Additional file 3 of B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes
Creators: name: Ahmad, Syed F.
name: Jehangir, Maryam
name: Adauto L. Cardoso
name: Wolf, Ivan R.
name: Margarido, Vladimir P.
name: Cabral-De-Mello, Diogo C.
name: O’Neill, Rachel
name: Valente, Guilherme T.
name: Martins, Cesar
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 3: Figure S1. A workflow of steps applied in the present study during the procedure of genomics analyses of B chromosomes in different species. Figure S2. Coverage plots of B-blocks of A. correntinus with remarkable difference in the reads coverage between 0B and 1B samples. Figure S3. Coverage plots of B-blocks of A. flavolineata with remarkable difference in the reads coverage between 0B and 2B samples. Figure S4. Identification of B chromosome genomic blocks (A) and their repeats contents (B) in A. flavolineata. Figure S5. Identification of protein-coding genes located in B chromosomes of the A. mexicanus, using the number of mapped reads that map to the CDSs found in the transcriptome, in the 0B (X axis) and 2B (Y axis). Each dot represents a coding sequence with only those labeled that recorded the log2 greater than 1.5. The plot is limited for 800 mapped reads to optimize the visualizations. Figure S6. Identification of protein-coding genes located in B chromosomes of the A. correntinus, using the number of mapped reads that map to the CDSs found in the transcriptome, in the 0B (X axis) and 1B (Y axis). Each dot represents a coding sequence with only those labeled that recorded the log2 greater than 1. The plot is limited for 800 mapped reads to optimize the visualizations. Figure S7. Coverage plots of (representative) coding sequences detected on the B chromosome of A. mexicanus using Log base 2 ratio. Each plot compares the reads depth of the transcript between 0B and 2B. Figure S8. Coverage plots of (representative) coding sequences detected on the B chromosome of A. correntinus using Log base 2 ratio. Each plot compares the reads depth of the transcript between 0B and 1B. Figure S9. Coverage plots of (representative) coding sequences detected on the B chromosome of A. flavolineata using Log base 2 ratio. Each plot compares the reads depth of the transcripts between 0B and 2B. Figure S10. Double FISH mapping of candidate blocks in A. flavolineata. Each panel represents mapping of two distinct blocks (7 and 14 – See Supplementary Table S2) labeled with digoxigenin (block 7 in red) and biotin (block 14 in green). A scattered pattern of markings of block 7 can be observed for the B chromosomes (white arrows), whereas telomeric and centromeric associated signals of blocks 7 and 14 are obvious for different A and X chromosomes. Figure S11. The methylation profile of microB blocks in A. mexicanus. (A) Graph shows the number of Bisulphite reads analyzed with B blocks and alignments. (B) Pie chart represents percentage of B block methylated Cs in different contexts with the highest percent in CpGs regions. (C) Pie chart highlights the number of hypomethylated (less than 50% methylated Cs), unmethylated, highly methylated and hypermethylated (more than 90% methylated Cs) B chromosome blocks. (D) Bisuphite coverage plots of hypermethylated blocks are shown as examples. Refer to Supplementary datasets (excel) for a complete list of methylated blocks with methylation level. Figure S12. FISH mapping of 45S rDNA (red labeling) in A. mexicanus. The micro B is indicated with an arrow showing no sign of 45S rDNA. Figure S13. Synteny dotplot of whole genome aligments between de novo B+ assembly and reference masked (coding) genome of A. mexicanus. Figure S14. Violin plots show the distribution of length for various types of genomic rearrangements from 0 to 5000 bp range. Figure S15. Synteny dotplot (synmap version, unfiltered) of self alignments of B blocks (A. mexicanus). Figure S16. Synteny dotplot (synmap version, unfiltered) of self alignments of B blocks (A. correntinus). Figure S17. Synteny dotplot (synmap version, unfiltered) of self alignments of B blocks (A. flavolineata).