The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses

Abstract

Supernumerary B chromosomes (Bs) are extra karyotype units in addition to A chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. A classical concept based on cytogenetics and genetics is that Bs are selfish and abundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-born field that we call "B-omics". We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B chromosomes are enriched with genes for many significant biological functions, including but not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution.

Keywords: cytogenetics; evolution; genes; genome; next generation sequencing.

Figure 1

Occurrence of B chromosomes (Bs) in major eukaryotic groups. The bar chart shows the number of B carrier species for different categories, sourced from the B-chrom database [7] (http://www.bchrom.csic.es/). A representation of various commonly used model B carrier species, under the investigation of omics, is shown with karyotype data and information about the geography of research institutes. The revolution of omics-based techniques has gained remarkable attention of B chromosome biologist all over the word working with a huge range of species.

Figure 2

An overview of “B-omics” comprised of multi-omics technologies applied to ongoing research of B chromosomes.

Figure 3

A new model of B evolution. We propose an updated model to illustrate B origin and evolution. Initially, the evolutionary hotspots in multi-chromosomal genomic DNA undergo different events such as transposition, duplications and/or genomic rearrangements; which can be considered as principal evolutionary forces. These events cause the origin of “B precursor DNA” that becomes isolated from the A chromosomes by any genomic rearrangement. The B precursor DNA could contain B essential genes (for example histones, DNA binding and packaging proteins), which are expressed to form B chromatin and its reorganization followed by the accumulation of additional DNA including repeats and genes. This ultimately results in the formation of a nascent proto-B through a series of evolutionary events as depicted. See the topic 2: “Genome composition, origin and evolution of B”, for details.

Figure 4

Gene ontology (GO) enrichment analysis of B-linked genes reported in diverse species [25,44,48,79]. Enriched terms are shown as the bubble plot using human as reference database. Different colors of bubbles show the intensity of enrichment for labeled function based on the log10 of P values, ranging from dark blue with highest level of enrichment. The X and Y axis do not have any intrinsic meaning.

Figure 5

NGS based methods for identification of B-linked genes. (a) A Summary of comparative genomics of samples with B chromosomes (B+) and without B chromosome (B-) steps for identification of putative sequences on B. (b) Genomics analysis of microdissected/flow sorted B.

Figure 6

An illustration of a combination of different technologies applied to achieve an accurate and error free assembly of B chromosomes. Long PacBio and Nanopore sequencing reads are generated for the B+ sample. The long reads are assembled producing a mixture of A chromosome and B-linked scaffolds. To separate the B-linked scaffolds from the rest of genome, Illumina short B- and B+ reads are mapped to this assembly. The mapped reads are counted for each scaffold and a coverage ratio for both B- and B+ is calculated. The B-linked scaffolds are isolated with the higher coverage of B+ than B- reads. Then, Hi-C libraries are created for B+ sample and mapped against the identified B-linked scaffolds. The scaffolds are merged into a single molecule now called the B-assembled chromosome utilizing the order and orientation information from Hi-C data. The BioNano assembly of B+ sample is performed and the hybrid maps are generated from the BioNano scaffolds and the B-assembled chromosome. The B chromosome assembly is validated by alignments of bacterial artificial chromosome (BAC) clone sequences and physical chromosome mapping confirmation based on the use of BAC clones as FISH probes. This step involves the process of identifying and correcting the errors with BAC clones spanning scaffolded B chromosome. The illustrated proposed methodology has been successfully applied to sex chromosome assembly. For more details refer to the methodology section of the article Mahajan et al. [112].

Figure 7

Evolutionary fate of the B in the light of gene evolution. After the B chromosome polymorphism appears, certain genes in A genomes suppress the B parasitic genes that are required for the drive of B during cell cycle transmission. These A genes neutralize the harmfulness of the parasitic drive by switching off the B genes because of mutations induced during their evolution. This mechanism might output three different possibilities: (1) B genes might not experience any mutations and remain switched off due to which the drive is completely lost resulting in the B extinction; (2) the B parasitic genes undergo some mutations to escape from neutralization effects and thus regain their functions so that drive is maintained leading to the regeneration of the B; or (3) both parasitic and useful genes present on B might experience mutations so that parasitic genes regain their function and ensure the regeneration of the B while useful genes might also be expressed, resulting in the formation of a new phenotype. The third scenario is evidenced from the B-linked genes found in fungi (see review, [36]), in which these genes might encounter selection to useful phenotype. This is achieved as a result of compartmentalization of the genome into core and accessories parts where the later part can serve as extra material for adaptive evolution.