Fig. 3

Detection of protein-coding genes residing in the B chromosomes of Astyanax scabripinnis and A. paranae. a Detection of protein-coding genes in the B chromosome of Astyanax scabripinnis by mapping gDNA Illumina reads obtained from three B-carrying (1B) and three B-lacking (0B) individuals on a de novo transcriptome built with Illumina reads coming from ovary RNA libraries from two individuals. Scatter plot showing the mean copy number for 47,216 CDSs in 0B and 1B females. The CDSs which, in presence of one B chromosome, showed a genomic fold change [gFC = log₂(1B/0B)] higher than 0.585 in the three B-carrying individuals (431 contigs in total, see Supplementary Table 11) are shown in light red color, and those failing to reach this threshold are noted in gray color. In addition, the 21 protein-coding genes which were validated by qPCR in A. scabripinnis and A. paranae are noted in dark red color for the contig showing the highest gFC value. b Distribution of coverage in copy numbers for CDSs in 1B and 0B individual in A. paranae. Light red indicates the 2019 out of 32,830 CDSs with gFC in A. paranae higher than 0.585 and dark red indicated the 21 genes validated with qPCR. Note that only bt1a1 and ccnd3 genes do not meet the gFC criteria, but bt1a1 was validated in these species using PCR. c Protein-coding gene content of the B chromosomes is highly similar among species. The figure shows the comparison of gFC values between A. scabripinnis and A. paranae for the CDS meeting the copy number criteria in A. scabripinnis 0B individuals. The gFC values found for the 21 B chromosome genes found in both species were positively correlated (Spearman rank correlation: rs = 0.27, t = 3.11, P = 0.002). Color patterns coincide with those in panel a