The evolutionary history of the allopolyploid Squalius alburnoides (Cyprinidae) complex in the northern Iberian Peninsula

Understanding the population structure, population dynamics and processes that give rise to polyploidy and helps to maintain it is central to our knowledge of the evolution of asexual vertebrates. Previous studies revealed high genetic diversity and several reproductive pathways in the southern populations of the Squalius alburnoides hybrid complex. In contrast, lower genetic variability and the associated limited chance of introducing new genetic combinations may threaten the survival of the northern Mondego populations. We analysed the genetic diversity and structure of nine populations of S. alburnoides in the Iberian Peninsula using microsatellite loci to provide further insights on the evolutionary history of this complex. Special attention was given to the less-studied northern populations (Mondego and Douro basins). Marked population structure, a high frequency of private alleles and a high diversity of some biotypes in the Douro basin indicate that some northern populations may not be at high risk of extinction, contrary to what was expected. The genetic diversity found in the northern Douro populations contradicts the general trend of remarkable genetic impoverishment northwards that occurs in other species and regions. The results indicate the possible existence of a glacial refugium in the Rabaçal River, corroborating findings in other species of this region. Historical events seem to have affected the geographical patterns of genetic variability found among and within the northern and southern populations of this complex and contributed to different patterns of genome composition. Therefore, historical events might have a major role in the long-term persistence of some polyploid hybrid taxa.     

多倍体植物中基因表达模式的变化

植物杂交和多倍化能导致基因组结构发生变化,并显著影响了基因表达,因此认为杂交和多倍化是促进植物进化的一个重要力量。近些年大量的研究表明植物多倍化后基因表达模式发生了复杂的改变,包括基因沉默、基因表达的基因组偏向性及组织特异性、基因激活等现象,本文对这些现象及其特点和机制进行了综述。     

Evolution of duplicate gene expression in polyploid and hybrid plants

Allopolyploidy is a prominent mode of speciation in flowering plants. On allopolyploidy, genomic changes can take place, including chromosomal rearrangement and changes in gene expression; these processes continue over evolutionary time. Recent studies of gene expression in polyploid and hybrid plants, reviewed here, have examined expression in natural polyploids and synthetic neopolyploids as well as in diploid and F(1) hybrids. Considerable changes in gene expression have been observed in allopolyploids, including up- or downregulation of expression in the polyploids compared with their parents, unequal expression of duplicated genes, and silencing of one copy. Genes in a variety of functional categories show altered expression, and the patterns vary considerably by gene. Some changes seem to be stochastic, whereas others are repeatable. Gene expression changes can be organ specific. Reciprocal silencing of duplicates in different organs has been observed, suggesting subfunctionalization and long-term retention of duplicates. It has become clear that hybridization has a much greater effect than chromosome doubling on gene expression in allopolyploids. Diploid and triploid F(1) hybrids can show alterations of expression levels compared with their parents. Parent-of-origin effects on gene expression have been examined, and loss of gene imprinting has been shown. Some gene expression changes in polyploids and hybrids can be correlated with phenotypic effects. Demonstrated mechanisms of gene expression changes include DNA methylation, histone modifications, and antisense RNA. Several hypotheses have been proposed for why gene expression is altered in allopolyploids and hybrids.     

Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus,Nemertea): hybridization,polyploidy and the Meselson effect

Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L. pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated π_N/π_S ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among‐species allele sharing and read‐count distribution, however, reveals that L. pseudolacteus is a triploid hybrid between Atlantic populations of L. sanguineus and L. lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L. pseudolacteus and conclude that (i) the peculiarities of L. pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.     

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.     

Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta

Background

Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to have formed less than one million years ago, along with its putative diploid progenitors (O. punctata and O. officinalis), are quite suitable for the study of polyploid genome evolution using a comparative genomics approach.

Results

Here, we performed a comparative study of a large genomic region surrounding the Shattering4 locus in O. minuta, as well as in O. punctata and O. officinalis. Duplicated genomes in O. minuta have maintained the diploid genome organization, except for several structural variations mediated by transposon movement. Tandem duplicated gene clusters are prevalent in the Sh4 region, and segmental duplication followed by random deletion is illustrated to explain the gene gain-and-loss process. Both copies of most duplicated genes still persist in O. minuta. Molecular evolution analysis suggested that these duplicated genes are equally evolved and mostly manipulated by purifying selection. However, cDNA-SSCP analysis revealed that the expression patterns were dramatically altered between duplicated genes: nine of 29 duplicated genes exhibited expression divergence in O. minuta. We further detected one gene silencing event that was attributed to gene structural variation, but most gene silencing could not be related to sequence changes. We identified one case in which DNA methylation differences within promoter regions that were associated with the insertion of one hAT element were probably responsible for gene silencing, suggesting a potential epigenetic gene silencing pathway triggered by TE movement.

Conclusions

Our study revealed both genetic and epigenetic mechanisms involved in duplicated gene silencing in the allotetraploid O. minuta.     

Polymorphism of major ribosomal gene chromosomal sites (NOR-phenotypes) in the hybridogenetic fish <Emphasis Type="Italic">Squalius alburnoides</Emphasis> complex (Cyprinidae) assessed through crossing experiments

Chromosomal locations of major ribosomal sites, i.e. NOR-phenotypes, were assigned in Squalius alburnoides complex using sequential chromomycin A₃ (CMA₃)- and silver (Ag)-staining. This hybridogenetic Iberian minnow comprises diploid, triploid and tetraploid forms that arose by interspecific hybridisation between S. pyrenaicus and an unknown species. Inheritance of NOR patterns was studied by means of crossing experiments involving most diploid–polyploid forms of the S. alburnoidescomplex with identified specific genotype constitution. In all the specimens studied, the NORs were localised in the short arms of submetacentric chromosomes. Although S. pyrenaicus presented only one pair of NOR-bearing chromosomes, the data from experimental crosses evidenced that S. alburnoides complex was characterised by a multiple NOR phenotype composed of one chromosome pair with stable NORs and two chromosome pairs with NOR site polymorphism of presence/absence type. These data suggest that the karyotype of the unknown parental species of the S. alburnoidescomplex should have a multiple NOR pattern and emphasised the role of the all-male diploid linage in the dynamics and evolutionary potential of the S.alburnoidescomplex allowing the preservation of the missing ancestor genome. Cross-analyses evidenced that in spite of the high polymorphic nature of NORs in this fish complex, we have no reason to reject the hypothesis that their inheritance patterns were in accordance with Mendelian segregation.     

Untangling Nucleotide Diversity and Evolution of the H Genome in Polyploid Hordeum and Elymus Species Based on the Single Copy of Nuclear Gene DMC1

Numerous hybrid and polypoid species are found within the Triticeae. It has been suggested that the H subgenome of allopolyploid Elymus (wheatgrass) species originated from diploid Hordeum (barley) species, but the role of hybridization between polyploid Elymus and Hordeum has not been studied. It is not clear whether gene flow across polyploid Hordeum and Elymus species has occurred following polyploid speciation. Answering these questions will provide new insights into the formation of these polyploid species, and the potential role of gene flow among polyploid species during polyploid evolution. In order to address these questions, disrupted meiotic cDNA1 (DMC1) data from the allopolyploid StH Elymus are analyzed together with diploid and polyploid Hordeum species. Phylogenetic analysis revealed that the H copies of DMC1 sequence in some Elymus are very close to the H copies of DMC1 sequence in some polyploid Hordeum species, indicating either that the H genome in theses Elymus and polyploid Hordeum species originated from same diploid donor or that gene flow has occurred among them. Our analysis also suggested that the H genomes in Elymus species originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools. Nucleotide diversity (π) of the DMC1 sequences on H genome from polyploid species (π = 0.02083 in Elymus, π = 0.01680 in polyploid Hordeum) is higher than that in diploid Hordeum (π = 0.01488). The estimates of Tajima''s D were significantly departure from the equilibrium neutral model at this locus in diploid Hordeum species (P<0.05), suggesting an excess of rare variants in diploid species which may not contribute to the origination of polyploids. Nucleotide diversity (π) of the DMC1 sequences in Elymus polyploid species (π = 0.02083) is higher than that in polyploid Hordeum (π = 0.01680), suggesting that the degree of relationships between two parents of a polyploid might be a factor affecting nucleotide diversity in allopolyploids.     

Multiple origins and nrDNA internal transcribed spacer homeologue evolution in the Glycine tomentella (Leguminosae) allopolyploid complex

Despite the importance of polyploidy in the evolution of plants, patterns of molecular evolution and genomic interactions following polyploidy are not well understood. Nuclear ribosomal DNA is particularly complex with respect to these genomic interactions. The composition of nrDNA tandem arrays is influenced by intra- and interlocus concerted evolution and their expression is characterized by patterns such as nucleolar dominance. To understand these complex interactions it is important to study them in diverse natural polyploid systems. In this study we use direct sequencing to isolate and characterize nrDNA internal transcribed spacer (ITS) homeologues from multiple accessions of six different races in the Glycine tomentella allopolyploid complex. The results indicate that in most allopolyploid accessions both homeologous nrDNA repeats are present, but that there are significant biases in copy number toward one homeologue, possibly resulting from interlocus concerted evolution. The predominant homeologue often differs between races and between accessions within a race. A phylogenetic analysis of ITS sequences provides evidence for multiple origins in several of the polyploid races. This evidence for diverse patterns of nrDNA molecular evolution and multiple origins of polyploid races will provide a useful system for future studies of natural variation in patterns of nrDNA expression.     

Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review

The Iberian minnow Leuciscus alburnoides represents a complex of diploid and polyploid forms with altered modes of reproduction. In the present paper, we review the recent data on the origin, reproductive modes, and inter-relationships of the various forms of the complex, in order to predict its evolutionary potential. The complex follows the hybrid-origin model suggested for most other asexual vertebrates. Diploid and triploid females from the southern river basins exhibit reproductive modes that cannot be conveniently placed into the categories generally recognised for these vertebrate complexes, which imply continuous shifting between forms, where genomes derived from both parental ancestors are cyclically lost, gained or replaced. Replacement of nuclear genomes allow the introduction of novel genetic material, that may compensate for the disadvantages of asexual reproduction. Contrasting with most other vertebrate complexes, L. alburnoides males are fertile and play an important role in the dynamics of the complex. Moreover, diploid hybrid males may have initiated a tetraploidization process, when a diploid clonal sperm fertilised a diploid egg. This direct route to tetraploidy by originating fish with the right constitution for normal meiosis (symmetric), may eventually lead to a new sexually reproducing polyploid species. This case-study reinforces the significance of hybridisation and polyploidy in evolution and diversification of vertebrates.     

Genomes,multiple origins,and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3-D gene sequences

Relationships among the various diploid and polyploid taxa that comprise Glycine tomentella have been hypothesized from crossing studies, isozyme data, and repeat length variation for the 5S nuclear ribosomal gene loci. However, several key questions have persisted, and detailed phylogenetic evidence from homoeologous nuclear genes has been lacking. The histone H3-D locus is single copy in diploid Glycine species and has been used to elucidate relationships among diploid races of G. tomentella, providing a framework for testing genome origins in the polyploid complex. For all six G. tomentella polyploid races (T1-T6), alleles at two homoeologous histone H3-D loci were isolated and analyzed phylogenetically with alleles from diploid Glycine species, permitting the identification of all of the homoeologous genomes of the complex. Allele networks were constructed to subdivide groups of homoeologous alleles further, and two-locus genotypes were constructed using these allele classes. Results suggest that some races have more than one origin and that interfertility within races has led to lineage recombination. Most alleles in polyploids are identical or closely related to alleles in diploids, suggesting recency of polyploid origins and spread beyond Australia. These features parallel the other component of the Glycine subgenus Glycine polyploid complex, G. tabacina, one of whose races shares a diploid genome with a G. tomentella polyploid race.     

Genomic in situ hybridization (GISH) discriminates between the A and the B genomes in diploid and tetraploid Setaria species.

Genomic in situ hybridization (GISH) was used to investigate genomic relationships between different Setaria species of the foxtail millet gene pool (S. italica) and one interspecific F1 hybrid. The GISH patterns obtained on the two diploid species S. viridis (genome A) and S. adhaerans (genome B), and on their F1 hybrid showed clear differentiation between these two genomes except at the nucleolar organizing regions. Similar GISH patterns allowed differentiation of S. italica from S. adhaerans. However, GISH patterns did not distinguish between the genomes of S. italica and its putative wild ancestor S. viridis. GISH was also applied to polyploid Setaria species and enabled confirmation of the assumed allotetraploid nature of S. faberii and demonstration that both S. verticillata and S. verticillata var. ambigua were also allotetraploids. All these tetraploid species contained two sets of 18 chromosomes each, one from genome A and the other from genome B. Only one polyploid species, S. pumila, was shown to bear an unknown genomic composition that is not closely related either to genome A or to genome B.     

植物多倍体中的基因组印记

植物多倍体在自然界中广泛存在,这说明拥有多套遗传物质使得多倍体的适应进化具有优势。新多倍体形成后,一些基因组范围的变化较迅速地发生在多倍体形成开端,另一些在长期进化中发生。由于受到遗传、表观等因素的影响,亲本对于新形成多倍体基因组的贡献不均衡。这种偏向于某个亲本基因组的显性优势,称为基因组印记。植物多倍体中的基因组印记表现为基因组偏向性的序列消除、不均衡基因表达、基因沉默,这些受到基因组合并及DNA甲基化、核仁显性等表观因素影响。本文旨在为多倍体基因组进化及育种的相关研究提供参考。