Allopolyploid Genome Research Articles

Maintenance of plastid RNA editing activities independently of their target sites

RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.

Allopolyploidy in Wheat Induces Rapid and Heritable Alterations in DNA Methylation Patterns of Cellular Genes and Mobile Elements

Whereas accumulating recent evidences indicate that allopolyploid formation in plants is accompanied by rapid and non-Mendelian genomic changes, some other works showed genomic stasis in both nascent and natural allopolyploids. To further study the issue, we performed global DNA fingerprinting of a newly synthesized allohexaploid wheat and its natural counterpart, the common wheat, by AFLP analysis. It was found that ca. 20% bands showed deviation from parental additivity in both synthetic and the natural common wheat. Sequence analysis indicates that a majority of the changed bands represent known-function genes and transposable elements. DNA gel blot analysis showed that the main type of changes in the amphiploid is epigenetic in nature, i.e., alteration in DNA methylation patterns. Two types of alterations in methylation, random and non-random, were detected, and both types were stably inherited. Possible causes and implications of the epigenetic changes in allopolyploid genome evolution and speciation are discussed.

Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes

Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.

Spartina anglica C. E. Hubbard: a natural model system for analysing early evolutionary changes that affect allopolyploid genomes

Spartina anglica arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced East American Spartina alterniflora and following genome duplication of the hybrid (S. x townsendii). This system allows investigations of the early evolutionary changes that accompany stabilization of a new allopolyploid species in natural populations. Various molecular data indicate that S. anglica has resulted from a unique parental genotype. This young species contains two distinctly divergent homoeologous genomes that have not undergone extensive change since their reunion. No burst of retroelements has been encountered in the F 1 hybrid or in the allopolyploid, suggesting a 'structural genomic stasis' rather than 'rapid genomic changes'. However, modifications of the methylation patterns in the genomes of S. x townsendii and S. anglica indicate that in this system, epigenetic changes have followed both hybridization and polyploidization.

Molecular characterization of a cryptic wheat-Thinopyrum intermedium translocation line: evidence for genomic instability in nascent allopolyploid and aneuploid lines

A putative translocation line (#32), together with a disomic addition line (TAI27) and an octo-amphiploid line (Zhong3) of common wheat and Thinopyrum intermedium were characterized by restriction fragment length polymorphism (RFLP) analysis, using probes covering all seven homoeologous groups of Triticeae. Line 32 was confirmed to be a cryptic translocation line, based on the detection of multiple introgressed hybridization fragments specific to Th. intermedium in the RFLP patterns, and the absence of a hybridization signal in GISH analysis. In addition, extensive genomic changes, as compared to the wheat parent, were detected on all three lines studied, with a great majority of changes showing concordance among the lines. Our data is consistent with the emerging view that nascent allopolyploid and aneuploid plant genomes are highly dynamic, which may generate novel introgressed materials for breeding.

Hybridization, polyploidy and speciation inSpartina(Poaceae)

SummaryHybridization and polyploidy are well illustrated in the genusSpartina. This paper examines how recent molecular approaches have helped our understanding of the past and recent reticulate history of species, with special focus on allopolyploid speciation.Spartinaspecies are tetraploid, hexaploid or dodecaploid perennials, most of them being native to the New World. The molecular phylogeny indicates an ancient split between the tetraploid and the hexaploid species, withS.argentinensisas sister to the hexaploid lineage. Recent hybridization and polyploidization events involved hexaploid species, resulting from introductions of the east‐AmericanS. alterniflora. In California, ongoing hybridizations with its sister speciesS. foliosaresult in introgressant hybrid swarms. In Europe, hybridization withS. maritimaresulted inS. × neyrautii(France) andS. × townsendii(England), with.S. alternifloraas the maternal parent. The allopolyploidS. anglicaresulted from chromosome doubling ofS. × townsendii.This young allopolyploid contains divergent homoeologous subgenomes that have not undergone significant changes since their reunion. Hybridization, rather than genome duplication, appears to have shaped the allopolyploid genome at both the structural and epigenetic levels.

Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids of Triticeae.

Allopolyploidy is preponderant in plants, which often leads to speciation. Some recent studies indicate that the process of wide hybridization and (or) genome doubling may induce rapid and extensive genetic and epigenetic changes in some plant species and genomic stasis in others. To further study this phenomenon, we analyzed three sets of synthetic allopolyploids in the Triticeae by restriction fragment length polymorphism (RFLP) using a set of expressed sequence tags (ESTs) and retrotransposons as probes. It was found that 40-64.7% of the ESTs detected genomic changes in the three sets of allopolyploids. Changes included disappearance of parental hybridization fragment(s), simultaneous appearance of novel fragment(s) and loss of parental fragment(s), and appearance of novel fragment(s). Some of the changes occurred as early as in the F1 hybrid, whereas others occurred only after allopolyploid formation. Probing with retrotransposons revealed numerous examples of disappearance of sequences. No gross chromosome structural changes or physical elimination of sequences were found. It is suggested that DNA methylation and localized recombination at the DNA level were probably the main causes for the genomic changes. Possible implications of the genomic changes for allopolyploid genome evolution are discussed.

Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae).

Spartina x townsendii arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced Spartina alterniflora, native to the eastern seaboard of North America. Duplication of the hybrid genome gave rise to Spartina anglica, a vigorous allopolyploid involved in natural and artificial invasions on several continents. This system allows investigation of the early evolutionary changes that accompany stabilization of new allopolyploid species. Because allopolyploidy may be a genomic shock, eliciting retroelement insertional activity, we examined whether retrotransposons present in the parental species have been activated in the genome of S. anglica. For this purpose we used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposons-microsatellite amplified polymorphism (REMAP) markers, which are multilocus PCR-based methods detecting retrotransposon integration events in the genome. IRAP and REMAP allowed the screening of insertional polymorphisms in populations of S. anglica. The populations are composed mainly of one major multilocus genotype, identical to the first-generation hybrid S. x townsendii. Few new integration sites were encountered in the young allopolyploid genome. We also found strict additivity of the parental subgenomes in the allopolyploid. Both these findings indicate that the genome of S. anglica has not undergone extensive changes since its formation. This contrasts with previous results from the literature, which report rapid structural changes in experimentally resynthesized allopolyploids.

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa.

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.

Molecules, morphology and maps: New directions in evolutionary genetics

AbstractWith the characterization of a complete nucleotide sequence of a plant genome within sight, we are getting access to the ultimate source of data for evolutionary genetics. This achievement could hardly have been imagined twenty years ago. The rapid progress in methods is generating novel results that require a reassessment of our ideas about the relationship between the evolution of genomes and organisms, and of the relationship between genotype and phenotype. The widespread incongruence between chloroplast and nuclear (organismal) phylogenies was not previously suspected. It shows that introgression based on ‘wide crosses’ is a regular process in natural populations, and geneflow among species and genera must influence the distribution of genes and alleles as much as linear, phyletic inheritance. Speciation from hybrids at the diploid level seems to be stabilized by the creation of new epistatic interactions. Speciation via allopolyploidy also involves more than the additive action of the combined genomes; rearrangements and homogenization of non‐coding repetitive sequences seems to occur quickly, and repetitive rDNA sequences of the combined genomes are homogenized to one of the parental sequences or to a recombinant sequence. Diploidization of allopolyploid genomes involves the evolution of redundant genes. This has profound effects on morphological evolution. Extrapolation from the developmental genetics of model systems (e.g. Arabidopsis) has shown that single mutations in regulatory genes can explain major differences in diagnostic characters between taxa. This seems to be in conflict with the general assumption that morphological evolution proceeds gradually by the selection of allelic polymorphisms in populations. Where plants with major morphological character differences can be crossed to produce fertile offspring, genetic analysis aided by molecular marker maps confirms that major regulatory genes are involved. At the same time, such experiments suggest a hypothesis integrating saltatory evolution and population genetics. The key factor is genetic redundancy through duplicate or modifier genes that reduce the phenotypic penetrance of the major gene. A low incidence of the new, at first unadapted phenotype, possibly mainly under environmental stress conditions, facilitates selection for the proper genetic background and for a new ‘integrated genotype’. Such episodes of saltatory evolution are likely to be linked to reticulate evolution; wide hybrids are likely to break up the protective modifier networks and expose major gene effects, while polyploidy immediately generates genetic redundancy

Coevolution of A and B genomes in allotetraploid <i>Triticum dicoccoides</i>

Data is presented on the coevolution of A and B genomes in allotetraploid wheat Triticum dicoccoides (2n = 4x = 28, genome AABB) obtained by genomic in situ hybridization (GISH). Probing chromosomes of T. dicoccoides with DNA from the proposed A/B diploid genome ancestors shows evidence of enriching A-genome with repetitive sequences of B-genome type. Thus, ancestral S-genome sequences have spread throughout the AB polyploid genome to a greater extent than have ancestral A-genome sequences. The substitution of part of the A-genome heterochromatin clusters by satellite DNA of the B genome is detected by using the molecular banding technique. The cause may be interlocus concerted evolution and (or) colonization. We propose that the detected high level of intergenomic invasion in old polyploids might reflect general tendencies in speciation and stabilization of the allopolyploid genome.

Simple methods for isolating homoeologous loci from allopolyploid genomes

During allopolyploid formation, divergent sets of chromosomes are combined in a common nucleus. Accordingly, loci that are single-copy in progenitor diploid genomes become duplicated, homoeologous loci in allopolyploids. Although homoeologous loci have been identified using classical genetic and linkage mapping approaches, there are few examples of the isolation and molecular characterization of homoeologous loci from allopolyploids. Here we describe two methods for the isolation of orthologous duplicated loci and demonstrate the feasibility of the techniques using allotetraploid cotton. The methods utilize restriction-digested, size-fractionated genomic DNA as a template for either plasmid cloning or PCR amplification. This fractionation procedure, when combined with Southern hybridization and mapping information, can separate homoeologues from each other and from more divergent cross-hybridizing sequences (paralogues). Each homoeologue can be then be isolated from a pool of size-fractionated genomic DNA that is enriched for target loci. While these methods were specifically designed for isolating homoeologous loci from allotetraploids, they should be applicable to a broad spectrum of diploid and polyploid plants and be useful for studying both ancient and recent gene duplications. In addition, the procedures enrich for orthologous sequences, which can be used for phylogenetic analysis. Thus, a general approach is detailed for the isolation of nuclear genes for phylogeny reconstruction.Key words: polyploidy, homoeology, orthology, Gossypium.

Simple methods for isolating homoeologous loci from allopolyploid genomes

Simple methods for isolating homoeologous loci from allopolyploid genomes

Karyological analysis and genome size in Milium (Gramineae) with special reference to polyploidy and chromosomal evolution

Karyotypes, nuclear DNA amounts, and meiotic behaviour are presented for Milium effusum L. (2n = 28), Milium montianum Parl. (2n = 22), and two cytotypes of Milium vernale Bieb. (2n = 8, 10). The bimodal karyotype of M. montianum (8 large and 14 small chromosomes) is described for the first time. Evidence from C-banding and geographical distribution suggests an ancient interracial allopolyploid origin for M. effusum (2n = 28). Although M. montianum is undoubtedly allopolyploid, its parentage is unconfirmed. A strong resemblance between the M. vernale (2n = 8) karyotype and the eight large chromosomes in M. montianum suggests a common ancestry. It is possible that a diploid form of M. effusum contributed the remaining 14 chromosomes. A selective loss of DNA sequences from the smaller chromosomes during the subsequent reorganization of the allopolyploid genome may have enhanced the bimodality of the karyotype. Geographical distribution and a change in the breeding system support the direction of the change x = 5 to x = 4 in M. vernale. Allopolyploidy appears to have played a central role in the chromosome evolution and speciation of Milium.Key words: Milium (Gramineae), karyotype analysis, genome size, polyploidy, chromosome evolution.