Chromosomes with a life of their own

B chromosomes (Bs) can be described as 'passengers in the genome', a term that has been used for the repetitive DNA which comprises the bulk of the genome in large genome species, except that Bs have a life of their own as independent chromosomes. As with retrotransposons they can accumulate in number, but in this case by various processes of mitotic or meiotic drive, based on their own autonomous ways of using spindles, especially in the gametophyte phase of the life cycle of flowering plants. This selfish property of drive ensures their survival and spread in natural populations, even against a gradient of harmful effects on the host plant phenotype. Bs are inhabitants of the nucleus and they are subject to control by 'genes' in the A chromosome (As) complement. This interaction with the As, together with the balance between drive and harmful effects makes a dynamic system in the life of a B chromosome, notwithstanding the fact that we are only now beginning to unravel the story in a few favoured species. In this review we concentrate mainly on recent developments in the Bs of rye and maize, two of the species currently receiving most attention. We focus on their population dynamics and on the molecular basis of their structural organisation and mechanisms of drive, as well as on their mode of origin and potential applications in plant biotechnology.     

A Century of B Chromosomes in Plants: So What?

BACKGROUND: Supernumerary B chromosomes (Bs) are a major source of intraspecific variation in nuclear DNA amounts in numerous species of plants. They favour large genomes, and create polymorphisms for DNA variation in natural populations. By studying Bs we can gain useful knowledge about the organization, function and evolution of genomes. There are also significant biological questions concerning the origin and structural organization of Bs, and the way in which these selfish elements can establish themselves by exploiting the replicative machinery of their host genome nucleus. SCOPE: It is a sine qua non that Bs originate from the A chromosomes, in a variety of ways. We can study their modes of drive and ask how it is that chromosomes which apparently lack genes can have control over their own drive process which leads to their survival in natural populations. Molecular cytogenetic studies are opening up new avenues of investigation. Population equilibria for B frequencies are determined by a balance between accumulation and harmful effects. Bs are also subject to meiotic loss due to polysomy and to elimination at meiosis as univalents. These balancing forces can be seen in the context of host/parasite interaction, based on a dissection of the genetic elements in both As and Bs (in maize) which interact to bring about a stable equilibrium, at least for a snapshot in time. CONCLUSIONS: Aside from their intrinsic enigmatic properties, B chromosomes make useful experimental tools to study genome organization. Thus far they have not been exploited for their applications, other than through the use of A-B translocations used for gene mapping in maize; but there are opportunities to use them to modulate the frequency and distribution of recombination, to diploidize allopolyploids, to study centromeres and to be developed as plant artificial chromosomes; given that they can be structurally modified and their inheritance stabilized.     

Nature and evolution of B chromosomes in plants: A non-coding but information-rich part of plant genomes

This work reviews recent advances providing insights on the origin and evolution of B chromosomes (Bs) in representative plant species. Brachyome dichromosomatica has large and micro Bs. Both carry an inactive ribosomal gene cluster. The large Bs contain the B-specific Bd49 family, mainly located at the centromere. Multiple copies are present in the A chromosomes (As) of related species, whereas only a few copies exist in B. dichromosomatica As. The micro Bs share sequences with the As, the large Bs and have the B-specific repeats Bdm29 and Bdm54. It seems that the large and micro Bs are related in origin. It is very unlikely that the Bs originated by simple excision from the As. Rye Bs are composed of sequences predominantly shared with the As. B-specific sequences are located at the heterochromatic end of the long arm. Probably, they originated from the As after many rearrangements, with a tendency for duplication. The E3900 family derives from a Ty3 gypsy retrotransposon, but the D1100 family shows no evidence of genic origin. The overall composition of maize As and Bs is similar suggesting a common origin. Several B-specific sequences have been found, the most studied being pZmBs, which is located at the B centromere. It shows partial homology to the centromere of chromosome 4 and to the knobs. It is not known whether the B centromere derives from centromere 4, or whether both have a more distant common origin. The dynamics of Bs in populations depends on their non-Mendelian mechanisms of transmission, their effects on carrier fitness and on A genes modulating their parasitic properties. Three representative examples are reviewed. The Bs of Allium schoenoprassum are transmitted at a mean lower than Mendelian and adversely affect vigour and fertility. However, there is a differential selection operating in favour of B-containing seedlings. Rye Bs undergo strong drive, which is counteracted by harmful effects on fertility and instabilities at meiosis. Both nondisjunction and meiotic behaviour, and consequently the establishment of B polymorphisms, mainly depend on the Bs themselves. B nondisjunction in maize is controlled by the B, but the As control preferential fertilisation. Considering the non-equilibrium model, the Bs of Allium seem to have been neutralised by the A genome, the As of maize provide defence against B attack, whereas the Bs of rye are only slightly neutralized.     

B chromosomes and genome size in flowering plants.

B chromosomes are extra chromosomes found in some, but not all, individuals within a species, often maintained by giving themselves an advantage in transmission, i.e. they drive. Here we show that the presence of B chromosomes correlates to and varies strongly and positively with total genome size (excluding the Bs and corrected for ploidy) both at a global level and via a comparison of independent taxonomic contrasts. B chromosomes are largely absent from species with small genomes; however, species with large genomes are studied more frequently than species with small genomes and Bs are more likely to be reported in well-studied species. We controlled for intensity of study using logistic regression. This regression analysis also included effects of degree of outbreeding, which is positively associated with Bs and genome size, and chromosome number, which is negatively associated with Bs and genome size, as well as variable ploidy (more than one ploidy level in a species). Genome size, breeding system and chromosome number all contribute independently to the distribution of B chromosomes, while variable ploidy does not have a significant effect. The genome size correlates are consistent with reduced selection against extra DNA in species with large genomes and with increased generation of B sequences from large A genomes.     

B染色体起源的研究进展

B染色体(简写为Bs)起源的传统观点是认为它起源于携带者所在物种的基因组.目前又发现了许多新的证据来推测Bs的起源.它可能具有两种起源:种内起源和种间起源(起源于另一物种的基因组),且有证据表明同一物种的Bs可能是多次起源,同时对Bs的起源机制也作了总结.认为B8起源的研究已取得了一定的进展,但要给Bs起源下一个确切的结论仍需要大量的实验证据.     

Prevalence of B chromosomes in Orthoptera is associated with shape and number of A chromosomes

We analyze the prevalence of B chromosomes in 1,601 species of orthopteran insects where chromosome number and shape are known. B chromosomes have been reported in 191 of these species. Bs are not uniformly distributed among orthopteran superfamilies, with evident hotspots in the Pyrgomorphoidea (32.3% of species carrying Bs), Grylloidea (14.9%), Acridoidea (14.6%) and Tetrigoidea (14.3%). As expected under the theory of centromeric drive, we found a correlation between B chromosome presence and A chromosome shape-Bs are more frequent in karyotypes with more acrocentric A chromosomes. We also found that Bs are less common in species with high chromosome numbers and appear to be most common at the modal chromosome number (2n = 24). Study effort, measured for each genus, was not associated with B prevalence, A chromosome shape or A chromosome number. Our results thus provide support for centromeric drive as an important and prevalent force in the karyotypic evolution of Orthoptera, just as it appears to be in mammals. We suggest that centromeric drive may provide a mechanistic explanation for White's principle of karyotypic orthoselection.     

Genetic control of B chromosome transmission in Aegilops speltoides (Poaceae)

The transmission of B chromosomes in Aegilops speltoides was studied in 1B and 3B plants. 1B plants tend to lose the B, while the Bs are accumulated in 3B plants with respect to Mendelian expectation. The experimental conditions permitted us to deduce the number of Bs transmitted in the egg cells. The quantitative character “mean number of Bs transmitted in the egg cells” shows a large variation in both types of plants. We have carried out a mass selection experiment, selecting those plants with the highest and the lowest values for this character. A genetic component of such variation was demonstrated because significant selection gain was obtained for high transmission rate in 1B plants, and low transmission rate in 3B plants. We have also estimated some fitness variables and their relationship with B transmission by the egg cell. We found that vigor variables are not correlated with B transmission variation. However, in 3B plants there is a significant negative correlation between B transmission rate and fertility, measured as grains per plant and grains per spikelet. It seems that natural selection acts at this level, balancing the strength of the drive and preventing the excessive increase of B number.     

Selfish DNA and breeding system in flowering plants

In many species, some individuals carry one or more B chromosomes: extra, or supernumerary chromosomes not part of the normal complement. In most well-studied cases, Bs lower the fitness of their carrier and persist in populations only because of accumulation mechanisms analogous to meiotic drive. It has been suggested that such genomic parasites are expected to persist only in outcrossed sexual species, in which uninfected lines of descent can be continuously reinfected; in inbred or asexual species, all selection is between lines of descent, and the genomic parasites are either lost or must evolve into commensals or mutualists. Here we present a simple population genetic model of the effect of outcrossing rate on the frequency of B chromosomes, and find that outcrossing facilitates the spread of parasitic Bs, but inhibits the spread of mutualists. Data compiled from the literature on breeding system and B chromosomes of British plants indicate that Bs are much more likely to be reported from obligately outcrossed species than inbred species. These results support the ideas that most B chromosomes are parasitic, and that breeding systems play a central role in the biology of selfish genes.     

The distribution of B chromosomes across species

In this review we look at the broad picture of how B chromosomes are distributed across a wide range of species. We review recent studies of the factors associated with the presence of Bs across species, and provide new analyses with updated data and additional variables. The major obstacle facing comparative studies of B chromosome distribution is variation among species in the intensity of cytogenetic study. Because Bs are, by definition, not present in all individuals of a species, they may often be overlooked in species that are rarely studied. We give examples of corrections for differences in study effort, and show that after a variety of such corrections, strong correlations remain. Several major biological factors are associated with the presence of B chromosomes. Among flowering plants, Bs are more likely to occur in outcrossing than in inbred species, and their presence is also positively correlated with genome size and negatively with chromosome number. They are no more frequent in polyploids than in diploids, nor in species with multiple ploidies. Among mammals, Bs are more likely to occur in species with karyotypes consisting of mostly acrocentric chromosomes. We find no evidence for an association with chromosome number or genome size in mammals, although the sample for genome size is small. The associations with breeding system and acrocentric chromosomes were both predicted in advance, but those with genome size and chromosome number were discovered empirically and we can offer only tentative explanations for the very strong associations we have uncovered. Our understanding of why B chromosomes are present in some species and absent in others is still in its infancy, and we suggest several potential avenues for future research.     

Imitate to integrate: reviewing the pathway for B chromosome integration in Trypoxylon (Trypargilum) albitarse (Hymenoptera, Sphecidae)

B chromosomes are genomic "intruders" normally characterized by their total dispensability counteracted by a variety of drive mechanisms, which assures their presence regardless of their harmful effects on the host genome. From an evolutionary standpoint, the relationship between standard (A) and B chromosomes can go through different pathways, from an everlasting arms race to a cordial B integration. Examples underlying the first situation are fairly common; B integration, however, has been more a theoretical than a practical possibility. The B chromosome in the haplodiploid solitary wasp Trypoxylon albitarse is probably the first example of a "mimetic" B, which is being integrated into the A genome by limiting itself to one B per haploid genome, the same dosage as the A chromosomes. Here we review some of the findings underlying this hypothesis and discuss the T. albitarse B strategy as a possible mechanism for B chromosome integration as a regular member of the chromosome complement in haplodiploid organisms.     

The parasitic effects of rye B chromosomes might be beneficial in the long term

Rye B chromosomes (Bs) have strong parasitic effects on fertility. B carrying plants are less fertile than 0B ones, whereas the Bs have no significant effects on plant vigour. On the other hand, it has been reported that B transmission is under genetic control in such a way that H line plants transmit the Bs at high frequency, whereas the Bs in the low B transmission rate line (L) fail to pair at metaphase I and are frequently lost. In the present work we analyse variables affecting vigour and fertility considering not only the number of Bs of each plant, but also its H or L status and the B number of its maternal parent. Our results show that the Bs not only decrease female fertility of the B carrier, but the fertility of its progeny, with the exception of 0B plants coming from a 4B mother, which are the most fertile. In this way B chromosomes can be considered as a selective factor. Pollen abortion was higher in B carriers, in the progeny of B carriers and in H plants, but 4B plants coming from B carrying mothers produce less aborted pollen, indicating that a high B number is more deleterious if it is transmitted in the pollen grains. A similar result was obtained for endosperm quality estimated as grain weight, because it is negatively influenced by the Bs in 4B plants coming from a 0B mother. H plants were always less fertile than L ones, indicating that alleles increasing the loss of Bs in the L line will be probably selected as a defence of the A genome against the invasive Bs of the H line. Flower number is not affected by the Bs.     

The B chromosomes in Brachycome

This review presents a historical account of studies of B chromosomes in the genus Brachycome Cass. (synonym: Brachyscome) from the earliest cytological investigations carried out in the late 1960s though to the most recent molecular analyses. Molecular analyses provide insights into the origin and evolution of the B chromosomes (Bs) of Brachycome dichromosomatica, a species which has Bs of two different sizes. The larger Bs are somatically stable whereas the smaller, or micro, Bs are somatically unstable. Both B types contain clusters of ribosomal RNA genes that have been shown unequivocally to be inactive in the case of the larger Bs. The large Bs carry a family of tandem repeat sequences (Bd49) that are located mainly at the centromere. Multiple copies of sequences related to this repeat are present on the A chromosomes (As) of related species, whereas only a few copies exist in the A chromosomes of B. dichromosomatica. The micro Bs share DNA sequences with the As and the larger Bs, and they also have B-specific repeats (Bdm29 and Bdm54). In some cases repeat sequences on the micro Bs have been shown to occur as clusters on the A chromosomes in a proportion of individuals within a population. It is clear that none of these B types originated by simple excision of segments from the A chromosomes.     

B chromosomes in populations of mammals

B chromosomes (Bs) have been found in 55 out of 4629 living species of mammals. The summarized data show great variability in types of mammalian Bs, including differences in size, shape and molecular composition. This variability extends to the origin, mode of transmission and population dynamics. In general, B chromosomes in mammals do not differ from Bs found in other animal or plant species, but some peculiarities do exist. Most species in which Bs are found are widespread. Some data support the view that Bs may contribute to the successful expansion of some of these species, but it is possible that Bs are just more easily scored in them due to their frequent occurrence. Most of these species are also characterized by cycling fluctuations of abundance and characteristic social organization that produce conditions favorable for Bs to spread. All areas of research on Bs in mammals suffer from lack of data, emphasizing the necessity for intensified research on the molecular structure and ways of maintenance of Bs in populations.     

B chromosomes in Brazilian rodents

B chromosomes are now known in eight Brazilian rodent species: Akodon montensis, Holochilus brasiliensis, Nectomys rattus, N. squamipes, Oligoryzomys flavescens, Oryzomys angouya, Proechimys sp. 2 and Trinomys iheringi. Typically these chromosomes are heterogeneous relative to size, morphology, banding patterns, presence/absence of NORs, and presence/absence of interstitial telomeric signals after FISH. In most cases, Bs are heterochromatic and late replicating. Active NORs were detected in two species: Akodon montensis and Oryzomys angouya. As a rule, Bs behave as uni or bivalents in meiosis, there is no pairing between Bs and autosomes or sex chromosomes and also their synaptonemal complexes are isopycnotic with those in A chromosomes.     

Genetic differentiation in populations of the yellow-necked mouse,Apodemus flavicollis,harbouring B chromosomes in different frequencies

Two alternative models are used to explain maintenance of polymorphism of B chromosomes (Bs) in populations of a great number of species. The parasitic model suggests deleterious effects of Bs on fitness of carriers, while the heterotic model assumes that, in the absence of drive, equilibrium is produced by beneficial effects of Bs at low numbers. In order to determine the potential contribution of Bs to genetic differentiation and diversity, four populations of Apodemus flavicollis, differing in frequency of Bs (from 0.23 to 0.38) and settled in ecologically different habitats, were analyzed by 471 AFLP markers. Although numerous loci were demonstrated to be population specific, none of them was associated with individuals with Bs. AMOVA showed that the presence of Bs does not affect population differentiation, pointing to greater genetic similarity of Bs to A chromosomes. The greatest genetic diversity (0.241) was found in the population settled in optimal conditions for this species featured by the lowest frequency of animals with Bs (0.23). We found that the majority of loci marked as loci under directional selection, are characteristic of either a population with lower or one with a higher frequency of Bs. Several loci detected as outliers were associated with environmental variables that could directly and/or indirectly influence population dynamics of A. flavicollis. Thus, we suggest that the different frequency of Bs carriers in populations is related to adaptive differentiation to diverse habitats, which is in accordance with the heterotic model of Bs maintenance.     

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and <Emphasis Type="Italic">Apodemus</Emphasis> B chromosomes

Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.     

The effect of B chromosomes on fitness components inAegilops speltoides Tausch

The effect of B chromosomes (Bs) on various components of vigour and fertility inAegilops speltoides was studied. We designed three types of synthetic populations. In the first type we compared plants from the localities Haifa (which has Bs in nature) and Ashkelon (which has not). Non significant differences were found between the plants from both populations, and between B carriers and non carriers among Haifa individuals. In the second synthetic population we compared 0B, 1B, 2B, 3B and 5B plants from Haifa. We found that vigour variables were not affected by the presence of Bs, while fertility variables were significantly correlated with B number, in such a way that 1B plants produce more grains per plant than any other constitution, while 5Bs produce a remarkable deleterious effect. In the third type of synthetic populations we compared plants with 0B and 1B, 0B and 2B, 0B and 3B, and 0B and 5B. In this case we also found that 1B plants were the most fertile, but the variation of reproductive fitness was higher from plot to plot within the same B class than among B classes. We conclude that the effect of B chromosomes on the fitness variables that we have estimated is close to neutrality in this species. We discuss the relation between the strength of the mechanism of accumulation and the deleterious effects of B chromosomes.     

Absence of qualitative genes controlling interspecific pairing in rye B chromosomes

Summary The meiotic behaviour of hybrids between Secale cereale carrying B chromosomes and S. vavilovii has been studied in order to estimate the effects of B chromosomes on hybrid meiotic pairing. The possible effect of Bs on the meiotic pairing of the offspring from backcrosses with S. vavilovii has been studied also. The results obtained clearly indicate that no detectable differences existed in chromosome pairing of hybrids with or without B chromosomes. The hypothetical existence of epistatic genes on cereale genome masking the effect of Bs has been rejected after the results obtained in backcrosses. Therefore, lack of qualitative genes controlling interspecific pairing on rye B chromosomes has been concluded. A quantitative effect of B chromosomes was detected only when they were in alien cytoplasm.     

TRANSMISSION AND SIGNIFICANCE OF B CHROMOSOMES IN ANTHURIUM WAROCQUEANUM

Somatic and meiotic chromosomes of one plant of Anthurium warocqueanum J. Moore and its selfed offspring were analyzed. The parent showed 2n = 30 + 3B in both somatic cells and pollen mother cells. The B chromosomes divided normally in somatic cells, but meiotic associations of Bs varied. Three configurations of three B chromosomes were observed at metaphase I of parent meiosis: one trivalent, one bivalent and one univalent, or three univalents. The number of B chromosomes in offspring ranged from 0 to 6, indicating their transmission from both male and female gametes. Offspring with two B chromosomes appeared in greatest frequency. It was hypothesized that both male and female gametes of the 3 B parent frequently contained one B chromosome through the normal distribution of the bivalent Bs at meiosis and the elimination of the univalent B chromosome due to lagging. Examination of pollen mother cells of offspring also revealed irregular behavior of B chromosomes. With a high number of B chromosomes, normal A chromosome bivalent formation seemed to be reduced. No phenotypic effects of B chromosomes were observed.     

Intraspecific crosses resulting in the first occurrence of eight and nine B chromosomes in Prochilodus lineatus (Characiformes, Prochilodontidae)

B chromosomes are supernumerary elements present in about 15% of eukaryotic species and are most frequently heterochromatic, behave parasitically, show a transmission rate higher than standard (A) chromosomes, and can provoke harmful effects on carriers. In the current work, Prochilodus lineatus individuals carrying eight and nine B chromosomes were obtained by induced crossing performed involving breeders with different B chromosome numbers in their cells. The high B chromosome numbers found in the offspring were recorded for the first time in this species. The use of cytogenetic techniques applied in the present study revealed that regardless of the increase in number of B chromosomes in the genome of these individuals, those elements did not presented active genes, and showed their normal heterochromatic characteristic.