Aneuploidization under segmental allotetraploidy in rice and its phenotypic manifestation

Key message

We report a repertoire of diverse aneuploids harbored by a newly synthesized segmental allotetraploid rice population with fully sequenced sub-genomes and demonstrate their retention features and phenotypic consequences.

Abstract

Aneuploidy, defined as unequal numbers of different chromosomes, is a large-effect genetic variant and may produce diverse cellular and organismal phenotypes. Polyploids are more permissive to chromosomal content imbalance than their diploid and haploid counterparts, and therefore, may enable more in-depth investigation of the phenotypic consequences of aneuploidy. Based on whole-genome resequencing, we identify that ca. 40% of the 312 selfed individual plants sampled from an early generation rice segmental allotetraploid population are constitutive aneuploids harboring 55 distinct aneuploid karyotypes. We document that gain of a chromosome is more prevalent than loss of a chromosome, and the 12 rice chromosomes have distinct tendencies to be in an aneuploid state. These properties of aneuploidy are constrained by multiple factors including the number of genes residing on the chromosome and predicted functional connectivity with other chromosomes. Two broad categories of aneuploidy-associated phenotypes are recognized: those shared by different aneuploids, and those associated with aneuploidy of a specific chromosome. A repertoire of diverse aneuploids in the context of a segmental allotetraploid rice genome with fully sequenced sub-genomes provides a tractable resource to explore the roles of aneuploidy in nascent polyploid genome evolution and helps to decipher the mechanisms conferring karyotypic stabilization on the path to polyploid speciation and towards artificial construction of novel polyploid crops.

     

NORs and counterstain-enhanced fluorescence studies in Cyprinidae of different ploidy level

The ribosomal RNA gene expression in the genomes of evolutionary diploid (Scardinius erythrophthalmus, Leucaspius delineatus, Tinca tinca) and polyploid species (Cyprinus carpio, Carassius carassius, Carassius auratus gibelio, Carassius auratus auratus) of Cyprinidae has been investigated by means of a silver nitrate technique. The diploid species investigated exhibited only one pair of chromosomes with nucleolus organizers (NOR). Higher numbers of rRNA-expressing chromosomal sites in several evolutionary polyploid species (Carassins) gave evidence against a complete functional diploidization, at least with regard to the NOR bearing chromosomes in these species. The NORs displayed a heterochromatic brilliant chromomycin A₃ fluorescence. No distamycin-A/DAPI-bright heterochromatic blocks were detected in the genomes of the Cyprinidae.     

Quantitative DNA variation between and within chromosome complements of Vigna species (Fabaceae)

Cytogenetical investigations, so far, on the organisation and evolution of the genomes of Vigna species have proved difficult due to small chromosome size, large chromosome number and uniformity in chromosome shape and size within and between the complements. In this investigation the nature and extent of DNA variation between thirteen diploid and one polyploid species have been estimated. The DNA variation between diploid species was small and species clustered around a mean value of 2.7 pg. The polyploid species had a greater DNA value of 4.95 pg. No significant variation in 2C DNA content was found between accessions of V. radiata. A comparison of the distribution of DNA among the chromosomes within complements has shown that the excess DNA acquired in evolution was distributed evenly in all chromosomes despite significant differences in chromosome size. The relative changes in chromatin area and DNA density which accompany evolutionary DNA variation was also compared.     

Reproductive modes,ploidy distribution,and supernumerary chromosome frequencies of the flatworm Polycelis nigra (Platyhelminthes: Tricladida)

The hermaphroditic flatworm, Polycelis nigra, is characterized by two reproductive biotypes which differ with respect to ploidy; sexual individuals are diploid (n = 8, 2× = 16) and pseudogamous parthenogenetic individuals are polyploid (typically 3×). We have collected and karyotyped individuals from 15 sampling sites (13 in mid to northern Italy, one in Great Britain and one in The Netherlands). We found that biotypes can exist alone or in sympatry, and identified purely diploid, mixed diploid-polyploid, and purely polyploid populations. Karyotype data show that in addition to the normal autosome complement, B chromosomes of differing morphology as well as stable aneuploid chromosomes (extra-A) were found almost exclusively in polyploids (11 of 12 sites). We extensively sampled Lago di Toblino (northern Italy), a pure polyploid population characterized by a submetacentric to metacentric, mitotically stable B chromosome, as well as a stable extra-A chromosome. Here, individuals having 1–3 B chromosomes were more abundant (61%) than those having no B's, implying that B chromosome infection has little detrimental effect when occurring in low numbers. Furthermore, 66% of individuals from this population possessed extra-A chromosomes, although it is unclear whether these elements are aneuploid autosomes or B chromosomes of different morphology. The ubiquity of these chromosomes, within asexuals in particular, is suggestive of a correlation between the origination of the elements and the evolution of polyploidy, or may reflect increased tolerance of parthenogenetic genomes to aneuploidy. This revised version was published online in July 2006 with corrections to the Cover Date.     

普通小麦7B染色体两类低拷贝专化DNA序列的特性

研究表明 ,多倍体小麦基因组中存在一类低拷贝、染色体专化的DNA序列 ,其在多倍体形成时常表现出不稳定性。这类序列被认为在异源多倍体的建立和稳定中起着关键作用。为进一步研究这一问题 ,对通过染色体显微切割从普通小麦 (TriticumaestivumL .)中分离的 5个 7B染色体专化DNA序列的特性进行了研究。以这些序列为探针对大量的多倍体小麦和它们的二倍体祖先物种进行了Southern杂交分析。结果表明 ,这些序列可被分为两种类型 :其中的 4个序列与所有的多倍体物种均杂交 ,但是在二倍体水平上 ,它们却只与和多倍体小麦B基因组紧密相关的物种杂交 ,这说明这些序列是在二倍体物种分化以后产生的 ,然后垂直传递给多倍体 ;其中的 1个序列与所有的二倍体及多倍体物种均杂交 ,暗示在多倍体形成后这些序列从A和D基因组中消除了。用这一序列分别与一个人工合成的六倍体和四倍体小麦进行Southern杂交的结果表明 ,序列消除是一个迅速的事件而且很可能与这些序列的甲基化状态有关。认为这些低拷贝的染色体专化序列对于多倍体形成后部分同源染色体之间的进一步分化起着重要作用。     

CHROMOSOME BEHAVIOR IN HYBRID FERNS: A REINTERPRETATION OF APPALACHIAN DRYOPTERIS

Analyses of chromosome pairing behavior in fern hybrids, as evidenced by the degree of bivalent and/or univalent formation at meiotic prophase, have frequently been employed in studies of evolutionary relationships within polyploid fern complexes. Pairing is often seen to involve genomic numbers of chromosomes. Many examples exist, however, that indicate pairing on subgenomic levels. If this type of behavior is not recognized in analyses of F₁ hybrids and their polyploid derivatives, interpretations of evolutionary relationships based upon pairing behavior may be misleading. Contrary to some views, sterile triploid hybrids possessing less than three distinct genomes may play a significant role in the formation of reticulate polyploid complexes. This possibility must be considered in interpretations of these complexes. With these factors in mind, the Appalachian Dryopteris complex has been reinterpreted. The reinterpretation provides explanations for several unexplained inconsistencies in previous interpretations.     

Extraordinary conservation of entire chromosomes in insects over long evolutionary periods

Comparison of the genomes of different Drosophila species has shown that six different chromosomes, the so‐called ‘‘Muller elements,” constitute the building blocks for all Drosophila species. Here, we confirm previous results suggesting that this conservation of the Muller elements extends far beyond Drosophila, to at least tephritid fruit flies, thought to have diverged from drosophilids 60–70 mYr ago. Less than 10 percent of genes differ in chromosome location between the two insect groups. Within chromosomes, however, the order is highly scrambled, as expected from the comparison between Drosophila species. The data also support the notion that the sex chromosomes of tephritid flies originated from an ancestor of the dot chromosome 4 of Drosophila. Overall, therefore, no new chromosome has been created for perhaps a billion generations over the two evolutionary lines. This stability at the chromosome level, which appears to extend to all Diptera including mosquitoes, is in stark contrast to other groups such as mammals, birds, fish and plants, in which chromosome numbers and organization vary enormously among species that have diverged over much fewer generations.     

Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring

Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish (Coregonus clupeaformis). We examined chromosomes in pure embryos, and healthy and malformed backcross embryos. While pure individuals displayed chromosome numbers corresponding to the expected diploid number (2n = 80), healthy backcrosses showed evidence of mitotic instability through an increased variance of chromosome numbers within an individual. In malformed backcrosses, extensive aneuploidy corresponding to multiples of the haploid number (1n = 40, 2n = 80, 3n = 120) was found, suggesting meiotic breakdown in their F₁ parent. However, no detectable chromosome rearrangements between parental forms were identified. Genomic instability through aneuploidy thus appears to contribute to reproductive isolation between dwarf and normal lake whitefish, despite their very recent divergence (approx. 15–20 000 generations). Our data suggest that genetic incompatibilities may accumulate early during speciation and limit hybridization between nascent species.     

Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes

The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales – a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R ² = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers.     

Chromosome Studies of 10 Species of Aconitum in China

This paper deals with chromosomal numbers and morphology of 10 species of Aconitum in China. According to the basic number of the genus (x=8), these species can be referred to diploid, tetraploid, hexaploid and octoploid. Correlation is found between chromosomal numbers, sizes and structures. The perennial species with a rhizome are mostly diploid, with chromosomes larger than those in the biennial species with a tuber, and their chromosome pairs 3-7 are mostly subterminal ones, whereas most biennial species are polyploid, and their chromosome pairs 3-7 are almost submetacentric. The evolutionary trends of chromosome from diploid to polyploid, large to small, st to sm are considered possible. The data are agreed with the idea that rhizomal species are more primitive than tuberous ones. The existence of two types of karyotypes in these 10 species is a further support of taxonomic division of two subgenera, subgen. Paraconitum and subgen. Aconitum. In addition, some species are taxonomically discussed.     

Meiotic chromosomes of the tree frog Smilisca baudinii (Anura: Hylidae)

The Mexican tree frog Smilisca baudinii, is a very common frog in Central America. In spite their importance to keep the ecological equilibrium of the rainforest, its biology and genetics are poorly known. In order to contribute with its biological knowledge, we described the typical meiotic karyotype based in standard cytogenetic protocols to specimens collected in Tabasco, Mexico. The study was centered in the analysis of 131 chromosome spreads at meiotic stage from two adults of the species (one female and one male). The metaphase analysis allowed the establishment of the modal haploid number of 1n = 12 bivalent chromosomes. The chromosomic formulae from the haploid bivalent karyotype was integrated by 12 biarmed chromosomes characterized by twelve pairs of metacentric-submetacentric (msm) chromosomes. The meiotic counting gives the idea that diploid chromosome number is integrated by a complement of 2n = 24 biarmed chromosomes. The presence of sex chromosomes from female and male meiotic spreads was not observed. Current results suggest that S. baudinii chromosome structure is well shared among Hylidae family and "B" chromosomes are particular structures that have very important evolutionary consequences in species diversification.     

Chromosomes and polyploidy in Lenophyllum (Crassulaceae)

Gametic chromosome numbers of 22, 32, 33, and 44 in five species of Lenophyllum suggest that they may be polyploids on a basic 11, but this number has not been found. Three species have 8-12 distinctively large chromosomes that do not pair with each other in their hybrids and probably belong to the same genome. In hybrids of many polyploid Mexican Crassulaceae preferential pairing occurs between corresponding chromosomes of their multiple genomes, which indicates that they are autopolyploids. However, little or no preferential pairing occurs between chromosomes of Lenophyllum in its hybrids, and its species appear to be allopolyploids. The putative parents are unknown.     

Polyploid inter-specific hybrids in the genus Fragaria

Conclusion In conclusion we think it necessary to lay stress on the great faculty to form diploid gametes, and in result polyploid forms shown by allFragaria species, as has been noted by the majority of investigators having worked with these plants.In result of our investigations of diploid-hexaploid and octoploid-hexaploid hybrids, we have found 16 cases of doubling of the chromosome number in sexual cells of hybrids, and 5 cases of doubling in pure species. A cytological analysis of all F₂ hybrids at our disposal (the number of chromosomes has been counted in 14 plants out of 25), as well as of back crosses (the number of chromosomes has been counted in 2 plants out of 6), will doubtless considerably increase this number. The differences in the chromosome sets (7 chromosomes being a whole set) of the species used in crossing, evidently, greatly promotes the above mentioned phenomenon.Starting from experimental data, there may be two ways of explaining the origin of the polyploid series ofFragaria, with 14, 28, 42, 56 somatic chromosomes, found under natural conditions. The first way is that of hybridisation, as a source of origin of polyploid species, (with different chromosome sets) with subsequent doubling of the chromosome number, giving rise to allopolyploids. In regards to the second way, cross pollination is but an external stimulating influence, similar to a series of other factors disturbing the normal course of reduction division, and giving rise to autopolyploids (analogous to the origin of our tetraploid). It is evident, that high polyploid species of the strawberry have originated in the first way.With 1 plate     

SPC-P1: a pathogenicity-associated prophage of Salmonella paratyphi C

Background

The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy.

Results

The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries.

Conclusions

The negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes.     

Rapid structural and epigenetic changes in polyploid and aneuploid genomes

Recent work with plants has demonstrated that genome instability can be triggered by a change in chromosome number arising from either whole genome duplications (polyploidy) or loss/gain of individual chromosomes (aneuploidy). This genome instability is manifested as rapid structural and epigenetic alterations that can occur somatically or meiotically within a few generations after heteroploid formation. The intrinsic instability of newly formed polyploid and aneuploid genomes has relevance for genome evolution and human carcinogenesis, and points toward recombinational and epigenetic mechanisms that sense and respond to chromosome numerical changes. BioEssays 21:761–767, 1999. © 1999 John Wiley & Sons, Inc.     

Chromosome numbers and evolutionary patterns in the Aster Occidentalis (Asteraceae) polyploid complex of western North America

The 15 species studied have chromosome numbers predominantly based onx=8, and intraspecific polyploidy is frequent. The numbersx=13 andx=18 in two species are hypothesized to represent dibasic alloploidy rather than aneuploidy. The group forms a hybrid complex, with 11 basic diploids thus far discovered and with much morphological variation observed among species at the hexaploid and higher polyploid levels. Both alloploidy and introgression probably contribute to this pattern of variability. The known diploids are assigned to eight species, with the suggestion that further taxonomic division may be warranted as the group becomes better known. Seven recognized species exist only as polyploids. Because of their reticulate relationships, the polyploid populations form an extensively intergading series of morphological types. It is cautioned that excessive taxonomic splitting, based on minor polyploid variants, might lead to an unwieldy and impractical classification for the group.     

Intergenomic single nucleotide polymorphisms as a tool for bacterial artificial chromosome contig building of homoeologous Brassica napus regions

Background

Homoeologous sequences pose a particular challenge if bacterial artificial chromosome (BAC) contigs shall be established for specific regions of an allopolyploid genome. Single nucleotide polymorphisms (SNPs) differentiating between homoeologous genomes (intergenomic SNPs) may represent a suitable screening tool for such purposes, since they do not only identify homoeologous sequences but also differentiate between them.

Results

Sequence alignments between Brassica rapa (AA) and Brassica oleracea (CC) sequences mapping to corresponding regions on chromosomes A1 and C1, respectively were used to identify single nucleotide polymorphisms between the A and C genomes. A large fraction of these polymorphisms was also present in Brassica napus (AACC), an allopolyploid species that originated from hybridisation of A and C genome species. Intergenomic SNPs mapping throughout homoeologous chromosome segments spanning approximately one Mbp each were included in Illumina’s GoldenGate® Genotyping Assay and used to screen multidimensional pools of a Brassica napus bacterial artificial chromosome library with tenfold genome coverage. Based on the results of 50 SNP assays, a BAC contig for the Brassica napus A subgenome was established that spanned the entire region of interest. The C subgenome region was represented in three BAC contigs.

Conclusions

This proof-of-concept study shows that sequence resources of diploid progenitor genomes can be used to deduce intergenomic SNPs suitable for multiplex polymerase chain reaction (PCR)-based screening of multidimensional BAC pools of a polyploid organism. Owing to their high abundance and ease of identification, intergenomic SNPs represent a versatile tool to establish BAC contigs for homoeologous regions of a polyploid genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-560) contains supplementary material, which is available to authorized users.     

Cytological studies on meiotic configurations of intraspecific aneuploids ofCarex blepharicarpa (Cyperaceae) in Japan

Chromosome configurations at meiotic metaphase I ofCarex blepharicarpa were determined for 245 individuals collected from 11 localities in the Chugoku District of Japan. Nine intraspecific aneuploids, 2n=26–33 and 41, were found. The most common diploid number was 29, and found in 73 individuals. No clear geographical pattern was suggested by a distribution of these aneuploids. A consecutive series of chromosome numbers from 2n=26 to 32 was found in two populations from Okayama Prefecture. At meiotic metaphase I, univalents and multivalents were found, and one to three trivalents were observed in each aneuploid. Heteromorphic chain trivalents comprising large, medium and small chromosomes were prevalent. Homomorphic trivalents, which are thought to be originated from chromosome duplications caused by unreduced gametes, were found in only one individual with 2n=41. The high frequency of heteromorphic trivalents in this species indicates that most aneuploidy probably results from fission and/or fusion of chromosomes.     

Development of a wheat single gene FISH map for analyzing homoeologous relationship and chromosomal rearrangements within the Triticeae

Key message

A cytogenetic map of wheat was constructed using FISH with cDNA probes. FISH markers detected homoeology and chromosomal rearrangements of wild relatives, an important source of genes for wheat improvement.

Abstract

To transfer agronomically important genes from wild relatives to bread wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) by induced homoeologous recombination, it is important to know the chromosomal relationships of the species involved. Fluorescence in situ hybridization (FISH) can be used to study chromosome structure. The genomes of allohexaploid bread wheat and other species from the Triticeae tribe are colinear to some extent, i.e., composed of homoeoloci at similar positions along the chromosomes, and with genic regions being highly conserved. To develop cytogenetic markers specific for genic regions of wheat homoeologs, we selected more than 60 full-length wheat cDNAs using BLAST against mapped expressed sequence tags and used them as FISH probes. Most probes produced signals on all three homoeologous chromosomes at the expected positions. We developed a wheat physical map with several cDNA markers located on each of the 14 homoeologous chromosome arms. The FISH markers confirmed chromosome rearrangements within wheat genomes and were successfully used to study chromosome structure and homoeology in wild Triticeae species. FISH analysis detected 1U-6U chromosome translocation in the genome of Aegilops umbellulata, showed colinearity between chromosome A of Ae. caudata and group-1 wheat chromosomes, and between chromosome arm 7S#3L of Thinopyrum intermedium and the long arm of the group-7 wheat chromosomes.     

Chromosome and nucleotide sequence differentiation in genomes of polyploid Triticum species

Summary The nature of genome change during polyploid evolution was studied by analysing selected species within the tribe Triticeae. The levels of genome changes examined included structural alterations (translocations, inversions), heterochromatinization, and nucleotide sequence change in the rDNA regions. These analyses provided data for evaluating models of genome evolution in polyploids in the genus Triticum, postulated on the basis of chromosome pairing at metaphase I in interspecies hybrids.The significance of structural chromosome alterations with respect to reduced MI chromosome pairing in interspecific hybrids was assayed by determining the incidence of heterozygosity for translocations and paracentric inversions in the A and B genomes of T. timopheevii ssp. araraticum (referred to as T. araraticum) represented by two lines, 1760 and 2541, and T. aestivum cv. Chinese Spring. Line 1760 differed from Chinese Spring by translocations in chromosomes 1A, 3A, 4A, 6A, 7A, 3B, 4B, 7B and possibly 2B. Line 2541 differed from Chinese Spring by translocations in chromosomes 3A, 6A, 6B and possibly 2B. Line 1760 also differed from Chinese Spring by paracentric inversions in arms 1AL and 4AL whereas line 2541 differed by inversions in 1BL and 4AL (not all chromosomes arms were assayed). The incidence of structural changes in the A and B genomes did not coincide with the more extensive differentiation of the B genomes relative to the A genomes as reflected by chromosome pairing studies.To assay changing degrees of heterochromatinization among species of the genus Triticum, all the diploid and polyploid species were C-banded. No general agreement was observed between the amount of heterochromatin and the ability of the respective chromosomes to pair with chromosomes of the ancestral species. Marked changes in the amount of heterochromatin were found to have occurred during the evolution of some of the polyploids.The analysis of the rDNA region provided evidence for rapid fixation of new repeated sequences at two levels, namely, among the 130 bp repeated sequences of the spacer and at the level of the repeated arrays of the 9 kb rDNA units. These occurred both within a given rDNA region and between rDNA regions on nonhomologous chromosomes. The levels of change in the rDNA regions provided good precedent for expecting extensive nucleotide sequence changes associated with differentiation of Triticum genomes and these processes are argued to be the principal cause of genome differentiation as revealed by chromosome pairing studies.