A novel approach to assemble the complex B chromosome using a combination of modern genomics technologies
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Universidade Estadual Paulista (Unesp)
B chromosomes (Bs) are nonvital extra chromosomes found in diverse eukaryotic species including fungi, plants and animals. Among hundreds of investigated species, cichlid genomes offer fascinating models for studying B chromosome biology. Despite the extensive investigations, Bs are poorly understood mainly in relation to mechanisms of their own evolutionary survival as well as their structural and functional impact on genome organization. Our previous studies identified several sequences (genes and repeats) on the B of the cichlid fish Astatotilapia latifasciata but the complete genomic map of B chromosome has been missing. Here, we generated a chromosome- scale A. latifasciata genome with the B chromosome assembly by adopting integrative approach that combined deep coverage Pacific Biosciences single-molecule real-time (Pacbio long reads), high-throughput chromatin conformation capture (Hi-C) mapping, and Illumina (short-reads) sequencing. The assembled genome spans a total of 0.93 giga base pairs (Gb) genome with contig and scaffold N50 values of 3.4 and 36.2 mega base pairs (Mb) respectively. Compared with our previous Illumina based assembly, this upgraded genome is much more complete, and accurate. The annotation of core eukaryotic genes and universal single-copy orthologs has also been significantly improved and a total 150 Mb region has now been recovered, which was missing (in the previous assembly). We identified 759 protein-coding genes in the 34 Mb genomic content of B chromosome, of which at most of the genes showed a reduced level of expression as compared to A chromosomes. Our results demonstrate a substantial higher amount of transposable elements (TEs) mainly long terminal repeats (LTRs) retrotransposons (mean density 47.6) on the B chromosome as compared to the standard A chromosome set (mean density 10.45). We further applied whole- genome chromosome conformation capture (Hi-C) and in silico modeling methods to characterize the three dimensional (3D) architecture of and A and B chromosomes in the A. latifasciata genome. Remarkably, we observed a differential level organization of the chromatin into topologically associated domains (TADs) between 0B and 1B genomes. On a global level, the Hi-C interaction matrices of 1B genome are characterized by a relative gain of long-range and loss of short-range interactions within chromosomes indicating the impact of B chromosome on three-dimensional landscape of genome. Additionally, comparative analysis of A. latifasciata genome with othercichlids genomes enabled us to detect the phylogenomic diversification and chromosomal rearrangements including fusions and inversions providing interesting insights in co-ancestral cichlids gene evolution.
Cichlid genome, Supernumerary chromosome, Hi-C, 3D genome, Genes evolution