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.

B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes

“…Enrichment analysis detected diverse GO terms for important biological roles such as metabolism, cell adhesions, reproduction, stimulus response, localization, morphogenesis and methylation. Genes with such functions were also reported to be located on B chromosomes in previous studies (see a comprehensive and updated list of B genes in the review by Ahmad and Martins [ 2 ] ). Among the B enriched functions, we found that most of them are involved in developmental processes, particularly morphogenesis.…”

“…B chromosomes (Bs) are additional and non-essential extra chromosomes, which show non-Mendelian inheritance and lack the ability of meiotic pairing unlike the normal A chromosomes [ 1 , 2 ]. The genomic characterization of Bs has remained elusive, since the discovery of Bs [ 3 ] about 112 years ago.…”

“…It is supposed that around 15% of eukaryotic species contain Bs [ 4 ], including animals, plants and fungi reported thus far [ 5 ], but several questions about their evolutionary origin and function remain unanswered. At first, Bs were presumed neutral or genetically inert elements of the genome, but later it was found that Bs may have either a detrimental or beneficial role (reviewed in Ahmad and Martins [ 2 ]). Bs have been found to decrease fertility in maize [ 6 , 7 ], whereas in extreme situations they may also reduce the genome fitness and eliminate all paternal chromosomes in the wasp Nasonia vitripennis [ 8 ], and can contain protein coding genes [ 9 , 10 ].…”

“…However, these techniques provide limited material and thus do not fully reveal the relationship of homologous sequences between A and B chromosomes and the complete gene content of Bs. During the last decade, next generation sequencing (NGS) technologies have substantially elevated B chromosome research into a new era of “B-omics” [ 2 ]. The multi-omics revolution has offered new opportunities to resolve the classical limitations of cytogenetics analyses.…”

Addressing Long-Standing Questions with Advanced Approaches: The 4th B Chromosome Conference

“…He presented a set of genes discovered in 2 species of Astyanax and in the grasshopper A. flavolineata . Furthermore, S. Ahmad reviewed a long list of previously reported B chromosome genes described in fungi, plants, insects, fish, and mammals [Ahmad and Martins, 2019]. The functional annotation demonstrates that Bs have accumulated copies of many genes involved in several important biological processes, including cell cycle control and chromosome formation.…”