Figure 3 - uploaded by Douglas E Soltis
Content may be subject to copyright.
Karyotyping using FISH and GISH reprobing. (a, c, e, g and i) FISH probes were as follows: centromeric TPRMBO (lilac), subtelomeric TGP7 (red), interstitial TTR3 (green) and 18 S rDNA (yellow/orange). (b, d, f, h and j) GISH reprobing of the same chromosome preparations using total genomic DNA of the parents, T. dubius (green) and T. porrifolius (red). Diamond symbols are placed below aneuploid chromosomes. Arrows indicate the position of translocation breakpoints revealed by GISH. Arrowheads indicate missing FISH markers that did coincide with a translocation detected with GISH. (a and b) 2866-11-1, (c and d) 2866-15-1, (e and f) 2869-9-1, (g and h) 2869-10-1 and (i and j) 2876-10-1. Scale bar, 5 μm.
Source publication
Cytological studies have shown many newly formed allopolyploids (neoallopolyploids) exhibit chromosomal variation as a result of meiotic irregularities, but few naturally occurring neoallopolyploids have been examined. Little is known about how long chromosomal variation may persist and how it might influence the establishment and evolution of allo...
Contexts in source publication
Context 1
... of individual chromosomes was also possible when taking into account chromosome size, arm length and the heterogeneous GISH signal along the chromosomes. Figure 3). Although there was no conflicting information on chromosome origin provided by FISH and GISH, some small subterminal (or distal) reductions or losses of arrays were only resolvable with FISH probes specific to the TGP7 or TTR3 repeats ( Figure 3). ...
Context 2
... 3). Although there was no conflicting information on chromosome origin provided by FISH and GISH, some small subterminal (or distal) reductions or losses of arrays were only resolvable with FISH probes specific to the TGP7 or TTR3 repeats ( Figure 3). Subtelomeric TGP7 signals, for example, were missing on the long arm of C Po (Figures 3e and f), but there was no indication of an intergenomic translocation based on the GISH signals at this position. ...
Context 3
... both cases, no translocation heterozygotes were recovered, but both recombined and non- recombined homozygotes were observed. Only in one population (Oakesdale) was a homozygous reciprocal intergenomic translocation, on the long arm of chromosome A Du and A Po , present in all individuals analyzed (Supplementary Figures S3a and f). One individual, 2871-10-1, showed an additional translocation on an A Po chromosome, with the breakpoint appearing to be close to the 5S rDNA array (Supplementary Figure S3c). ...
Context 4
... in one population (Oakesdale) was a homozygous reciprocal intergenomic translocation, on the long arm of chromosome A Du and A Po , present in all individuals analyzed (Supplementary Figures S3a and f). One individual, 2871-10-1, showed an additional translocation on an A Po chromosome, with the breakpoint appearing to be close to the 5S rDNA array (Supplementary Figure S3c). ...
Context 5
... observation also applies to the T. miscellus populations that were analyzed previously ( Chester et al., 2012). Only one reciprocal intergenomic translocation in the Oakesdale population of T. mirus (Supplementary Figure S3) and one reciprocal intergenomic translocation in the Spokane-2 population of T. miscellus (Chester et al., 2012) appeared close to fixation. Interest- ingly, these translocations both occurred in similar regions on the group A chromosomes. ...
Citations
... For example, both naturally occurring and synthetic T. miscellus and T. mirus exhibit true aneuploidy (e.g. 2n = 23 or 25 rather than the expected and typical 2n = 24), compensated aneuploidy (in which 2n = 24 but with unequal doses of some parental chromosomes), and intergenomic translocations (Lim et al., 2008;Chester et al., 2012Chester et al., , 2015Spoelhof et al., 2017). In addition, dynamic genetic changes, including gene loss and gene silencing, in the two newly formed Tragopogon polyploids have been well documented (e.g. ...
Polyploidy is an important evolutionary force, yet epigenetic mechanisms, such as DNA methylation, that regulate genome‐wide expression of duplicated genes remain largely unknown. Here, we use Tragopogon (Asteraceae) as a model system to discover patterns and temporal dynamics of DNA methylation in recently formed polyploids.
The naturally occurring allotetraploid Tragopogon miscellus formed in the last 95–100 yr from parental diploids Tragopogon dubius and T. pratensis. We profiled the DNA methylomes of these three species using whole‐genome bisulfite sequencing.
Genome‐wide methylation levels in T. miscellus were intermediate between its diploid parents. However, nonadditive CG and CHG methylation occurred in transposable elements (TEs), with variation among TE types. Most differentially methylated regions (DMRs) showed parental legacy, but some novel DMRs were detected in the polyploid. Differentially methylated genes (DMGs) were also identified and characterized.
This study provides the first assessment of both overall and locus‐specific patterns of DNA methylation in a recent natural allopolyploid and shows that novel methylation variants can be generated rapidly after polyploid formation. Together, these results demonstrate that mechanisms to regulate duplicate gene expression may arise soon after allopolyploid formation and that these mechanisms vary among genes.
... The two measures were uncorrelated on an individual basis (n = 124, R 2 = 0.0034, p = 0.52), and, despite their larger seed weight, germination was typically lower (and more variable) in polyploids than in diploids. The lower average seed viability among allopolyploids may be a downstream effect of meiotic abnormalities or genomic rearrangements that are often observed in young allopolyploids, including Tragopogon (Ramsey and Schemske, 2002;Comai, 2005;Lim et al., 2008;Tate et al., 2009;Szadkowski et al., 2010;Chester et al., 2012Chester et al., , 2015Spoelhof et al., 2017). Instead of enhancing germination rate, larger seeds may simply lead to larger seedlings-plant height at the initial measurement (24 DAG) was positively correlated with average mature seed weight (n = 128, R 2 = 0.21, p < 0.001), which could enhance the competitive ability of polyploid seedlings (Leishman et al., 2000). ...
Premise:
Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time we compare phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids.
Methods:
Our large common-garden experiment measured traits in growth, development, physiology, and reproductive fitness and analyzed differences between allopolyploids and their parental species and between synthetic and natural allopolyploids.
Key results:
As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to non-existent trait differences.
Conclusions:
In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization. This article is protected by copyright. All rights reserved.
... Although Ad. nelumboides is a tetraploid species, a previous microsatellite study suggested that this species behaves a genetic diploid (Kang et al. 2008). Rapid chromosomal and genomic changes following WGD (Song et al. 1995;Leitch and Bennett 1997;Chester et al. 2012;Soltis et al. 2012;Chester et al. 2015), including karyotypic variation (intrachromosomal and intragenomic rearrangements) and gene silencing (and even loss), may explain genetic diploidization in Ad. nelumboides. In fact, pseudogenization and gene deletion by recombination have been considered to be major mechanisms for fractionation, as a particularly important component of diploidization (Li et al. 2021). ...
Whole genome duplication has been recognized as a major process in speciation of land plants, especially in ferns. Whereas genome downsizing contributes greatly to the post-genome shock responses of polyploid flowering plants, diploidization of polyploid ferns diverges by maintaining most of the duplicated DNA and is thus expected to be dominated by genic processes. As a consequence, fern genomes provide excellent opportunities to study ecological speciation enforced by expansion of protein families via polyploidy. To test the key predictions of this hypothesis, we reported the de novo genome sequence of Adiantum nelumboides, a tetraploid homosporous fern. The obtained draft genome had a size of 6.27 Gb assembled into 11,767 scaffolds with the contig N50 of 1.37 Mb. Repetitive DNA sequences contributed with about 81.7%, a remarkably high proportion of the genome. With 69,568 the number of predicted protein-coding genes exceeded those reported in most other land plant genomes. Intragenomic synteny analyses recovered 443 blocks with the average block size of 1.29 Mb and the average gene content of 16 genes. The results are consistent with the hypothesis of high ancestral chromosome number, lack of substantial genome downsizing, and dominance of genic diploidization. As expected in the calciphilous plants, a notable number of detected genes were involved in calcium uptake and transport. In summary, the genome sequence of a tetraploid homosporous fern not only provides access to a genomic resource of a derived fern, but also supports the hypothesis of maintenance of high chromosome numbers and duplicated DNA in young polyploid ferns.
... GISH was first used in a study of the subgenomic organisation of Hordeum × Secale intergeneric hybrid in 1989 [144]. Since then, this method has been widely used to determine the ancestral/parental genomes in the hybrids and allopolyploids [145] that belong to genera such as Arabidopsis [146], Brassica [147,148], Coffea [149], Gossypium [150], Nicotiana [151], Tragopogon [152], Spartina [153] and many others. For example, using GISH, a putative diploid parental species has been proposed for the allotetraploid Chenopodium berlandieri (genome composition AABB): a B genome donor similar to C. ficifolium and an A genome donor similar to C. watsonii (Figure 4) [108]. ...
... The application of GISH enabled the ancestral subgenomes in both allotetraploids to be determined, however, an extensive chromosomal polymorphism between different individuals was revealed, including intergenomic translocations and aneuploidy, which were manifested by the presence of monosomic and trisomic plants [171]. Aneuploidy was found to be frequent in all of the populations of T. miscellus [172] and T. mirus [152] that have been studied to date. Interestingly, the plants that exhibited aneuploidy were either characterised by the expected chromosome number through reciprocal monosomy-trisomy/nullisomy-tetrasomy of the homoeologues (compensated aneuploidy) or the loss of homoeologues (non-compensated aneuploidy). ...
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two-or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome-and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
... Extensive chromosome reshuffling and aneuploidy were observed in wheat allopolyploids [8,35], Brassica allopolyploids [39] and Tragopogon neo-allopolyploids [40,41]. However, no aneuploidy was detected in the analyzed allotetraploid C. ×hytivus, possibly because that the zygotes containing aneuploidy cannot develop into full shape seeds, and then were neglected when collecting seeds or selecting for germination. ...
Background:
Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid parental karyotypes have not been studied in detail. The allotetraploid Cucumis ×hytivus (HHCC, 2n = 38) was obtained from interspecific hybridization between C. sativus (CC, 2n = 14) and C. hystrix (HH, 2n = 24) followed by chromosome doubling. The results of this study thus offer an excellent opportunity to explore the meiotic properties of allopolyploids with dysploid parental karyotypes.
Results:
In this report, we describe the meiotic properties of five chromosomes (C5, C7, H1, H9 and H10) and two genomes in interspecific hybrids and C. ×hytivus (the 4th and 14th inbred family) through oligo-painting and genomic in situ hybridization (GISH). We show that 1) only two translocations carrying C5-oligo signals were detected on the chromosomes C2 and C4 of one 14th individual by the karyotyping of eight 4th and 36 14th plants based on C5- and C7-oligo painting, and possible cytological evidence was observed in meiosis of the 4th generation; 2) individual chromosome have biases for homoeologous pairing and univalent formation in F1 hybrids and allotetraploids; 3) extensive H-chromosome autosyndetic pairings (e.g., H-H, 25.5% PMCs) were observed in interspecific F1 hybrid, whereas no C-chromosome autosyndetic pairings were observed (e.g. C-C); 4) the meiotic properties of two subgenomes have significant biases in allotetraploids: H-subgenome exhibits higher univalent and chromosome lagging frequencies than C-subgenome; and 5) increased meiotic stability in the S14 generation compared with the S4 generation, including synchronous meiosis behavior, reduced incidents of univalent and chromosome lagging.
Conclusions:
These results suggest that the meiotic behavior of two subgenomes has dramatic biases in response to interspecific hybridization and allopolyploidization, and the meiotic behavior harmony of subgenomes is a key subject of meiosis evolution in C. ×hytivus. This study helps to elucidate the meiotic properties and evolution of nascent allopolyploids with the dysploid parental karyotypes.
... In addition, multiple origins have been demonstrated in both of these neopolyploids: T. miscellus and T. mirus formed at least 21 and 11 times, respectively (Soltis, Plunkett, Novak, & Soltis, 1995;Symonds, Soltis, & Soltis, 2010). The dynamic genomes of the two newly formed Tragopogon polyploids have been well demonstrated from various perspectives, including chromosomal variation (Chester et al., 2012;Chester, Riley, Soltis, & Soltis, 2015;Lim et al., 2008;Spoelhof et al., 2017), gene loss (Buggs et al., 2009(Buggs et al., , 2012Buggs, Chamala, et al., 2010;Tate et al., 2006;Tate, Joshi, Soltis, Soltis, & Soltis, 2009) and gene expression changes (Buggs et al., 2009(Buggs et al., , 2011Buggs, Chamala, et al., 2010;Buggs, Elliott, et al., 2010;Koh et al., 2010;Tate et al., 2006). ...
Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9‐based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing site‐specific mutations in Tragopogon protoplasts. Agrobacterium‐mediated transformation with Cas9‐sgRNA constructs targeting the phytoene desaturase gene (TraPDS) was implemented in this model polyploid system. Sequencing of PCR amplicons from the target regions indicated simultaneous mutations of two alleles and four alleles of TraPDS in albino shoots from T. porrifolius (2x) and T. mirus (4x), respectively. The average proportions of successfully transformed calli with the albino phenotype were 87% and 78% in the diploid and polyploid, respectively. This appears to be the first demonstration of CRISPR/Cas9‐based genome editing in any naturally formed neopolyploid system. Although a more efficient tissue culture system should be developed in Tragopogon, application of a robust CRISPR/Cas9 system will permit unique studies of biased fractionation, the gene‐balance hypothesis and cytonuclear interactions in polyploids. In addition, the CRISPR/Cas9 platform enables investigations of those genes involved in phenotypic changes in polyploids and will also facilitate novel functional biology studies in Asteraceae. Our workflow provides a guide for applying CRISPR/Cas9 to other non‐genetic model plant systems.
This article is protected by copyright. All rights reserved.
... In natural populations as well as in synthetic lines of Tragopogon mirus and Tragopogon miscellus, two young allopolyploid species (<200 years old), normal bivalent formation and an array of meiotic abnormalities (including multivalent formation, lagging chromosomes, and the formation of anaphase I bridges) have been observed (Lim et al., 2008;Tate et al., 2009). In particular, intergenomic translocations and/or aneuploidy were identified, but variation typically followed a compensated pattern (Chester et al., 2013(Chester et al., , 2015. These key reports of such extensive chromosome rearrangements in nature are similar to those observed in experimental B. napus allopolyploids (Xiong et al., 2011). ...
Traditional sugarcane cultivars (Saccharum officinarum) proved highly susceptible to diseases, and this led breeders to progress to interspecific crosses resulting in disease resistance. A backcrossing program to S. officinarum was then required to boost sucrose content. Clonal selection across generations and incorporation of other germplasm into cultivated backgrounds established the (narrow) genetic base of modern cultivars (Saccharum spp.), which have a man-made genome. The genome complexity has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution, architecture, and cytogenetics. However, there is a critical shortage of information on chromosome behavior throughout meiosis in modern cultivars. In this study, we examined the microsporogenesis of a contemporary variety, providing a detailed analysis of the meiotic process and chromosome association at diakinesis, using FISH with centromeric probes. Chromosomal abnormalities were documented by examining high quality preparations of pollen mother cells (700 in total). Approximately 70% of the cells showed abnormalities, such as metaphase chromosomes not lined up at the plate, lagging chromosomes and chromosomal bridges, and tetrad cells with micronuclei. Some dyads with asynchronous behavior were also observed. Due to the hybrid composition of the sugarcane genome, we suggest that bivalent incomplete pairing may occur in the first prophase leading to univalency. The presence of rod bivalents showing the lagging tendency is consistent with a reduction in chiasma frequency. Finally, the presence of chromatin bridges indicates the indirect occurrence of chromosomal inversions, although chromosome fragments were not clearly recognized. Possible reasons for such meiotic abnormalities and the large prevalence of bivalent formation are discussed.
... The parental origin of an allopolyploid is typically inferred from a combination of morphological, cytogenetic, and molecular evidence. Hypotheses of parental origin can be tested and refined by genomic in situ hybridization (GISH; i.e., mapping of genomic DNAs of the putative parental taxa to allopolyploid chromosomes; Jang and Weiss-Schneeweiss 2015), additionally allowing for the assessment of the extent of interactions between the parental subgenomes in allopolyploids (Chester et al. , 2015Mandáková et al. 2013Mandáková et al. , 2014. Several phylogenetic methods for reconstructing species networks have been developed that can address, for instance, the assignment of allopolyploid homoeologues to their corresponding parental genomes and building the species networks from multilabeled trees (Than et al. 2008;Jones et al. 2013;Marcussen et al. 2012Marcussen et al. , 2015Bertrand et al. 2015). ...
Abstract
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid. Whereas parentage is typically inferred from cytogenetic and phylogenetic data, age inference is hampered by the reticulate nature of the phylogenetic relationships. Treating subgenomes of allopolyploids as if they belonged to different species (i.e., no recombination among subgenomes) and applying cross-bracing (i.e., putting a constraint on the age difference of nodes pertaining to the same event), we can infer the age of allopolyploids within the framework of the multi-species coalescent within BEAST2. Together with a comprehensive characterization of the repetitive DNA fraction using the RepeatExplorer pipeline, we apply the dating approach in a group of closely related allopolyploids and their progenitor species in the plant genus Melampodium (Asteraceae). We dated the origin of both the allotetraploid, M. strigosum, and its two allohexaploid derivatives, M. pringlei and M. sericeum, which share both parentage and the direction of the cross, to the Pleistocene (less than 1.4 Ma). Thus, Pleistocene climatic fluctuations may have triggered formation of allopolyploids possibly in short intervals, contributing to difficulties in inferring the precise temporal order of allopolyploid species divergence of M. sericeum and M. pringlei. The relatively recent origin of the allopolyploids likely played a role in the near-absence of major changes in the repetitive fraction of the polyploids’ genomes. The repetitive elements most affected by the post-polyploidization changes represented retrotransposons of the Ty1-copia lineage Maximus and, to a lesser extent, also Athila elements of Ty3-gypsy family.
... MBE most pervasive en route to large-scale karyotype alterations and hence catalyzes rapid genome evolution. In plants, investigations in diverse taxa have documented that newly formed polyploid genomes are intrinsically unstable with nascent WGDs being often accompanied by extensive karyotypic repatterning (Pires et al. 2004;Han et al. 2005;Otto 2007;Lim et al. 2008;Xiong et al. 2011;Chester et al. 2012;Zhang, Bian, Gou, Zhou et al. 2013;Chester et al. 2015). However, many issues regarding nascent WGD-invoked karyotypic instability remain to be fully explored. ...
Whereas a distinct karyotype with defined chromosome number and structure characterizes each biological species, it is intrinsically labile. Polyploidy or whole genome duplication (WGD) has played a pervasive and ongoing role in the evolution of all eukaryotes, and is the most dramatic force known to cause rapid karyotypic reconfiguration, especially at the initial stage. However, issues concerning transgenerational propagation of karyotypic heterogeneity and its translation to phenotypic diversity in nascent allopolyploidy, at the population level, have yet to be studied in detail. Here, we report a large-scale examination of transgenerationally propagated karyotypic heterogeneity and its phenotypic manifestation in an artificially constructed allotetraploid with a genome composition of AADD, i.e., involving two of the three progenitor genomes of polyploid wheat. Specifically, we show that (i) massive organismal karyotypic heterogeneity is precipitated after 12 consecutive generations of selfing from a single euploid founder individual; (ii) there exist dramatic differences in aptitudes between subgenomes and among chromosomes for whole-chromosome gain and/or loss and structural variations; (iii) majority of the numerical and structural chromosomal variations are concurrent due to mutual contingency and possible functional constraint; (iv) purposed and continuous selection and propagation for euploidy over generations did not result in enhanced karyotype stabilization; and (v) extent of karyotypic variation correlates with variability of phenotypic manifestation. Together, our results document that allopolyploidization catalyzes rampant and transgenerationally heritable organismal karyotypic heterogeneity that drives population-level phenotypic diversification, which lends fresh empirical support to the still contentious notion that WGD enhances organismal evolvability.
... Polyploidy, dysploidy, and aneuploidy are thought to have played important roles in the karyotype evolution of eukaryotes 28,29 . Dysploidy can cause increases or decreases in basic chromosome numbers through chromosome fission or fusion, respectively. ...
Mulberry (Morus spp.), in family Moraceae, is a plant with important economic value. Many polyploid levels of mulberry have been determined. In the present study, the fluorescence in situ hybridization (FISH) technique was applied in Morus notabilis, using four single-copy sequences, telomere repeats, and 5S and 25S rDNAs as probes. All the mitotic chromosomes were clearly identified and grouped into seven pairs of homologous chromosomes. Three dot chromosome pairs were distinguished by the FISH patterns of the 25S rDNA probe and a simple sequence repeat (SSR2524). According to the FISH signals, chromosome length and morphology, detailed meiotic diakinesis karyotype was constructed. Interestingly, only six bivalent chromosomes were observed in diakinesis cells. The 25S rDNA probe was used to illustrate chromosome alterations. The results indicated that mitotic chromosomes 5 and 7 fused into diakinesis chromosome 5 during the meiotic phase. In mitotic cells, the fused chromosome 5 broke into chromosomes 5 and 7. A chromosomal fusion-fission cycle between the meiotic and mitotic phases in the same individual is reported here for the first time. This finding will contribute to the understanding of karyotype evolution in plants.
