Interpopulation variation in the satellite DNA from grasshoppers with B-chromosomes

Transcribing the enigma: the B chromosome as a territory of uncharted RNAs

B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.

Satellite DNA Is an Inseparable Fellow Traveler of B Chromosomes

Next-Generation Sequencing (NGS) has revealed that B chromosomes in several species are enriched in repetitive DNA, mostly satellite DNA (satDNA). This raises the question of whether satDNA is important to B chromosomes for functional reasons or else its abundance on Bs is simply a consequence of properties of B chromosomes such as their dispensability and late replication. Here we review current knowledge in this respect and contextualize it within the frame of practical difficulties to perform this kind of research, the most important being the absence of good full genome sequencing for B-carrying species, which is an essential requisite to ascertain the intragenomic origin of B chromosomes. Our review analysis on 16 species revealed that 38% of them showed B-specific satDNAs whereas only one of them (6%) carried an inter-specifically originated B chromosome. This shows that B-specific satDNA families can eventually evolve in intraspecifically arisen B chromosomes. Finally, the possibility of satDNA accumulation on B chromosomes for functional reasons is exemplified by B chromosomes in rye, as they contain B-specific satDNAs which are transcribed and occupy chromosome locations where they might facilitate the kind of drive shown by this B chromosome during pollen grain mitosis.

Satellite DNA and heterochromatin variants: the case for unequal mitotic crossing over

Variations of constitutive heterochromatin (heteromorphisms) appear to be a general feature of eucaryotes. A variety of molecular and cytogenetic evidence supports the hypothesis that heteromorphisms result from unequal double-strand exchanges during mitotic DNA replication. Constitutive heterochromatin consists of highly repeated DNA sequences that are not transcribed. Thus, heteromorphisms are tolerated without overt phenotypic effect. Several of the highly repeated DNAs that comprise constitutive heterochromatin have been shown to contain site-specific endonuclease recognition sequences interspersed at regular intervals dependent upon nucleosome structure. These interspersed short repeated sequences could mediate unequal crossovers, resulting in quantitative variability of constitutive heterochromatin and satellite DNA. De novo variations of constitutive heterochromatin may be useful as markers of exposure to mutagens and/or carcinogens.

The DNAs of the A and B chromosomes of the mealy bug, Pseudococcus obscurus

When the DNA of mealy bugs carrying B chromosomes (+B:DNA( was compared to the DNA of individuals not possessing Bs (-B:DNA), no significant differences were found using isopycnic centrifugations in CsCl or thermal denaturation analyses. Both DNAs had buoyant densities of 1.693 g/cm3 in neutral CsCl gradients and 1.748 g/cm3 in alkaline CsCl gradients. Satellite DNAs were not detected. The average Tm of +B:DNA was 67.9 degrees C in 0.1 SSC while -B:DNA had an average Tm of 67.4 degrees C in the same solution. However, in situ molecular hybridizations with complementary RNAs (cRNAs) transcribed in vitro from each type of DNA showed considerable differences with regard to the amount of labeling of B chromosomes. Using cRNA to +B:DNA, the average number of silver grains over a B chromosome was 2.1 X the average number of silver grains over individual non-B chromosomes (A chromosomes). In contrast, the ratio (B/A) using cRNA to -B:DNA was less than 0.14. The results are interpreted as meaning that very little DNA is shared in common by both A and B chromosomes.

Telomeric satellite DNA functions in regulating recombination

Molecular and cytogenetical analyses of three sibling species of Australian grasshopper, Atractomorpha australis, A. species-1 and A. similis, resolves one of the long standing problems of highly repeated DNA. In this system satellite DNA functions in regulating the level and position of recombination, irrespective of whether the repeated DNA is located in telomeric or centric regions. Even though the three species do not differ in their euchromatic genome sizes, their relative DNA contents are 1.00/1.10/1.41, the difference in genome size being due solely to visible centric or telomeric blocks of heterochromatin. Antibiotic analytical and preparative ultracentrifugation, in situ hybridization and renaturation kinetic analyses reveal that a large cryptic satellite of A. similis constitutes the heterochromatic telomeric blocks of nearly all autosomes and that the DNA of this satellite is highly repeated. Comparison of these grasshopper data with published literature of heterochromatic rearrangements in Drosophila and with heterochromatin distribution and recombination patterns in diploid plant species reveals that in every case heterochromatin is implicated in some form of alteration in the meiotic recombination system.

Population cytology of the genus Phaulacridium

Ten of the 27 populations of Phaulacridium marginale collected from South Island, New Zealand, during the 1973 meiotic season were polymorphic for extra heterochromatin. This was present either as B chromosomes or as super-numerary segments on the shortest autosomes. In some populations both polymorphisms were present simultaneously, sometimes at high frequencies. Three different types of B chromosome were seen; large telocentric, small telocentric and small metacentric isochromosomes though only one type was seen in any one population. Segments on the telocentric S9 and S10 chromosomes were located distally. On the S11 chromosome, however, the extra segment was present as a short arm, thus making the chromosome submetacentric. This latter situation is similar to that in the related species Ph vittatum. The frequency of B's in the OM population appeared to be stable over years and there was no indication of any meiotic "drive" or "drag" in the males. The frequency of occurrence of B chromosomes in a population correlated negatively with annual rainfall (low B frequencies in regions of high rainfall). Neither type of extra heterochromatin had any significant effect on either mean cell chiasma frequency or on log variance of this metric. Possible synergism between B's and segments is discussed from the preliminary analysis of the OM population. The probable origins and age of the polymorphisms are discussed in detail.