric. st = subtelocentric. A. jordani and A. mexicanus can be considered synonymous, since both references analyzed the blind tetra fish [24, 25]. Table S2. Statistics of 21 B-linked genes in A. scabripinnis and A. paranae. Genomic fold change (gFC) was calculated as the log2(1B/0B) quotient between the mean nucleotide coverages along transcript length. HC = High coverage region. LC = Low coverage region. IC = Irregular Coverage. UC = Uniform Coverage. Figures in the “ind. gFC ≥ 0.585” column indicates the number of 1B A. scabripinnis individuals which met this condition. In the “qPCR” columns, 1 indicates validation of gene presence on the B chromosome. Table S3. Validation of B-linked genes by qPCR. Genomic fold change (gFC) was calculated as the log2(1B/0B) quotient between the mean nucleotide coverages along transcript length. IC = Irregular Coverage. UC = Uniform Coverage. CI = confidence interval. The blank spaces indicate experiments not performed. In the “Binary information” columns, 1 means qPCR validation. Asc = A. scabripinnis. Apa = A. paranae. Abo = A. bockmanni. Afa = A. fasciatus. Table S4. Counts of reference (Ref) and alternative (Alt = B-specific) variants in all gDNA and RNA libraries analyzed in A. scabripinnnis and A. paranae. Table S5. Nucleotide variation found in the B chromosome gene paralogs of A. scabripinnis. To score the number of variants, we distinguished between substitutions (s), deletions (d) or insertions (i) with respect to the A chromosome paralogs. We considered deletions and insertions as a single mutation event when they involved two or more consecutive nucleotides. dS = number of synonymous substitutions. dN = number of non-synonymous substitutions. ps = proportion of variable sites. Table S6. Gene expression profile and transcription intensity of B chromosomes. See Methods for details. Table S7. Localities, diploid chromosome number (2n) and number of samples (N) of the Astyanax individuals analyzed cytogenetically in this study. All populations harbor a large metacentric B chromosome. Table S8. Description of the materials analyzed by quantitative PCR. Table S9. Description of the Illumina-sequenced materials. Table S10. Primers designed in this study for PCR amplification of B-linked genes.