The impact of polyploidy on grass genome evolution

Does time matter? Intraspecific diversity of ribosomal RNA genes in lineages of the allopolyploid model grass Brachypodium hybridum with different evolutionary ages

BACKGROUND

Polyploidisation often results in genome rearrangements that may involve changes in both the single-copy sequences and the repetitive genome fraction. In this study, we performed a comprehensive comparative analysis of repetitive DNA, with a particular focus on ribosomal DNA (rDNA), in Brachypodium hybridum (2n = 4x = 30, subgenome composition DDSS), an allotetraploid resulting from a natural cross between two diploid species that resemble the modern B. distachyon (2n = 10; DD) and B. stacei (2n = 20; SS). Taking advantage of the recurrent origin of B. hybridum, we investigated two genotypes, Bhyb26 and ABR113, differing markedly in their evolutionary age (1.4 and 0.14 Mya, respectively) and which resulted from opposite cross directions. To identify the origin of rDNA loci we employed cytogenetic and molecular methods (FISH, gCAPS and Southern hybridisation), phylogenetic and genomic approaches.

RESULTS

Unlike the general maintenance of doubled gene dosage in B. hybridum, the rRNA genes showed a remarkable tendency towards diploidisation at both locus and unit levels. While the partial elimination of 35S rDNA units occurred in the younger ABR113 lineage, unidirectional elimination of the entire locus was observed in the older Bhyb26 lineage. Additionally, a novel 5S rDNA family was amplified in Bhyb26 replacing the parental units. The 35S and 5S rDNA units were preferentially eliminated from the S- and D-subgenome, respectively. Thus, in the more ancient B. hybridum lineage, Bhyb26, 5S and 35S rRNA genes are likely expressed from different subgenomes, highlighting the complexity of polyploid regulatory networks.

CONCLUSION

Comparative analyses between two B. hybridum lineages of distinct evolutionary ages revealed that although the recent lineage ABR113 exhibited an additive pattern of rDNA loci distribution, the ancient lineage Bhyb26 demonstrated a pronounced tendency toward diploidisation manifested by the reduction in the number of both 35S and 5S loci. In conclusion, the age of the allopolyploid appears to be a decisive factor in rDNA turnover in B. hybridum.

Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis

Polyploidization plays an important role in plant speciation and adaptation. To address the role of polyploidization in grass diversification, we studied Phragmites australis, an invasive species with intraspecific variation in chromosome numbers ranging from 2n = 36 to 144. We utilized a combined analysis of ploidy estimation, phylogeny, population genetics and model simulations to investigate the evolution of P. australis. Using restriction site-associated DNA sequencing (RAD-seq), we conducted a genome-wide analysis of 88 individuals sourced from diverse populations worldwide, revealing the presence of six distinct intraspecific lineages with extensive genetic admixture. Each lineage was characterized by a specific ploidy level, predominantly tetraploid or octoploid, indicative of multiple independent polyploidization events. The population size of each lineage has declined moderately in history while remaining large, except for the North American native and the US Land types, which experienced constant population size contraction throughout their history. Our investigation did not identify direct association between polyploidization events and grass invasions. Nonetheless, we observed octoploid and hexaploid lineages at contact zones in Romania, Hungary, and South Africa, suggestively due to genomic conflicts arising from allotetraploid parental lineages.

Polyploidy in maize: from evolution to breeding

Polyploidy played an important role in the evolution of the three most important crops: wheat, maize and rice, each of them providing a unique model for studying allopolyploidy, segmental alloploidy or paleopolyploidy. However, its genetic and evolutionary role is still vague. The undelying mechanisms and consequences of polyploidy remain fundamental objectives in the study of eukaryotes. Maize is one of the underutilized crops at the polyploid level. This species has no stable natural polyploids, the existing ones being artificially obtained. From the experimental polyploid series of maize, only the tetraploid forms (4n = 40) are of interest. They are characterized by some valuable morphological, physiological and biochemical features, superior to the diploid forms from which they originated, but also by some drawbacks such as: reduced fertility, slower development, longer vegetation period, low productivity and adaptedness. Due to these barriers to using tetraploids in field production, maize tetraploids primarily found utility in scientific studies regarding genetic variability, inbreeding, heterosis and gene dosage effect. Since the first mention of a triploid maize plant to present, many scientists and schools, devoted their efforts to capitalize on the use of polyploidy in maize. Despite its common disadvantages as a crop, significant progress in developing tetraploid maize with good agronomic performance was achieved leading to registered tetraploid maize varieties. In this review we summarize and discuss the different aspects of polyploidy in maize, such as evolutionary context, methods of induction, morphology, fertility issue, inheritance patterns, gene expression and potential use.

Doubled haploid technology and synthetic apomixis: Recent advances and applications in future crop breeding

Doubled haploid (DH) technology and synthetic apomixis approaches can considerably shorten breeding cycles and enhance breeding efficiency. Compared with traditional breeding methods, DH technology offers the advantage of rapidly generating inbred lines, while synthetic apomixis can effectively fix hybrid vigor. In this review, we focus on (i) recent advances in identifying and characterizing genes responsible for haploid induction (HI), (ii) the molecular mechanisms of HI, (iii) spontaneous haploid genome doubling, and (iv) crop synthetic apomixis. We also discuss the challenges and potential solutions for future crop breeding programs utilizing DH technology and synthetic apomixis. Finally, we provide our perspectives about how to integrate DH and synthetic apomixis for precision breeding and de novo domestication.

Non-B-form DNA is associated with centromere stability in newly-formed polyploid wheat

Non-B-form DNA differs from the classic B-DNA double helix structure and plays a crucial regulatory role in replication and transcription. However, the role of non-B-form DNA in centromeres, especially in polyploid wheat, remains elusive. Here, we systematically analyzed seven non-B-form DNA motif profiles (A-phased DNA repeat, direct repeat, G-quadruplex, inverted repeat, mirror repeat, short tandem repeat, and Z-DNA) in hexaploid wheat. We found that three of these non-B-form DNA motifs were enriched at centromeric regions, especially at the CENH3-binding sites, suggesting that non-B-form DNA may create a favorable loading environment for the CENH3 nucleosome. To investigate the dynamics of centromeric non-B form DNA during the alloploidization process, we analyzed DNA secondary structure using CENH3 ChIP-seq data from newly formed allotetraploid wheat and its two diploid ancestors. We found that newly formed allotetraploid wheat formed more non-B-form DNA in centromeric regions compared with their parents, suggesting that non-B-form DNA is related to the localization of the centromeric regions in newly formed wheat. Furthermore, non-B-form DNA enriched in the centromeric regions was found to preferentially form on young LTR retrotransposons, explaining CENH3's tendency to bind to younger LTR. Collectively, our study describes the landscape of non-B-form DNA in the wheat genome, and sheds light on its potential role in the evolution of polyploid centromeres.

Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer

The accumulation of proline in response to the most diverse types of stress is a widespread defense mechanism. In prokaryotes, fungi, and certain unicellular eukaryotes (green algae), the first two reactions of proline biosynthesis occur through two distinct enzymes, γ-glutamyl kinase (GK E.C. 2.7.2.11) and γ-glutamyl phosphate reductase (GPR E.C. 1.2.1.41), encoded by two different genes, ProB and ProA, respectively. Plants, animals, and a few unicellular eukaryotes carry out these reactions through a single bifunctional enzyme, the Δ1-pyrroline-5-carboxylate synthase (P5CS), which has the GK and GPR domains fused. To better understand the origin and diversification of the P5CS gene, we use a robust phylogenetic approach with a broad sampling of the P5CS, ProB and ProA genes, including species from all three domains of life. Our results suggest that the collected P5CS genes have arisen from a single fusion event between the ProA and ProB gene paralogs. A peculiar fusion event occurred in an ancestral eukaryotic lineage and was spread to other lineages through horizontal gene transfer. As for the diversification of this gene family, the phylogeny of the P5CS gene in plants shows that there have been multiple independent processes of duplication and loss of this gene, with the duplications being related to old polyploidy events.

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.

Molecular evolution and diversification of phytoene synthase (PSY) gene family

Phytoene synthase (PSY) is a crucial enzyme required for carotenoid biosynthesis, encoded by a gene family conserved in carotenoid-producing organisms. This gene family is diversified in angiosperms through distinct duplication events. Understanding diversification patterns and the evolutionary history of the PSY gene family is important for explaining carotenogenesis in different plant tissues. This study identified 351 PSY genes in 166 species, including Viridiplantae, brown and red algae, cyanobacteria, fungi, arthropods, and bacteria. All PSY genes displayed conserved intron/exon organization. Fungi and arthropod PSY sequences were grouped with prokaryote PSY, suggesting the occurrence of horizontal gene transfer. Angiosperm PSY is split into five subgroups. One includes the putative ortholog of PSY3 (Subgroup E3) from eudicots, and the other four subgroups include PSY from both monocots and eudicots (subgroups E1, E2, M1, and M2). Expression profile analysis revealed that PSY genes are constitutively expressed across developmental stages and anatomical parts, except for the eudicot PSY3, with root-specific expression. This study elucidates the molecular evolution and diversification of the PSY gene family, furthering our understanding of variations in carotenogenesis.

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.

Analysis of Homologous Regions of Small RNAs MIR397 and MIR408 Reveals the Conservation of Microsynteny among Rice Crop-Wild Relatives

MIRNAs are small non-coding RNAs that play important roles in a wide range of biological processes in plant growth and development. MIR397 (involved in drought, low temperature, and nitrogen and copper (Cu) starvation) and MIR408 (differentially expressed in response to environmental stresses such as copper, light, mechanical stress, dehydration, cold, reactive oxygen species, and drought) belong to conserved MIRNA families that either negatively or positively regulate their target genes. In the present study, we identified the homologs of MIR397 and MIR408 in Oryza sativa and its six wild progenitors, three non-Oryza species, and one dicot species. We analyzed the 100 kb segments harboring MIRNA homologs from 11 genomes to obtain a comprehensive view of their community evolution around these loci in the farthest (distant) relatives of rice. Our study showed that mature MIR397 and MIR408 were highly conserved among all Oryza species. Comparative genomics analyses also revealed that the microsynteny of the 100 kb region surrounding MIRNAs was only conserved in Oryza spp.; disrupted in Sorghum, maize, and wheat; and completely lost in Arabidopsis. There were deletions, rearrangements, and translocations within the 100 kb segments in Oryza spp., but the overall microsynteny of the region was maintained. The phylogenetic analyses of the precursor regions of all MIRNAs under study revealed a bimodal clade of common origin. This comparative analysis of miRNA involved in abiotic stress tolerance in plants provides a powerful tool for future Oryza research. Crop wild relatives (CWRs) offer multiple traits with potential to decrease the amount of yield loss owing to biotic and abiotic stresses. Using a comparative genomics approach, the exploration of CWRs as a source of tolerance to these stresses by understanding their evolution can be further used to leverage their yield potential.

Polystyrene nanoplastics affect seed germination, cell biology and physiology of rice seedlings in-short term treatments: Evidence of their internalization and translocation

Agroecosystems represent more and more a huge long-term sink for plastic compounds which inevitably undergo fragmentation, generating micro- and nano-plastics, with potential adverse effects on soil chemistry and living organisms. The present work was focused on the short-term effects of two different concentrations of polystyrene nanoplastics (PSNPs) (0.1 or 1 g L^-1 suspensions) on rice seedlings starting from seed germination, hypothesizing that possible acute effects on seedlings could depend on oxidative damage trigged by PSNPs internalization. As shown by TEM analysis, PSNPs were absorbed by roots and translocated to the shoots, affected root cell ultrastructure, the germination process, seedling growth and root mitotic activity, inducing cytogenetic aberration. Treatments were not correlated with increase in oxidative stress markers, but rather with a different pattern of their localization both in roots and in shoots, impairing H₂O₂ homeostasis and membrane damage, despite the adequate antioxidant response recorded. The harmful effects of PSNPs on cell biology and physiology of rice seedlings could be caused not only by a direct action by the PSNPs but also by changes in the production/diffusion of ROS at the tissue/cellular level.

Tetraploids expanded beyond the mountain niche of their diploid ancestors in the mixed-ploidy grass Festuca amethystina L

One promising area in understanding the responses of plants to ongoing global climate change is the adaptative effect of polyploidy. This work examines whether there is a coupling between the distribution of cytotypes and their biogeographical niche, and how different niches will affect their potential range. The study uses a range of techniques including flow cytometry, gradient and niche analysis, as well as distribution modelling. In addition, climatic, edaphic and habitat data was used to analyse environmental patterns and potential ranges of cytotypes in the first wide-range study of Festuca amethystina-a mixed-ploidy mountain grass. The populations were found to be ploidy homogeneous and demonstrate a parapatric pattern of cytotype distribution. Potential contact zones have been identified. The tetraploids have a geographically broader distribution than diploids; they also tend to occur at lower altitudes and grow in more diverse climates, geological units and habitats. Moreover, tetraploids have a more extensive potential range, being six-fold larger than diploids. Montane pine forests were found to be a focal environment suitable for both cytotypes, which has a central place in the environmental space of the whole species. Our findings present polyploidy as a visible driver of geographical, ecological and adaptive variation within the species.

The 10,000-Year Success Story of Wheat!

Wheat is one of the most important cereal crops in the world as it is used in the production of a diverse range of traditional and modern processed foods. The ancient varieties einkorn, emmer, and spelt not only played an important role as a source of food but became the ancestors of the modern varieties currently grown worldwide. Hexaploid wheat (Triticum aestivum L.) and tetraploid wheat (Triticum durum Desf.) now account for around 95% and 5% of the world production, respectively. The success of this cereal is inextricably associated with the capacity of its grain proteins, the gluten, to form a viscoelastic dough that allows the transformation of wheat flour into a wide variety of staple forms of food in the human diet. This review aims to give a holistic view of the temporal and proteogenomic evolution of wheat from its domestication to the massively produced high-yield crop of our day.

The genus Deschampsia and the epithet " alpina"

The epithet "alpina" has been recurrently used in the genus Deschampsia to name plants located in northern regions of Europe, Asia and North America, as a species (Deschampsiaalpina (L.) Roem. & Schult.), but also in infraspecific categories (Deschampsiacespitosasubsp.alpina Tzvel. and Deschampsiacespitosavar.alpina Schur.). The morphological and molecular available evidence suggests the existence of a single species, Deschampsiacespitosa (L.) P. Beauv., in which individuals belonging to the same morphological gradient have received different names in different taxonomic categories throughout its wide distribution range. An evaluation of the available names indicates that all uses of the epithet "alpina" are illegitimate. A new combination is proposed at the infraspecific level as Deschampsiacespitosasubsp.neoalpina Chiapella, Xue & Greimler.

Genome Size, Chromosome Number and Morphological Data Reveal Unexpected Infraspecific Variability in Festuca (Poaceae)

Polyploidy has played an important evolutionary role in the genus Festuca (Poaceae), and several ploidy levels (ranging from 2n = 2x = 14 to 2n = 12x = 84) have been detected to date. This study aimed to estimate the genome size and ploidy level of two subspecies belonging to the F. yvesii polyploid complex by flow cytometry and chromosome counting. The phenotypic variation of the cytotypes was also explored, based on herbarium material. The genome size of F. yvesii subsp. lagascae has been estimated for the first time. Nuclear 2C DNA content of F. yvesii subsp. summilusitana ranged from 21.44 to 31.91 pg, while that of F. yvesii subsp. lagascae was from 13.60 to 22.31 pg. We report the highest ploidy level detected for Festuca (2n = 14x = 98) and previously unknown cytotypes. A positive correlation between holoploid genome size and chromosome number counts shown herein was confirmed. The morphometric approach showed a slight trend towards an increase in the size of some organs consistent with the variation in the ploidy level. Differences in characters were usually significant only among the most extreme cytotypes of each subspecies, but, even in this case, the high overlapping ranges prevent their distinction.

Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry (Fragaria × ananassa)

Strawberries produce numerous volatile compounds that contribute to the unique flavors of fruits. Among the many volatiles, γ-decalactone (γ-D) has the greatest contribution to the characteristic fruity aroma in strawberry fruit. The presence or absence of γ-D is controlled by a single locus, FaFAD1. However, this locus has not yet been systematically characterized in the octoploid strawberry genome. It has also been reported that the volatile content greatly varies among the strawberry varieties possessing FaFAD1, suggesting that another genetic factor could be responsible for the different levels of γ-D in fruit. In this study, we explored the genomic structure of FaFAD1 and determined the allele dosage of FaFAD1 that regulates variations of γ-D production in cultivated octoploid strawberry. The genome-wide association studies confirmed the major locus FaFAD1 that regulates the γ-D production in cultivated strawberry. With the hybrid capture-based next-generation sequencing analysis, a major presence-absence variation of FaFAD1 was discovered among γ-D producers and non-producers. To explore the genomic structure of FaFAD1 in the octoploid strawberry, three bacterial artificial chromosome (BAC) libraries were developed. A deletion of 8,262 bp was consistently found in the FaFAD1 region of γ-D non-producing varieties. With the newly developed InDel-based codominant marker genotyping, along with γ-D metabolite profiling data, we revealed the impact of gene dosage effect for the production of γ-D in the octoploid strawberry varieties. Altogether, this study provides systematic information of the prominent role of FaFAD1 presence and absence polymorphism in producing γ-D and proposes that both alleles of FaFAD1 are required to produce the highest content of fruity aroma in strawberry fruit.

Genetic diversity of Asian and European common wheat lines assessed by fluorescence in situ hybridization

Understanding the genetic diversity of wheat is important for wheat breeding and improvement. However, there have been limited attempts to evaluate wheat diversity using fluorescence in situ hybridization (FISH). In this study, the chromosomal structures of 149 wheat accessions from 13 countries located between the latitudes of 30°N and 45°N, the principal growing region for wheat, were characterized using FISH with pTa535 and pSc119.2 probes. The ranges of the numbers of FISH types in the A-, B-, and D-genome chromosomes were 2-8, 3-7, and 2-4, respectively, and the average numbers in the A and B genomes were greater than in the D genome. Chromosomal translocations were detected by these probes, and previously undescribed translocations were also observed. Using the FISH, the genetic relationships among the 149 common wheat lines were divided into three groups (G1, G2, and G3). G1 mainly consisted of southern European lines, G2 consisted of most lines from Japan and some lines from western Asia, China, and Korea, and G3 consisted of the other lines from southern Europe and most of the lines from western Asia, China, and Korea. FISH karyotypes of wheat chromosomes distinguished chromosomal structural variations, revealing the genetic diversity among wheat varieties. Furthermore, these results provide valuable information for the further genetic improvement of wheat in China.

Origins and chromosome differentiation of Thinopyrum elongatum revealed by PepC and Pgk1 genes and ND-FISH

Thinopyrum elongatum is an important gene pool for wheat genetic improvement. However, the origins of the Thinopyrum genomes and the nature of the genus' intraspecific relationships are still controversial. In this study, we used single-copy nuclear genes and non-denaturing fluorescence in situ hybridization (ND-FISH) to characterize genome constitution and chromosome differentiation in Th. elongatum. According to phylogenetic analyses based on PepC and Pgk1 genes, there was an E genome with three versions (E^e, E^b, E^x) and St genomes in the polyploid Th. elongatum. The ND-FISH results of pSc119.2 and pAs1 revealed that the karyotypes of diploid Th. elongatum and Th. bessarabicum were different, and the chromosome differentiation occurred among accessions of the diploid Th. elongatum. In addition, the tetraploid Th. elongatum has two groups of ND-FISH karyotype, indicating that the tetraploid Th. elongatum might be a segmental allotetraploid. In summary, our results suggested that the diploid Th. elongatum, Th. Bessarabicum, and Pseudoroegneria were the donors of the E^e, E^b, and St genomes to the polyploid Th. elongatum, respectively.

Histone H3K27 dimethylation landscapes contribute to genome stability and genetic recombination during wheat polyploidization

Bread wheat (Triticum aestivum) is an allohexaploid that was formed via two allopolyploidization events. Growing evidence suggests histone modifications are involved in the response to 'genomic shock' and environmental adaptation during polyploid formation and evolution. However, the role of histone modifications, especially histone H3 lysine-27 dimethylation (H3K27me2), in genome evolution remains elusive. Here we analyzed H3K27me2 and H3K27me3 profiles in hexaploid wheat and its tetraploid and diploid relatives. Although H3K27me3 levels were relatively stable among wheat species with different ploidy levels, H3K27me2 intensities increased concurrent with increased ploidy levels, and H3K27me2 peaks were colocalized with massively amplified DTC transposons (CACTA family) in euchromatin, which may silence euchromatic transposons to maintain genome stability during polyploid wheat evolution. Consistently, the distribution of H3K27me2 is mutually exclusive with another repressive histone mark, H3K9me2, that mainly silences transposons in heterochromatic regions. Remarkably, the regions with low H3K27me2 levels (named H3K27me2 valleys) were associated with the formation of DNA double-strand breaks in genomes of wheat, maize (Zea mays) and Arabidopsis. Our results provide a comprehensive view of H3K27me2 and H3K27me3 distributions during wheat evolution, which support roles for H3K27me2 in silencing euchromatic transposons to maintain genome stability and in modifying genetic recombination landscapes. These genomic insights may empower breeding improvement of crops.

Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families

Protein domains can be regarded as sections of protein sequences capable of folding independently and performing specific functions. In addition to amino-acid level changes, protein sequences can also evolve through domain shuffling events such as domain insertion, deletion, or duplication. The evolution of protein domains can be studied by tracking domain changes in a selected set of species with known phylogenetic relationships. Here, we conduct such an analysis by defining domains as “features” or “descriptors,” and considering the species (target + outgroup) as instances or data-points in a data matrix. We then look for features (domains) that are significantly different between the target species and the outgroup species. We study the domain changes in 2 large, distinct groups of plant species: legumes (Fabaceae) and grasses (Poaceae), with respect to selected outgroup species. We evaluate 4 types of domain feature matrices: domain content, domain duplication, domain abundance, and domain versatility. The 4 types of domain feature matrices attempt to capture different aspects of domain changes through which the protein sequences may evolve—that is, via gain or loss of domains, increase or decrease in the copy number of domains along the sequences, expansion or contraction of domains, or through changes in the number of adjacent domain partners. All the feature matrices were analyzed using feature selection techniques and statistical tests to select protein domains that have significant different feature values in legumes and grasses. We report the biological functions of the top selected domains from the analysis of all the feature matrices. In addition, we also perform domain-centric gene ontology (dcGO) enrichment analysis on all selected domains from all 4 feature matrices to study the gene ontology terms associated with the significantly evolving domains in legumes and grasses. Domain content analysis revealed a striking loss of protein domains from the Fanconi anemia (FA) pathway, the pathway responsible for the repair of interstrand DNA crosslinks. The abundance analysis of domains found in legumes revealed an increase in glutathione synthase enzyme, an antioxidant required from nitrogen fixation, and a decrease in xanthine oxidizing enzymes, a phenomenon confirmed by previous studies. In grasses, the abundance analysis showed increases in domains related to gene silencing which could be due to polyploidy or due to enhanced response to viral infection. We provide a docker container that can be used to perform this analysis workflow on any user-defined sets of species, available at https://cloud.docker.com/u/akshayayadav/repository/docker/akshayayadav/protein-domain-evolution-project.

Hidden Hybridization and Habitat Differentiation in a Mediterranean Macrophyte, the Euryhaline Genus Ruppia

In many aquatic plant taxa, classification based on morphology has always been difficult. Molecular markers revealed that the complexity in several of these aquatic taxa could be addressed to recurrent hybridization events and cryptic species diversity. The submerged macrophyte genus Ruppia is one of these aquatic genera with a complex taxonomy due to the absence of clear distinguishable traits and several hybridization events. Two species co-exist throughout Europe, R. maritima and R. spiralis (previously known as R. cirrhosa), but recent molecular studies also found several indications of hybridization, introgression and chloroplast capture between these species. However, the full extent and frequency of hybridization and introgression in this genus has not been studied so far, nor is it clear how these hybrid lineages can co-exist locally with their parental species. In this paper, we wanted to detect whether a single coastal wetland where both species co-exist can act as a Ruppia hybrid zone. As a case study, we chose the Camargue, a Mediterranean coastal wetland that harbors a wide diversity in aquatic habitats, especially in terms of salinity and hydro-regime. We sampled several Ruppia populations within this wetland. To identify each sample and reconstruct the local genetic structure of the two parental species and their hybrids, we used both chloroplast and nuclear microsatellite markers. Afterward, we tested whether different species had different habitat preferences. Our results confirmed that R. maritima and R. spiralis are two strongly divergent species with different reproductive ecologies and different habitat preferences. This prevents frequent hybridization and consequently we could not detect any trace of a recent hybridization event. However, we found several populations of later-generation hybrids, including a population of R. maritima x hybrid backcrosses. The hybrid populations occupy a different habitat and are genetically distinct from their parental species, although they tend to be morphological similar to parental R. maritima. Although local hybridization and introgression in Ruppia is less frequent than we expected, the taxonomy of Ruppia is complicated due to ancient hybridizations and several back-crossings.

The effects of hybridization and genome doubling in plant evolution via allopolyploidy

Polyploidy is a pervasive and recurring phenomenon across the tree of life, which occurred at variable time scales, ecological amplitudes and cell types, and is especially prominent in the evolutionary histories of plants. Importantly, many of the world's most important crops and noxious invasive weeds are recent polyploids. Polyploidy includes two major types, autopolyploidy, referring to doubling of a single species genome, and allopolyploidy referring to doubling of two or more merged genomes via biological hybridization of distinct but related species. The prevalence of both types of polyploidy implies that both genome doubling alone and doubling coupled with hybridization confer selective advantages over their diploid progenitors under specific circumstances. In cases of allopolyploidy, the two events, genome doubling and hybridization, have both advantages and disadvantages. Accumulated studies have established that, in allopolyploidy, some advantage(s) of doubling may compensate for the disadvantage(s) of hybridity and vice versa, although further study is required to validate generality of this trend. Some studies have also revealed a variety of non-Mendelian genetic and genomic consequences induced by doubling and hybridization separately or concertedly in nascent allopolyploidy; however, the significance of which to the immediate establishment and longer-term evolutionary success of allopolyploid species remain to be empirically demonstrated and ecologically investigated. This review aims to summarize recent advances in our understanding of the roles of hybridization and genome doubling, in separation and combination, in the evolution of allopolyploid genomes, as well as fruitful future research directions that are emerging from these studies.

Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids

Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

BACKGROUND

Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved in plant growth and immunity are known to shape compositions of microbial communities, the effects of host evolution on microbial communities are not well understood.

RESULTS

We show evidence that both host speciation and domestication shape seed bacterial and fungal community structures. Genome types of rice contributed to compositional variations of both communities, showing a significant phylosymbiosis with microbial composition. Following the domestication, abundance inequality of bacterial and fungal communities also commonly increased. However, composition of bacterial community was relatively conserved, whereas fungal membership was dramatically changed. These domestication effects were further corroborated when analyzed by a random forest model. With these changes, hub taxa of inter-kingdom networks were also shifted from fungi to bacteria by domestication. Furthermore, maternal inheritance of microbiota was revealed as a major path of microbial transmission across generations.

CONCLUSIONS

Our findings show that evolutionary processes stochastically affect overall composition of microbial communities, whereas dramatic changes in environments during domestication contribute to assembly of microbiotas in deterministic ways in rice seed. This study further provides new insights on host evolution and microbiome, the starting point of the holobiome of plants, microbial communities, and surrounding environments.

Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies

Herbicide resistant (HR) weeds are of major concern in modern agriculture. This situation is exacerbated by the massive adoption of herbicide-based technologies along with the overuse of a few active ingredients to control weeds over vast areas year after year. Also, many other anthropological, biological, and environmental factors have defined a higher rate of herbicide resistance evolution in numerous weed species around the world. This review focuses on two central points: 1) how these factors have affected the resistance evolution process; and 2) which cultural practices and new approaches would help to achieve an effective integrated weed management. We claim that global climate change is an unnoticed factor that may be acting on the selection of HR weeds, especially those evolving into non-target-site resistance mechanisms. And we present several new tools -such as Gene Drive and RNAi technologies- that may be adopted to cope with herbicide resistance spread, as well as discuss their potential application at field level. This is the first review that integrates agronomic and molecular knowledge of herbicide resistance. It covers not only the genetic basis of the most relevant resistance mechanisms but also the strengths and weaknesses of traditional and forthcoming agricultural practices.

The Evolutionary Dynamics of a Novel Miniature Transposable Element in the Wheat Genome

The discovery of Mariam, a wheat-unique miniature transposable element family, was reported in our previous study. We have also shown the possible impact of Mariam insertions on the expression of wheat genes. However, the evolutionary dynamics of Mariam was not studied in detail. In this study, we have assessed the insertion sites of Mariam family in different wheat species. In-silico analysis of Mariam insertions has allowed the discovery of two different sequence versions of Mariam, and that Mariam might have been recently active in wild emmer wheat genome (T. turgidum ssp diccocoides). In addition, the analysis of Mariam insertional polymorphism has facilitated the discovery of large genomic rearrangement events, such as deletions and introgressions in the wheat genome. The dynamics of Mariam family sheds light on the evolution of wheat.

Molecular cytogenetics of valuable Arctic and sub-Arctic pasture grass species from the Aveneae/Poeae tribe complex (Poaceae)

Abstract

Background

Grasslands in the Arctic tundra undergo irreversible degradation due to climatic changes and also over-exploitation and depletion of scarce resources. Comprehensive investigations of cytogenomic structures of valuable Arctic and sub-Arctic grassland species is essential for clarifying their genetic peculiarities and phylogenetic relationships, and also successful developing new forage grass cultivars with high levels of adaptation, stable productivity and longevity. We performed molecular cytogenetic characterization of insufficiently studied pasture grass species (Poaceae) from related genera representing two neighboring clades: 1) Deschampsia and Holcus; 2) Alopecurus, Arctagrostis and Beckmannia, which are the primary fodder resources in the Arctic tundra.

Results

We constructed the integrated schematic maps of distribution of these species in the northern, central and eastern parts of Eurasia based on the currently available data as only scattered data on their occurrence is currently available. The species karyotypes were examined with the use of DAPI-banding, multicolour FISH with 35S rDNA, 5S rDNA and the (GTT)₉ microsatellite motif and also sequential rapid multocolour GISH with genomic DNAs of Deschampsia sukatschewii, Deschampsia flexuosa and Holcus lanatus belonging to one of the studied clades. Cytogenomic structures of the species were specified; peculiarities and common features of their genomes were revealed. Different chromosomal rearrangements were detected in Beckmannia syzigachne, Deschampsia cespitosa and D. flexuosa; B chromosomes with distinct DAPI-bands were observed in karyotypes of D. cespitosa and H. lanatus.

Conclusions

The peculiarities of distribution patterns of the examined chromosomal markers and also presence of common homologous DNA repeats in karyotypes of the studies species allowed us to verify their relationships. The obtained unique data on distribution areas and cytogenomic structures of the valuable Arctic and sub-Arctic pasture species are important for further genetic and biotechnological studies and also plant breeding progress.

A two-step mutation process in the double WS1 homologs drives the evolution of burley tobacco, a special chlorophyll-deficient mutant with abnormal chloroplast development

MAIN CONCLUSION

The functional homologs WS1A and WS1B, identified by map-based cloning, control the burley character by affecting chloroplast development in tobacco, contributing to gene isolation and genetic improvement in polyploid crops. Burley represents a special type of tobacco (Nicotiana tabacum L.) cultivar that is characterized by a white stem with a high degree of chlorophyll deficiency. Although important progress in the research of burley tobacco has been made, the molecular mechanisms underlying this character remain unclear. Here, on the basis of our previous genetic analyses and preliminary mapping results, we isolated the White Stem 1A (WS1A) and WS1B genes using a map-based cloning approach. WS1A and WS1B are functional homologs with completely identical biological functions and highly similar expression patterns that control the burley character in tobacco. WS1A and WS1B are derived from Nicotiana sylvestris and Nicotiana tomentosiformis, the diploid ancestors of Nicotiana tabacum, respectively. The two genes encode zinc metalloproteases of the M50 family that are highly homologous to the Ethylene-dependent Gravitropism-deficient and Yellow-green 1 (EGY1) protein of Arabidopsis and the Lutescent 2 (L2) protein of tomato. Transmission electron microscopic examinations indicated that WS1A and WS1B are involved in the development of chloroplasts by controlling the formation of thylakoid membranes, very similar to that observed for EGY1 and L2. The genotyping of historical tobacco varieties revealed that a two-step mutation process occurred in WS1A and WS1B during the evolution of burley tobacco. We also discussed the strategy for gene map-based cloning in polyploid plants with complex genomes. This study will facilitate the identification of agronomically important genes in tobacco and other polyploid crops and provide insights into crop improvement via molecular approaches.

Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation

Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.

A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.

Parallelism and convergence in post-domestication adaptation in cereal grasses

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species

Chromosomal inversions occur in natural populations of many species, and may underlie reproductive isolation and local adaptation. Traditional methods of inversion discovery are labor-intensive and lack sensitivity. Here, we report the use of three-dimensional contact probabilities between genomic loci as assayed by chromosome-conformation capture sequencing (Hi-C) to detect multi-megabase polymorphic inversions in four barley genotypes. Inversions are validated by fluorescence in situ hybridization and Bionano optical mapping. We propose Hi-C as a generally applicable method for inversion discovery in natural populations.

Nucleolar Dominance in a Tetraploidy Hybrid Lineage Derived From Carassius auratus red var. () × Megalobrama amblycephala ()

Nucleolar dominance is related to the expression of 45S rRNA genes inherited from one progenitor due to the silencing of the other progenitor’s rRNA genes. To investigate nucleolar dominance associated with tetraploidization, we analyzed the changes regarding the genetic traits and expression of 45S rRNA genes in tetraploidy hybrid lineage including F₁ allotetraploids (4n = 148) and F₂ autotetraploids (4n = 200) derived from the distant hybridization of Carassius auratus red var. (2n = 100) () ×Megalobrama amblycephala (2n = 48) (). Results showed that nucleolar dominance from the females was established in F₁ hybrids and it was inherited in F₂ hybrids, suggesting that tetraploidization can lead to rapid establishment of nucleolar dominance in the hybrid origin’s tetraploid lineage. These results extend the knowledge of nucleolar dominance in polyploidy hybrid animals, which are of significance for the evolution of hybrids in vertebrates.

Morphometric traits in the fine-leaved fescues depend on ploidy level: the case of Festuca amethystina L

BACKGROUND

Polyploid specimens are usually characterized by greater exuberance: they reach larger sizes and/or have a larger number of some organs. Festuca amethystina L. belongs to the section Aulaxyper. Based on morphological features, four subspecies of F. amethystina have been already identified. On the other hand, it has two cytotypes: diploid and tetraploid. The main aim of our study was to distinguish morphological differences between the cytotypes of F. amethystina, assuming that its phenotype differs significantly.

METHODS

The nuclear DNA content was measured by flow cytometry in dry leaves from specimens originating from 13 populations of F. amethystina. Several macrometric and micrometric traits of stems, spikelets and leaf blades were taken into account in the comparative analysis of two cytotypes.

RESULTS

In the case of cytotypes, specimens of tetraploids were larger than diploids. The conducted morphometric analysis of leaf cross-sections showed significant differences between the cytotypes.

DISCUSSION

The research has confirmed for the first time that in the case of F. amethystina the principle of greater exuberance of polyploids is true. Differences between the cytotypes are statistically significant, however, they are not enough to make easy the distinction of cytotypes on the basis of the measurements themselves. Our findings favor the rule known in Festuca taxonomy as a whole, i.e. that the ploidy level can be one of the main classification criteria.

Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity

NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.

Epigenetic perspectives on the evolution and domestication of polyploid plant and crops

Polyploidy or whole genome duplication (WGD) is a prominent feature for genome evolution of some animals and all flowering plants, including many important crops such as wheat, cotton, and canola. In autopolyploids, genome duplication often perturbs dosage regulation on biological networks. In allopolyploids, interspecific hybridization could induce genetic and epigenetic changes, the effects of which could be amplified by genome doubling (ploidy changes). Albeit the importance of genetic changes, some epigenetic changes can be stabilized and transmitted as epialleles into the progeny, which are subject to natural selection, adaptation, and domestication. Here we review recent advances for general and specific roles of epigenetic changes in the evolution of flowering plants and domestication of agricultural crops.

Chromosomal distribution of pTa-535, pTa-86, pTa-713, 35S rDNA repetitive sequences in interspecific hexaploid hybrids of common wheat (Triticum aestivum L.) and spelt (Triticum spelta L.)

Fluorescent in situ hybridization (FISH) relies on fluorescent-labeled probes to detect specific DNA sequences in the genome, and it is widely used in cytogenetic analyses. The aim of this study was to determine the karyotype of T. aestivum and T. spelta hybrids and their parental components (three common wheat cultivars and five spelt breeding lines), to identify chromosomal aberrations in the evaluated wheat lines, and to analyze the distribution of polymorphisms of repetitive sequences in the examined hybrids. The FISH procedure was carried out with four DNA clones, pTa-86, pTa-535, pTa-713 and 35S rDNA used as probes. The observed polymorphisms between the investigated lines of common wheat, spelt and their hybrids was relatively low. However, differences were observed in the distribution of repetitive sequences on chromosomes 4A, 6A, 1B and 6B in selected hybrid genomes. The polymorphisms observed in common wheat and spelt hybrids carry valuable information for wheat breeders. The results of our study are also a valuable source of knowledge about genome organization and diversification in common wheat, spelt and their hybrids. The relevant information is essential for common wheat breeders, and it can contribute to breeding programs aimed at biodiversity preservation.

How much do we know about the frequency of hybridisation and polyploidy in the Mediterranean region?

Natural hybridisation and polyploidy are currently recognised as drivers of biodiversity, despite early scepticism about their importance. The Mediterranean region is a biodiversity hotspot where geological and climatic events have created numerous opportunities for speciation through hybridisation and polyploidy. Still, our knowledge on the frequency of these mechanisms in the region is largely limited, despite both phenomena are frequently cited in studies of Mediterranean plants. We reviewed information available from biodiversity and cytogenetic databases to provide the first estimates of hybridisation and polyploidy frequency in the Mediterranean region. We also inspected the most comprehensive modern Mediterranean Flora (Flora iberica) to survey the frequency and taxonomic distribution of hybrids and polyploids in Iberian Peninsula. We found that <6% of Mediterranean plants were hybrids, although a higher frequency was estimated for the Iberian Peninsula (13%). Hybrids were concentrated in few families and in even fewer genera. The overall frequency of polyploidy (36.5%) was comparable with previous estimates in other regions; however our estimates increased when analysing the Iberian Peninsula (48.8%). A surprisingly high incidence of species harbouring two or more ploidy levels was also observed (21.7%). A review of the available literature also showed that the ecological factors driving emergence and establishment of new entities are still poorly studied in the Mediterranean flora, although geographic barriers seem to play a major role in polyploid complexes. Finally, this study reveals several gaps and limitations in our current knowledge about the frequency of hybridisation and polyploidy in the Mediterranean region. The obtained estimates might change in the future with the increasing number of studies; still, rather than setting the complete reality, we hope that this work triggers future studies on hybridisation and polyploidy in the Mediterranean region.

Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat

Genome duplications aid in the formation of novel molecular networks through regulatory differentiation of the duplicated genes and facilitate adaptation to environmental change. Hexaploid wheat, Triticum aestivum, contains three homoeologous chromosome sets, the A-, B-, and D-subgenomes, which evolved through interspecific hybridization and subsequent whole-genome duplication. The divergent expression patterns of the homoeologs in hexaploid wheat suggest that they have undergone transcriptional and/or functional differentiation during wheat evolution. However, the distribution of transcriptionally differentiated homoeologs in gene regulatory networks and their related biological functions in hexaploid wheat are still largely unexplored. Therefore, we retrieved 727 publicly available wheat RNA-sequencing (RNA-seq) datasets from various tissues, developmental stages, and conditions, and identified 10,415 expressed homoeologous triplets. Examining the co-expression modules in the wheat transcriptome, we found that 66% of the expressed homoeologous triplets possess all three homoeologs grouped in the same co-expression modules. Among these, 15 triplets contain co-expressed homoeologs with differential expression levels between homoeoalleles across ≥ 95% of the 727 RNA-seq datasets, suggesting a consistent trend of homoeolog expression bias. In addition, we identified 2,831 differentiated homoeologs that showed gene expression patterns that deviated from those of the other two homoeologs. We found that seven co-expression modules contained a high proportion of such differentiated homoeologs, which accounted for ≥ 20% of the genes in each module. We also found that five of the co-expression modules are abundantly composed of genes involved in biological processes such as chloroplast biogenesis, RNA metabolism, putative defense response, putative posttranscriptional modification, and lipid metabolism, thereby suggesting that, the differentiated homoeologs might highly contribute to these biological functions in the gene network of hexaploid wheat.

History vs. legend: Retracing invasion and spread of Oxalis pes-caprae L. in Europe and the Mediterranean area

Oxalis pes-caprae L. is a South African geophyte that behaves as an invasive in the eurimediterranean area. According to a long-established hypothesis, O. pes-caprae may have invaded Europe and the Mediterranean area starting from a single plant introduced in the Botanical Garden of Malta at the beginning of the 19^th century. The aim of this work was to test this hypothesis, to track the arrival of O. pes-caprae in different countries of the Euro-Mediterranean area and to understand the pathways of spreading and particularly its starting point(s). Historical data attesting the presence of the plant in the whole Euro-Mediterranean region were collected from different sources: herbarium specimens, Floras and other botanical papers, plant lists of gardens, catalogs of plant nurseries and plant dealers. First records of the plant (both cultivated and wild) for each Territorial Unit (3rd level of NUTS) were selected and used to draw up a diachronic map and an animated graphic. Both documents clearly show that oldest records are scattered throughout the whole area, proving that the plant arrived in Europe and in the Mediterranean region more times independently and that its spreading started in different times from several different centers of invasion. Botanical gardens and other public or private gardens, nurseries and plant dealers, and above all seaside towns and harbors seemingly played a strategic role as a source of either intentional and unintentional introduction or spread. A geographic profiling analysis was performed to analyse the data. We used also techniques (Silhouette, Kmeans and Voronoi tessellation) capable of verifying the presence of more than one independent clusters of data on the basis of their geographical distribution. Microsatellites were employed for a preliminary analysis of genetic variation in the Mediterranean. Even if the sampling was insufficient, particularly among the populations of the original area, our data supported three main groups of populations, one of them corresponding to the central group of populations identified by GP analysis, and the other two corresponding, respectively, to the western and the eastern cluster of data. The most probable areas of origin of the invasion in the three clusters of observations are characterized by the presence of localities where the invasive plant was cultivated, with the exception of the Iberian cluster of observation where the observations in the field predate the data about known cultivation localities. Alternative possible reasons are also suggested, to explain the current prevalence of pentaploid short-styled plants in the Euro-Mediterranean area.

Empirical evidence of fixed and homeostatic patterns of polyploid advantage in a keystone grass exposed to drought and heat stress

A long-standing hypothesis in evolutionary biology is that polyploid plants have a fitness advantage over diploids in climatically variable or extreme habitats. Here we provide the first empirical evidence that polyploid advantage in these environments is caused by two distinct processes: homeostatic maintenance of reproductive output under elevated abiotic stress, and fixed differences in seed development. In an outdoor climate manipulation experiment using coastal to inland Australian populations of the perennial grass Themeda triandra Forssk., we found that total output of viable seed in drought- and heat-stressed tetraploid plants was over four times higher than in diploids, despite being equal under more favourable growing conditions. Tetraploids also consistently produced heavier seeds with longer hygroscopic awns, traits which increase propagule fitness in extreme environments. These differences add to fitness benefits associated with broader-scale local adaptation of inland T. triandra populations to drought stress. Our study provides evidence that nucleotypic effects of genome size and increased reproductive flexibility can jointly underlie polyploid advantage in plants in stressful environments, and argue that ploidy can be an important criterion for selecting plant populations for use in genetic rescue, restoration and revegetation projects, including in habitats affected by climate change.

Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum

Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes), and TOR (seven haplotypes). Comparative genomic approaches showed that these sugarcane loci presented a high degree of conservation of gene content and collinearity (synteny) with sorghum and rice orthologous regions, but were invaded by transposable elements (TE). All the homo/homeologous haplotypes of LFY, PHYC, and TOR are likely to be functional, because they are all under purifying selection (dN/dS ≪ 1). However, they were found to participate in a nonequivalently manner to the overall expression of the corresponding gene. SNPs, indels, and amino acid substitutions allowed inferring the S. officinarum or S. spontaneum origin of the TOR haplotypes, which further led to the estimation that these two sugarcane ancestral species diverged between 2.5 and 3.5 Ma. In addition, analysis of shared TE insertions in TOR haplotypes suggested that two autopolyploidization may have occurred in the lineage that gave rise to S. officinarum, after its divergence from S. spontaneum.

Peterson, Soreng RJ, Paszko B. Molecular phylogenetics of cool-season grasses in the subtribes Agrostidinae, Anthoxanthinae, Aveninae, Brizinae, Calothecinae, Koeleriinae and Phalaridinae (Poaceae, Pooideae, Poeae, Poeae chloroplast group 1)

Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3'-end of the external transcribed spacer (ETS)) and five plastid regions (matK, trnL-trnF, atpF-atpH, psbK-psbI, psbA-rps19-trnH), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia, Gaudinia, Koeleria, Rostraria, Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis/Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia, Leptophyllochloa, Sphenopholis, Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum, Trisetum cernuum, T. irazuense and T. macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetum subsect. Sibirica, and affinities of Lagurus ovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostis coarctata, Dichelachne, Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxia effusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Deyeuxia as a synonym of Calamagrostis s.str. Furthermore, the two species of Ammophila are not sister taxa and are nested among different groups of Calamagrostis s.str., supporting their classification in Calamagrostis. Agrostis, Lachnagrostis and Polypogon form a clade and species of each are variously intermixed in plastid and nuclear ribosomal trees. Additionally, all but one species from South America classified in Deyeuxia sect. Stylagrostis resolve in Holcinae p.p. (Deschampsia). The current phylogenetic results support recognition of the latter species in Deschampsia, and we also demonstrate Scribneria is part of this clade. Moreover, Holcinae is not monophyletic in its current circumscription because Deschampsia does not form a clade with Holcus and Vahlodea, which are sister taxa. The results support recognition of Deschampsia in its own subtribe Aristaveninae. Substantial further changes to the classification of these grasses will be needed to produce generic circumscriptions consistent with phylogenetic evidence. The following 15 new combinations are made: Calamagrostis × calammophila, C. breviligulata, C. breviligulata subsp. champlainensis, C. × don-hensonii, Deschampsia aurea, D. bolanderi, D. chrysantha, D. chrysantha var. phalaroides, D. eminens, D. eminens var. fulva, D. eminens var. inclusa, D. hackelii, D. ovata, and D. ovata var. nivalis. D. podophora; the new name Deschampsia parodiana is proposed; the new subtribe Lagurinae is described; and a second-step lectotype is designated for the name Deyeuxia phalaroides.

Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.

Ecological range shift in the polyploid members of the South American genus Fosterella (Bromeliaceae)

Background and Aims

The distribution of polyploidy along a relatively steep Andean elevation and climatic gradient is studied using the genus Fosterella L.B. Sm. (Bromeliaceae) as a model system. Ecological differentiation of cytotypes and the link of polyploidy with historical biogeographic processes such as dispersal events and range shift are assessed.

Methods

4',6-Diamidino-2-phenylindole (DAPI) staining of nuclei and flow cytometry were used to estimate the ploidy levels of 159 plants from 22 species sampled throughout the distribution range of the genus. Ecological differentiation among ploidy levels was tested by comparing the sets of climatic variables. Ancestral chromosome number reconstruction was carried out on the basis of a previously generated phylogeographic framework.

Key Results

This study represents the first assessment of intrageneric, intraspecific and partially intrapopulational cytotype diversity in a genus of the Bromeliaceae family. In Fosterella , the occurrence of polyploidy was limited to the phylogenetically isolated penduliflora and rusbyi groups. Cytotypes were found to be ecologically differentiated, showing that polyploids preferentially occupy colder habitats with high annual temperature variability (seasonality). The combined effects of biogeographic history and adaptive processes are presumed to have shaped the current cytotype distribution in the genus.

Conclusions

The results provide indirect evidence for both adaptive ecological and non-adaptive historical processes that jointly influenced the cytotype distribution in the predominantly Andean genus Fosterella (Bromeliaceae). The results also exemplify the role of polyploidy as an important driver of speciation in a topographically highly structured and thus climatically diverse landscape.

Comparative molecular cytogenetic characterization of seven Deschampsia (Poaceae) species

The genus Deschampsia P. Beauv (Poaceae) involves a group of widespread polymorphic species. Some of them are highly tolerant to stressful and variable environmental conditions, and D. antarctica is one of the only two vascular plants growing in Antarctic. This species is a source of useful for selection traits and a valuable model for studying an environmental stress tolerance in plants. Genome diversity and comparative chromosomal phylogeny within the genus have not been studied yet as karyotypes of most Deschampsia species are poorly investigated. We firstly conducted a comparative molecular cytogenetic analysis of D. antarctica (Antarctic Peninsula) and related species from various localities (D. cespitosa, D. danthonioides, D. elongata, D. flexuosa (= Avenella flexuosa), D. parvula and D. sukatschewii by fluorescence in situ hybridization with 45S and 5S rDNA, DAPI-banding and sequential rapid in situ hybridization with genomic DNA of D. antarctica, D. cespitosa, and D. flexuosa. Based on patterns of distribution of the examined markers, chromosomes of the studied species were identified. Within these species, common features as well as species peculiarities in their karyotypic structure and chromosomal distribution of molecular cytogenetic markers were characterized. Different chromosomal rearrangements were detected in D. antarctica, D. flexuosa, D. elongata and D. sukatschewii. In karyotypes of D. antarctica, D. cespitosa, D. elongata and D. sukatschewii, 0-3 B chromosomes possessed distinct DAPI-bands were observed. Our findings suggest that the genome evolution of the genus Deschampsia involved polyploidy and also different chromosomal rearrangements. The obtained results will help clarify the relationships within the genus Deschampsia, and can be a basis for the further genetic and biotechnological studies as well as for selection of plants tolerant to extreme habitats.

Adaptation of the Pivotal-Differential Genome Pattern for the Induction of Intergenomic Chromosome Recombination in Hybrids of Synthetic Amphidiploids within Triticeae Tribe

A pivotal-differential evolution pattern is when two allopolyploids share a common genome, which is called pivotal, and differ with respect to the other genome or genomes, called differential. This feature induces the intergenomic recombination between chromosomes of differential genomes, which can lead to speciation. Our study is a cytomolecular insight into this mechanism which was adapted for the induction of intergenomic chromosome recombination in hybrids of synthetic amphidiploids Aegilops biuncialis × S. cereale (UUMMRR) and triticale (AABBRR) where R-genome was pivotal. We observed chromosome recombination events which were induced by both: (1) random chromosome fragmentation and non-homologous chromosome end joining at mitosis of root meristem cells and (2) intergenomic chromosome associations at meiosis of pollen mother cells (PMCs) of F₁ hybrids. Reciprocal chromosome translocations were identified in six F₁ plants and 15 plants of F₂ generation using fluorescence in situ hybridization (FISH) with DNA clones (pTa-86, pTa-k374, pTa-465, pTa-535, pTa-k566, and pTa-713). We observed signals of pTa-86, pTa-535, and pTa-k566 probes in several chromosome breakpoints. The comparison of the DNA clone sequences distinguished a number of common motifs, which can be considered as characteristics of chromosome breakpoint loci. Immunodetection of synaptonemal complex proteins and genomic in situ hybridization analysis at meiosis of PMCs of F₁ hybrids showed, that the homologous pairing of pivotal R-genome chromosomes is crucial for the fertility of F₁ hybrids, however, these chromosomes can be also involved in the intergeneric recombination.

A cryptic species produced by autopolyploidy and subsequent introgression involving Medicago prostrata (Fabaceae)

Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species was formed through HHS by sampling eight nuclear loci and 22 individuals, with additional individuals from related species, using gene capture and Illumina sequencing. Phylogenetic inference and coalescent simulations were performed to infer the causes of gene tree incongruence. We found no evidence that phylogenetic differences among M. prostrata individuals were the result of HHS. Instead, an autopolyploid origin of tetraploids with introgression from tetraploids of the M. sativa complex is likely. We argue that tetraploid M. prostrata individuals constitute a new species, characterised by a partially non-overlapping distribution and distinctive alleles (from the M. sativa complex). No gene flow from tetraploid to diploid M. prostrata is apparent, suggesting partial reproductive isolation. Thus, speciation via autopolyploidy appears to have been reinforced by introgression. This raises the intriguing possibility that introgressed alleles may be responsible for the increased range exploited by tetraploid M. prostrata with respect to that of the diploids.