- 1 Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, SP Brazil Full list of author information is available at the end of the article. - The cytogenetics characterization of the blind cavefish revealed a karyo- type comprising 2n = 50 chromosomes with 1 or 2 microBs [20]. - However, no study has presented deeper genomic view of the B gene content and therefore analysis is required to reveal the genomic contents and understand B chromosome biology of this organism.. - Similarly, a comprehensive genomic analysis of the B chromosome in the cichlid fish, Astatotilapia latifasciata discovery that the B comprises of thousands of fragmented genes as well as potentially transcriptional active intact genes [36]. - Later, evidence was found that the Bs of the grass- hopper, Eyprepocnemis plorans, harbor at least ten genes, among which five genes are expressed [37]. - Here, we se- quenced and analyzed the B carrier genomes of the in- sect A. - Out of the 39 karyotyped individuals, 12 were ‘B+ males’, 8 ‘B- males’. - The karyotype analyses of the grasshopper A. - The X-axis and Y-axis represent read depth and genomic position of the B- block. - These regions having remark- ably higher coverage, called B blocks, were detected in the genomes of each of the three model species (Fig. - We also performed de novo assembly of the genomes for A. - Genomic characterization of the B chromosome uncovers its gene contents with diverse functions. - A list of the B-blocks with sequence length of at-least 200 bp or more is listed as Supplementary dataset (Supplementary dataset 1). - The mapping of the Illumina reads from the B- and B+ genomes on the coding sequences (CDS) of tran- scriptomes revealed a total of 38,071 reads for A. - Graphical repre- sentation of the B- and B+ showed the presence of CDSs over-represented in the B+ genomes (Fig. - the expected value if each B chromosome carried at least one copy of the CDS (see methods). - EIF4G1 Recognition of the mRNA cap Mitochondrion organization. - Some of the CDS did not align to the references, therefore we termed them as non- annotated or unknown. - To reveal the unique sequences found on the B chromo- somes, we first performed de novo assemblies of the B+. - Meics Nucleation of microtubules Spindle Assembly and Chromosome Segregation FBtr0304801 Mini spindles, isoform D msps Nucleation of microtubules Integrity of the Mitotic. - Catalyzes the rewinding of the stably unwound DNA. - In addition, fluorescence in-situ hybridization (FISH) of the two selected B-blocks further confirmed their abundance on the micro B (Fig. - flavolineata using the number of mapped reads that map to the CDSs found in the transcriptome of the 0B (X axis) and 2B (Y axis). - Therefore, we took advantage of the available bi-sulphite sequencing data in. - NCBI/SRA database of the cavefish to call methylation of the B chromosome sequences. - To analyze the methy- lation level of the micro B sequences in the cavefish gen- ome, we mapped the bi-sulphite treated reads to the B- blocks, which were sequenced previously by Gore et al.. - The Bismark mapping of bisulphite Illumina reads to the B blocks of the cavefish yielded a total of methylation call strings with a total of 32% mapping efficiency. - 4 Comparative plots of the exclusive sequences detected on the Bs of (a) A. - The mean coverage plots (left) of all exclusive blocks show the fraction of the genome with respective coverage. - However, we identified eight sites of rDNA clusters on the A chromosomes, with a preferential distribution to terminal portion of the short arms of resident chromosomes.. - 7 III, circos plot), which represent a majority of the B chromosome sequences. - assembly of the cavefish genome was mapped with the re- peat masked assembly representing only coding sequences to reveal the synteny patterns (Supplementary Fig. - We further traced the B associated patterns indicative of duplication and inversions through self-aligned syn- tenic dotplot analysis generated from the comparative analysis of B blocks of the three species (Fig. - syntenic dotplot shows that there is an overlap of the lines when the lines are projected to one axis or the other. - Interestingly, the GO enrichment analysis of the Bs in different organisms shared some common over represented functions such as metabolism, development and morphogenesis (Fig. - These results highlight the importance of genes associated with these functions in the evolutionary survival of the B inside the cell.. - We found that at least 246 Kb and 58 Kb of unique se- quences are exclusive of the Bs in A. - These NGS results are parallel to the size of the corresponding macro and micro Bs as were observed in their karyotypes, demonstrating that the coverage- based approach was successful in deciphering a consid- erable amount of sequences on the Bs. - To perform a deep survey of DNA repeats, we applied a combination of approaches to predict major TEs and their abundance in the genomes and to perform compar- isons of the B+ and B- repeat content. - We highlighted the major repetitive contents of the Bs and our analysis identified TEs, including retroelements, of the B chromosomes of multiple species. - Several stud- ies have previously found that Bs are generally enriched with TEs suggesting that TEs are the principal migrants of the Bs that may be key players in the insertion of other sequences from As into B chromo- somes during evolution. - In addition to the fragmented genes, there are complete genes that have remained intact, possibly due to their role in the evolutionary survival of the B chromosome. - Remarkably, the GO enrichment analyses of dif- ferent micro dissected Bs in different species revealed similar patterns of functions, thus providing evidence to corroborate the emerging hypothesis that the evolutionary success of the B chromosome lies on its gene contents.. - mexicanus, revealing male- specificity of the B chromosome, also point towards this phenomenon that the presence of Bs may have some role to determine the sex in Astyanax [64].. - However the similarity of few weak hits to mito- chondrial genes shows that such sequences sourced from mitochondria, might have been inserted into B of the A. - Most (more than 90%) of the exclusive B chromosome sequences of Astyanax were characterized as novel and unknown genes as well as some long non-coding RNA sequences.. - The epigenomic profiles of the microB in the cavefish genome provide a rough view of the methylation status of B chromosome sequences. - Although our data analysis supports that most of the B chromosome sequences in the cavefish are likely methylated mainly within CpG re- gions, it still remains to be seen whether there is any methylation based repression of any gene and whether these epigenetic changes might have any phenotypic variability effect. - Taken to- gether our analysis, suggest that DNA methylation of B chromosome sequences might be one of the principal mechanisms to mediate the repression of many B-. - The rearrangements analysis of the B- versus B+ ge- nomes suggests that the cavefish genome exhibits exten- sive rearrangements that might have shaped its extra- ordinary evolution for adaptation. - Moreover, the com- parison of the B blocks to their ancestral A genome re- gions allowed us to infer the evolutionary mechanism that led to Bs. - The different sizes of the B blocks ranging from few hundred to thousands bp indicate that the larger regions might have migrated to Bs after the formation of a proto B. - While we predict most of the fragments are pseudogenes, fur- ther analysis of transcription levels will assist in under- standing exact structure and function of these gene fragments. - An overview of the methodology is illustrated in Supple- mentary Fig. - correntinus were collected from its natural habitat in the Iguaçu River, in the stretch with around 25 km be- tween downstream of the Iguaçu Falls and its mouth on. - To create assembly references of genomes containing B chromosomes, we assembled the Illumina reads of the B+ samples for A. - We performed several trial runs of the assembly and chose. - The evaluation of the de novo assemblies was obtained using QUAST software [75] by computing several metric values (length, number, length variation, N50, gap length). - The sites with at least 15× reads coverage in B+ and B- genomes were selected, and the per-base coverage of the B+ and B- genomes were investigated using bedtools [76] to measure the mean B+/B- coverage ratio (MC). - These references were selected on the basis of the complete representation of genes and high-quality chromosome level assembly. - The identity percentage was calculated comparing the length of identified genes on Bs versus the total corresponding gene length in the annotation of the reference genomes. - The integ- rity percentage of each B-gene was calculated comparing its length to the corresponding gene length in the anno- tation of the reference genomes. - The dissociation curve was observed to confirm the specific amplification of the PCR products.. - The microscopic examination of the slides was done in an Olympus BX61 optical microscope.. - The microdissected B chromosome assemblies were per- formed on the basis of the pseudo-scaffolding strategy as proposed by Vij et al. - First we retrieved the list of B chromosome genes for each species from the Blastn output with the best BLAST hit having at least 200 base pairs of the query sequences overlapped with respective reference gene. - We then downloaded a complete annotation database of all genes of the refer- ence species from Ensembl. - Epigenomics profiling of the B chromosome in A.. - The methylation status of the micro-B sequences in A.. - First the fasta sequences of the B-blocks of A. - In the third step, methylation information was extracted from alignment output by running methy- lation extractor of the Bismark software.. - We filtered the alignments with the “delta filter” script of the MUMer and the output filtered files were parsed in the tab delimited files with the “show coords” tool.. - To reveal the homology of the B chromosome sequences of A.. - For this analysis we chose the largest blocks with size greater than 2 kb and did a comparison using using CoGE Syn- Map [96] to identify the evolutionary genomic patterns of the B chromosome. - Identification of protein-coding genes located in B chromosomes of the A. - Each plot compares the reads depth of the transcript between 0B and 2B. - Each plot compares the reads depth of the transcript between 0B and 1B. - Each plot com- pares the reads depth of the transcripts between 0B and 2B. - Genes integrity percentage of the B blocks of A. - Fasta sequences of the B blocks (A. - Fasta se- quences of the B blocks (A. - The funding body did not contribute to the design of the study or collection, analysis and interpretation of data and writing the manuscript.. - The sequencing reads of the B- and B+ samples of A.. - A contribution to the hypothesis of the genetic continuity of chromosomes. - The evolution of the genome. - Genetic characteristics of the B chromosomes in maize.. - Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus). - (Characiformes, Characidae) collected in middle Paraná river, Iguassu National Park: considerations on taxonomy and systematics of the genus.. - It ’ s a wonderful hypogean life: a guide to the troglomorphic fishes of the world. - Chromosomal mapping of repetitive DNAs in the grasshopper Abracris flavolineata reveal possible ancestry of the B chromosome and H3 histone spreading. - B chromosomes of the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray) contain inactive NOR-like sequences. - Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. - The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. - Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. - Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. - DNA content of the B chromosomes in grasshopper Podisma kanoi Storozh. - Landscape of transposable elements focusing on the B chromosome of the cichlid fish Astatotilapia latifasciata. - De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B. - chromosomes of the grasshopper Eyprepocnemis plorans. - Correction: chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt