Genome redundancy and plasticity within ancient and recent Brassica crop species

The crop species within the genus Brassica have highly replicated genomes. Three base 'diploid' species, Brassica oleracea , B. nigra and B. rapa , are likely ancient polyploids, and three derived allopolyploid species, B. carinata , B. juncea and B. napus , are created from the interspecific hybridization of these base genomes. The base Brassica genome is thought to have hexaploid ancestry, and both recent and ancient polyploidization events have been proposed to generate a large number of genome rearrangements and novel genetic variation for important traits. Here, we revisit and refine these hypotheses. We have examined the B. oleracea linkage map using the Arabidopsis thaliana genome sequence as a template and suggest that there is strong evidence for genome replication and rearrangement within the base Brassicas, but less evidence for genome triplication. We show that novel phenotypic variation within the base Brassicas can be achieved by replication of a single gene, BrFLC , that acts additively to influence flowering time. Within the derived allopolyploids, intergenomic heterozygosity is associated with higher seed yields. Some studies have reported that de novo genomic variation occurs within derived polyploid genomes, whereas other studies have not detected these changes. We discuss reasons for these different findings. Large translocations and tetrasomic inheritance can explain some but not all genomic changes within the polyploids. Transpositions and other small-scale sequence changes probably also have contributed to genomic novelty. Our results have shown that the Brassica genomes are remarkably plastic, and that polyploidy generates novel genetic variation through gene duplication, intergenomic heterozygosity and perhaps epigenetic change.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 665–674.     

Exploring the genomic mysteries of polyploidy in cotton

For several years allopolyploid cottons have been the subject of evolutionary investigations into the genomic mysteries of polyploidy. An array of genomic interactions have been documented, including interlocus concerted evolution, differential rates of genomic evolution and intergenomic sequence transfer. Substantial alterations in gene expression have occurred in response to allopolyploidization, including gene silencing and expression changes that vary by organ. Some of the molecular phenomena occurring in polyploids appear to be non-Mendelian. Many of the genomic and expression alterations have occurred on an evolutionary timescale, whereas others reflect more immediate consequences of genomic merger.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 573–581.     

Whole-genome duplications in South American desert rodents (Octodontidae)

The discovery of tetraploidy in the red viscacha rat, Tympanoctomys barrerae (4 n  = 102) has emphasized the evolutionary role of genome duplication in mammals. The tetraploid status of this species is corroborated here by in situ PCR and Southern blot analysis of a single-copy gene. The species meiotic configuration strongly suggests a hybrid derivation. To investigate the origin of T. barrerae further, the recently described Pipanacoctomys aureus was studied. This 92-chromosome species also has a duplicated genome size, redundant gene copy number and diploid-like meiotic pairing, consistent with an event of allotetraploidization. Phylogenetic analysis of mitochondrial sequences indicates sister-group relationships between these two tetraploid rodents. The new karyotypic data and the phylogenetic relationships suggest the participation of the ancestral lineages of Octomys mimax in the genesis of P. aureus . The high overall DNA similarity and shared band homology revealed by genomic Southern hybridization as well as matching chromosome numbers between O. mimax and the descendant tetraploid species support the notion of introgressive hybridization between these taxa.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 443–451.     

Polyploidy in vertebrate ancestry: Ohno and beyond

Over 30 years ago, Susumu Ohno proposed that two rounds of polyploidy occurred early in vertebrate evolution. We re-examine this proposal using three recent lines of evidence. First, total gene number estimates from completely sequenced genomes suggest an increase in total gene number somewhere along the vertebrate or prevertebrate lineage, compatible with Ohno's model. Second, analyses of homeobox and other genes from amphioxus reveal very extensive gene duplication specifically on the vertebrate lineage. This refines the timing of putative polyploidy to after the divergence of amphioxus and vertebrates. Third, the existence of four-fold paralogy regions in the human genome is suggestive of two rounds of polyploidy, although other explanations are possible. We propose an experimental test, based on chromosomal localization of genes in amphioxus, that should resolve whether paralogy regions are indeed remnants of duplication in vertebrate ancestry.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 425–430.     

Perspectives on polyploidy in plants – ancient and neo

It is timely to re-examine the phenomenon of polyploidy in plants. Indeed, the power of modern molecular technology to provide new insights, and the impetus of genomics, make polyploidy a fit, fashionable and futuristic topic for review. Some historical perspective is essential to understand the meaning of the terms, to recognize what is already known and what is dogma, and to frame incisive questions for future research. Polyploidy is important because life on earth is predominantly a polyploid phenomenon. Moreover, civilization is mainly powered by polyploid food – notably cereal endosperm. Ongoing uncertainty about the origin of triploid endosperm epitomizes our ignorance about somatic polyploidy. New molecular information makes it timely to reconsider how to identity polyploids and what is a polyploid state. A functional definition in terms of a minimal genome may be helpful. Genes are known that can raise or lower ploidy level. Molecular studies can test if, contrary to dogma, the relationship between diploids and polyploids is a dynamic two-way system. We still need to understand the mechanisms and roles of key genes controlling ploidy level and disomic inheritance. New evidence for genome duplications should be compared with old ideas about cryptopolyploidy, and new views of meiosis should not ignore premeiotic genome separation. In practice, new knowledge about polyploidy will be most useful only when it reliably predicts which crops can be usefully improved as stable autopolyploids and which genomes combined to create successful new allopolyloids.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 411–423.     

Endogenous pararetroviruses of allotetraploid Nicotiana tabacum and its diploid progenitors, N. sylvestris and N. tomentosiformis

Endogenous pararetroviruses (EPRVs) represent a new class of dispersed repetitive DNA in plants. The genomes of many Nicotiana species and other solanaceous plants are rich in EPRVs. Distinct EPRV families are present in N. sylvestris ( Ns ) and in N. tomentosiformis ( Nto ), the two diploid progenitors of allotetraploid N. tabacum . Nicotiana EPRVs represent an interesting type of repetitive sequence to analyse in polyploids because of their potential impact on plant fitness and the epigenetic architecture of plant genomes. The Ns EPRV family appears identical in N. sylvestris and N. tabacum , indicating little change has occurred in either species since polyploid formation. By contrast, the Nto EPRV family is larger in N. tomentosiformis than in N. tabacum , suggesting either preferential elimination from the polyploid genome or specific accumulation in the diploid genome following polyploidization. The lability of Nto EPRVs might be enhanced by a frequent association with gypsy retrotransposons. Although some EPRVs are probably benign, others are potentially pathogenic or, conversely, determinants of virus resistance. Normally quiescent EPRVs can be reactivated and cause symptoms of infection in hybrids of species that differ in their EPRV content. EPRVs that furnish immunity to the free virus exemplify the selective value of so-called 'junk' DNA. Variation in the abundance and distribution of EPRVs among related species can be useful in taxonomic and evolutionary studies.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 627–638.     

Genome downsizing in polyploid plants

All else being equal, polyploids are expected to have larger C-values (amount of DNA in the unreplicated gametic nucleus) than their diploid progenitors, increasing in direct proportion with ploidy. This expectation is observed in some polyploid series, especially those newly formed, but there are examples suggesting that C-values in particular polyploids are less than expected. The availability of the Angiosperm DNA C-values database ( http://www.rbgkew.org.uk/cval/homepage.html ) has allowed this question to be addressed across a broad range of angiosperms and has revealed striking results deviating from expectation: (i) mean 1C DNA amount did not increase in direct proportion with ploidy, and (ii) mean DNA amount per basic genome (calculated by dividing the 2C value by ploidy) tended to decrease with increasing ploidy. These results suggest that loss of DNA following polyploid formation, or genome downsizing, may be a widespread phenomenon of considerable biological significance. Recent advances in our understanding of the molecular events that take place following polyploid formation together with new data on how DNA amounts can both increase and decrease provide some insights into how genome downsizing may take place. The nature of the evolutionary forces that may be driving DNA loss are also discussed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 651–663.     

'Why polyploidy is rarer in animals than in plants': myths and mechanisms

Although polyploidy has been involved in speciation in both animals and plants, the general perception is often that it is too rare to have been a significant factor in animal evolution and its role in plant diversification has been questioned. These views have resulted in a bias towards explanations for what deters polyploidy, rather than the somewhat more interesting question of the mechanisms by which polyploidy arises and becomes established in both plants and animals. The evidence for and against some of the traditional views on polyploidy is reviewed, with an attempt to synthesize factors promoting evolution through genome duplication in both groups. It is predicted that polyploidy should be more common in temperate than in tropical breeders because environmental fluctuations may promote unreduced gamete formation, it should be most common in organisms with sufficient numbers of gametes that random meiotic problems can be overcome, and it should be more frequent when mechanisms to promote assortative mating are a direct byproduct of genome duplication.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 453–466.     

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.  ×  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 F₁ 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.  ×  townsendii and S. anglica indicate that in this system, epigenetic changes have followed both hybridization and polyploidization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 475–484.     

Genome-level evolution of resistance genes in Arabidopsis thaliana

Pathogen resistance genes represent some of the most abundant and diverse gene families found within plant genomes. However, evolutionary mechanisms generating resistance gene diversity at the genome level are not well understood. We used the complete Arabidopsis thaliana genome sequence to show that most duplication of individual NBS-LRR sequences occurs at close physical proximity to the parent sequence and generates clusters of closely related NBS-LRR sequences. Deploying the statistical strength of phylogeographic approaches and using chromosomal location as a proxy for spatial location, we show that apparent duplication of NBS-LRR genes to ectopic chromosomal locations is largely the consequence of segmental chromosome duplication and rearrangement, rather than the independent duplication of individual sequences. Although accounting for a smaller fraction of NBS-LRR gene duplications, segmental chromosome duplication and rearrangement events have a large impact on the evolution of this multigene family. Intergenic exchange is dramatically lower between NBS-LRR sequences located in different chromosome regions as compared to exchange between sequences within the same chromosome region. Consequently, once translocated to new chromosome locations, NBS-LRR gene copies have a greater likelihood of escaping intergenic exchange and adopting new functions than do gene copies located within the same chromosomal region. We propose an evolutionary model that relates processes of genome evolution to mechanisms of evolution for the large, diverse, NBS-LRR gene family.     

Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts

Glycine subgenus Glycine , the sister group to the cultivated soybean and its progenitor, have received considerable study over several decades. The combination of biosystematic data and an extensive germplasm collection has provided a strong foundation for molecular systematic studies in the group, including those on allopolyploids. These studies have shown that the various polyploid taxa known from the subgenus are all part of a single large allopolyploid complex, linked by shared diploid genomes. Many elements of the complex have arisen recently, and most show evidence of recurrent origins. However, there are also many dissimilarities among even closely related polyploids. Polyploids differ from one another in such ways as number of origins, amount of allelic diversity harboured at different loci, bidirectional vs. unidirectional origins, retention of ribosomal gene homoeologues, success as measured by geographical range and abundance, and patterns of gene expression.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 583–597.     

The genomics of speciation: investigating the molecular correlates of X chromosome introgression across the hybrid zone between Mus domesticus and Mus musculus

Understanding the genetic details of reproductive isolation is a key goal in the study of speciation. Hybrid zones, geographical regions where two species meet and exchange genes, can provide insight into the genetic basis of reproductive isolation. This is especially true in species with mapped molecular markers because patterns of gene flow can be compared among different genomic regions. Even greater insight can be obtained in species with complete genome sequences because gene identity, gene number and other features of interest can be assessed for genomic regions with different patterns of introgression. Here, we review recent studies on the well-characterized hybrid zone between Mus domesticus and M. musculus , including a detailed survey of patterns of introgression for 13 markers on the X chromosome. We then compare levels of introgression for these 13 regions to a number of genomic attributes inferred from the complete sequence of the X chromosome, with two purposes. First, we identify candidate genes for reproductive isolation by finding genes that map to an X-linked region of reduced introgression and that are only expressed in the male germ line or that show high rates of protein evolution in comparison with rat. Second, we ask whether patterns of gene flow are correlated with recombination rate, gene density, base composition, CpG island density, mutation rate and the rate of protein evolution, as might be expected if many genes contribute to reproductive isolation. We identify seven candidate genes for reproductive isolation between M. domesticus and M. musculus , and our analyses reveal no general correlations between levels of introgression and other measured sequence characteristics. These results underline the utility of the house mouse as a model system for the study of speciation.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 523–534.     

Genome data: what do we learn?

Genome sequence information has continued to accumulate at a spectacular pace during the past year. Details of the sequence and gene content of human chromosome 22 were published. The sequencing and annotation of the first two Arabidopsis thaliana chromosomes was completed. The sequence of chromosome 3 from Plasmodium falciparum, the second sequenced malaria chromosome, was reported, as was that of chromosome 1 from Leishmania major. The complete genomic sequences of five microbes were reported. Approaches to using data from completely sequenced microbial genomes in phylogenetic studies are being explored, as is the application of microarrays to whole genome expression analysis.     

Contribution to the karyological knowledge of Echinops (Asteraceae, Cardueae) and related genera

Twenty-six chromosome counts were made of several genera of the tribe Cardueae from various European and Asian provenances: Acantholepis (one species studied), Amphoricarpus (1), Chardinia (1), Echinops (14 species, 15 populations), Siebera (1), Staehelina (3) and Xeranthemum (4). Eleven of the reports are made for the first time, ten confirm previous counts, while the remainder report disparities with earlier records. The existence of different basic chromosome numbers and ploidy levels suggests dysploidy and polyploidy as the main mechanisms of chromosomal evolution in the taxa considered.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 337−344.     

New perspectives on the mechanisms of chromosome evolution in parasitic flowering plants

In an attempt to find any association between chromosomal characters and parasitism, a cytological study of parasitic flowering plants in Israel has been carried out. While no such association was found, evidence for three levels of chromosome evolution could be discerned: intra-chromosomal modifications, polyploidy per se , and genome restructuring in polyploids. Our conclusions may serve as a paradigm of the multiple pathways of chromosomal evolution in plants in general. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 117–122.     

Uniformity of karyotypes in Ligularia (Asteraceae: Senecioneae), a highly diversified genus of the eastern Qinghai–Tibet Plateau highlands and adjacent areas

Ligularia , a highly diversified genus in the eastern Qinghai–Tibet Plateau and adjacent areas, was chosen as a suitable subject in which to study speciation patterns in this 'hot spot' area at the chromosomal level. Chromosome numbers and karyotypes were studied in 23 populations of 14 species, most of which are endemic to this area. The basic number x  = 29 was confirmed for all species. Ligularia virgaurea was found to have diploid and triploid cytotypes, 2 n  = 58 and 87. Other species are only diploid, with 2 n  = 58. The karyotypes of all populations within any species, and all species spanning most sections and covering most of the morphological range in Ligularia , are very similar to each other, belonging to type 2A according to Stebbin's classification. This karyotype was also found in its close allies, e.g. Cremanthodium , Ligulariopsis , Parasenecio , and Sinacalia . Aneuploid reduction of chromosome number from 2 n  = 60 to 58 and karyotypic variation was found in Ligularia and its allies. Such a chromosomal pattern with few polyploids infers that variation of karyotype structure at the diploid level seems to be the predominant feature of chromosomal evolution in this group and sympatric speciation via hybridization and polyploidization has played a minor role in its species diversity.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 329–342.     

Microarray expression profiling resources for plant genomics

Large volumes of genomic data have been generated for several plant species over the past decade, including structural sequence data and functional annotation at the genome level. Various technologies such as expressed sequence tags (ESTs), massively parallel signature sequencing (MPSS) and microarrays have been used to study gene expression and to provide functional data for many genes simultaneously. This review focuses on recent advances in the application of microarrays in plant genomic research and in gene expression databases available for plants. Large sets of Arabidopsis microarray data are publicly available. Recently developed array platforms are currently being used to generate genome-wide expression profiles for several crop species. Coupled to these platforms are public databases that provide access to these large-scale expression data, which can be used to aid the functional discovery of gene function.     

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content

Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.