Genome evolution in polyploids

Extensive genome evolution distinguishes maize within a stable tribe of grasses

Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy - a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum. In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea, 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.

Revisiting Citrus Rootstocks Polyploidy as a Means to Improve Drought Resilience: Sometimes Less Is More

Polyploid varieties have been suggested as an alternative approach to promote drought tolerance in citrus crops. In this study, we compared the responses of diploid and tetraploid Sunki 'Tropical' rootstocks to water deficit when grafted onto 'Valencia' sweet orange trees and subjected to water withholding in isolation or competition experiments under potted conditions. Our results revealed that, when grown in isolation, tetraploid rootstocks took longer to show drought symptoms, but this advantage disappeared when grown in competition under the same soil moisture conditions. The differences in drought responses were mainly associated with variations in endogenous leaf levels of abscisic acid (ABA), hydrogen peroxide (H₂O₂) and carbohydrates among treatments. Overall, tetraploids were more affected by drought in individual experiments, showing higher H₂O₂ production, and in competition experiments, rapidly increasing ABA production to regulate stomatal closure and reduce water loss through transpiration. Therefore, our results highlight the crucial importance of evaluating diploid and tetraploid rootstocks under the same soil moisture conditions to better simulate field conditions, providing important insights to improve selection strategies for more resilient citrus rootstocks.

Genome-wide characterization of cytochrome P450 genes reveals the potential roles in fruit ripening and response to cold stress in tomato

Plant cytochrome P450 (CYP) superfamily, the largest enzyme metabolism family, has been identified in many species and plays a vital role in plant development and stress response via secondary metabolite biosynthesis. A comprehensive identification and functional investigation of CYPs in tomato plants would contribute to deeper understanding of their biological significance. In this study, 268 tomato CYP genes were identified and found to be unevenly located on 12 chromosomes. Based on the phylogenetic analysis, these 268 SlCYPs were classed into two distinct clades (A-type and non-A-type) and nine clans, including 48 families. Moreover, 67 tandem and 22 WGD (whole genome duplication)/segmental duplication events were detected, of which 12 SlCYP genes experienced both WGD/segmental and tandem duplication events, indicating that tandem duplication plays a major role in the expansion of the SlCYP family. Besides, 48 pairs containing 41 SlCYP and 44 AtCYP genes were orthologous, while 216 orthologous pairs were obtained between tomato and potato. The expression level of all SlCYP genes in tomato tissues at different development stages was analyzed, and most expressed SlCYPs showed a tissue-specific pattern. Meanwhile, 143 differentially expressed SlCYPs were identified under cold stress. Furthermore, the RT-qPCR results indicated that SlCYPs may be involved in fruit ripening and cold tolerance in tomato seedlings. These findings provide valuable insights into the evolutionary relationships and functional characteristics of SlCYPs, which can be utilized for further investigation of fruit metabolic pathways and cold tolerance in tomato.

Identification and Validation of Reference Genes for qRT-PCR Analysis of Petal-Color-Related Genes in Rosa praelucens

The flower's color is regarded as one of the most outstanding features of the rose. Rosa praelucens Byhouwer, an endemic and critically endangered decaploid wild rose species, is abundant in phenotypic diversity, especially in flower color variation, from white to different degrees of pink. The mechanism underlying this variation, e.g., the level of petal-color-related genes, is worth probing. Seven candidate reference genes for qRT-PCR analysis, including tubulin α chain (TUBA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H2B (Histone2A), eukaryotic translation elongation factor 1-α (EEF1A), 60S ribosomal protein (RPL37), eukaryotic translation initiation factor 1-α (EIF1A), and aquaporins (AQP), were detected from the transcriptome datasets of full blooming flowers of white-petaled and pink-petaled individuals, and their expression stabilities were evaluated through qRT-PCR analysis. According to stability rankings analysis, EEF1A showed the highest stability and could be chosen as the most suitable reference gene. Moreover, the reliability of EEF1A was demonstrated via qRT-PCR analysis of six petal-color-related target genes, the expression patterns of which, through EEF1A normalization, were found to be consistent with the findings of transcriptome analysis. The result provides an optimal reference gene for exploring the expression level of petal-color-related genes in R. praelucens, which will accelerate the dissection of petal-color-variation mechanisms in R. praelucens.

Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND

Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.

RESULTS

The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.

CONCLUSIONS

This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

Polyploidy as a strategy to increase taxane production in yew cell cultures: Obtaining and characterizing a Taxus baccata tetraploid cell line

Novel approaches to optimize the production of plant specialized metabolites are crucial to reach maximum productivity of plant biofactories. Plant polyploidization frequently enhances protein synthesis and thereby increases the biosynthesis of specialized metabolites. Paclitaxel is a valuable anticancer agent scarcely produced in nature. Therefore, plant biofactories represent a sustainable alternative source of this compound and related taxanes. With the aim of improving the productivity of Taxus spp. cell cultures, we induced polyploidy in vitro by treating immature embryos of Taxus baccata with colchicine. To obtain the polyploid cell lines, calli were induced from T. baccata plantlets previously treated with colchicine and ploidy levels were accurately identified using flow cytometry. In terms of cell morphology, tetraploid cells were about 3-fold bigger than the diploid cells. The expression of taxane pathway genes was higher in the tetraploid cell line compared to the diploid cells. Moreover, taxane production was 6.2-fold higher and the production peak was achieved 8 days earlier than in the diploid cell line, indicating a higher productivity. The obtained tetraploid cell line proved to be highly productive, constituting a step forward towards the development of a bio-sustainable production system for this chemotherapeutic drug.

Evolution of sex in crops: recurrent scrap and rebuild

Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.

Effects of homoeologous exchange on gene expression and alternative splicing in a newly formed allotetraploid wheat

Homoeologous exchange (HE) is a major mechanism generating post-polyploidization genetic variation with important evolutionary consequences. However, the direct impacts of HE on gene expression and transcript diversity in allopolyploids without the intertwined evolutionary processes remain to be fully understood. Here, we analyzed high-throughput RNA-seq data of young leaves from plant groups of a synthetic allotetraploid wheat (AADD), which contained variable numbers of HEs. We aimed to investigate if and to which extent HE directly impacts gene expression and alternative splicing (AS). We found that HE impacts expression of genes located within HE regions primarily via a cis-acting dosage effect, which led to significant changes in the total expression level of homoeologous gene pairs, especially for homoeologs whose original expression was biased. In parallel, HE also influences expression of a large number of genes residing in non-HE regions by trans-regulation leading to convergent expression of homoeologs. Intriguingly, when taking the original relative homoeolog expression states into account, homoeolog pairs under trans-effect are more prone to manifesting a convergent response to the HEs whereas those under cis-regulation tended to show further exacerbated subgenome-biased expression. Moreover, HE-induced quantitative, largely individual-specific, changes of AS events were detected. Similar to homoeologous expression, homoeo-AS events under trans-effect were more responsive to HE. HE therefore exerts multifaceted immediate effects on gene expression and, to a less extent, on individualized transcript diversity in nascent allopolyploidy.

Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the Invasive Sphagneticola trilobata and the Native S. calendulacea in South China, and Implications for Its Invasiveness

The role of hybridization is significant in biological invasion, and thermotolerance is a trait critical to range expansions. The South American Sphagneticola trilobata is now widespread in South China, threatening the native S. calendulacea by competition and hybridization. Furthermore, upon formation, their F1 hybrid can quickly replace both parents. In this study, the three taxa were used as a model to investigate the consequences of hybridization on cold tolerance, particularly the effect of subgenome dominance in the hybrid. Upon chilling treatments, physiological responses and transcriptome profiles were compared across different temperature points to understand their differential responses to cold. While both parents showed divergent responses, the hybrid’s responses showed an overall resemblance to S. calendulacea, but the contribution of homeolog expression bias to cold stress was not readily evident in the F1 hybrid possibly due to inherent bias that comes with the sampling location. Our findings provided insights into the role of gene expression in differential cold tolerance, and further contribute to predicting the invasive potential of other hybrids between S. trilobata and its congeners around the world.

Diversification and Functional Evolution of HOX Proteins

Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.

Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon

In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems¹. Polyploidizations are often associated with this plasticity in sexual systems^2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

BACKGROUND

Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid's parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization.

RESULTS

We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC's performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO's output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data.

CONCLUSIONS

The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO .

Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins

Polyploidization can have a significant ecological and evolutionary impact by providing substantially more genetic material that may result in novel phenotypes upon which selection may act. While the effects of polyploidization are broadly reviewed across the plant tree of life, the reproducibility of these effects within naturally occurring, independently formed polyploids is poorly characterized. The flowering plant genus Tragopogon (Asteraceae) offers a rare glimpse into the intricacies of repeated allopolyploid formation with both nascent (< 90 years old) and more ancient (mesopolyploids) formations. Neo- and mesopolyploids in Tragopogon have formed repeatedly and have extant diploid progenitors that facilitate the comparison of genome evolution after polyploidization across a broad span of evolutionary time. Here, we examine four independently formed lineages of the mesopolyploid Tragopogon castellanus for homoeolog expression changes and fractionation after polyploidization. We show that expression changes are remarkably similar among these independently formed polyploid populations with large convergence among expressed loci, moderate convergence among loci lost, and stochastic silencing. We further compare and contrast these results for T. castellanus with two nascent Tragopogon allopolyploids. While homoeolog expression bias was balanced in both nascent polyploids and T. castellanus, the degree of additive expression was significantly different, with the mesopolyploid populations demonstrating more non-additive expression. We suggest that gene dosage and expression noise minimization may play a prominent role in regulating gene expression patterns immediately after allopolyploidization as well as deeper into time, and these patterns are conserved across independent polyploid lineages.

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.

Genome-Wide Analysis, Evolutionary History and Response of ALMT Family to Phosphate Starvation in Brassica napus

Low phosphorus (P) availability is one of the major constraints to plant growth, particularly in acidic soils. A possible mechanism for enhancing the use of sparsely soluble P forms is the secretion of malate in plants by the aluminum-activated malate transporter (ALMT) gene family. Despite its significance in plant biology, the identification of the ALMT gene family in oilseed rape (Brassica napus; B. napus), an allotetraploid crop, is unveiled. Herein, we performed genome-wide identification and characterization of ALMTs in B. napus, determined their gene expression in different tissues and monitored transcriptional regulation of BnaALMTs in the roots and leaves at both a sufficient and a deficient P supply. Thirty-nine BnaALMT genes were identified and were clustered into five branches in the phylogenetic tree based on protein sequences. Collinearity analysis revealed that most of the BnaALMT genes shared syntenic relationships among BnaALMT members in B. napus, which suggested that whole-genome duplication (polyploidy) played a major driving force for BnaALMTs evolution in addition to segmental duplication. RNA-seq analyses showed that most BnaALMT genes were preferentially expressed in root and leaf tissues. Among them, the expression of BnaC08g13520D, BnaC08g15170D, BnaC08g15180D, BnaC08g13490D, BnaC08g13500D, BnaA08g26960D, BnaC05g14120D, BnaA06g12560D, BnaC05g20630D, BnaA07g02630D, BnaA04g15700D were significantly up-regulated in B. napus roots and leaf at a P deficient supply. The current study analyzes the evolution and the expression of the ALMT family in B. napus, which will help in further research on their role in the enhancement of soil P availability by secretion of organic acids.

Phenanthrene contamination and ploidy level affect the rhizosphere bacterial communities of Spartina spp

Spartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These events have resulted in a heightened tolerance to hydrocarbon contaminants, but the effects of this phenomenon on the rhizosphere microbial communities are unknown. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene was amplified and sequenced, whereas the abundances of the genes encoding for the PAH (polycyclic aromatic hydrocarbon) ring-hydroxylating dioxygenase (RHD) of Gram-negative and Gram-positive bacteria were quantified by real-time PCR. Both the contamination and the plant genotype significantly affected the bacterial communities. In particular, the allopolyploid S. anglica harbored a more diverse bacterial community in its rhizosphere. The interspecific hybrid and the allopolyploid also harbored significantly more copies of the PAH-RHD gene of Gram-negative bacteria in their rhizosphere than the parental species, irrespective of the contamination treatments. Overall, our results are showing that the recent polyploidization events in the Spartina affected its rhizosphere bacterial communities, both under normal and contaminated conditions, possibly increasing its phytoremediation potential.

Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids

Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.

Regions enriched for DNA repeats in chromosomes of Macrostomum mirumnovem, a species with a recent Whole Genome Duplication

The free-living flatworm Macrostomum mirumnovem is a neopolyploid species whose genome underwent a recent Whole Genome Duplication (WGD). In the result of chromosome fusions of the ancient haploid chromosome set, large metacentric chromosomes were formed. In addition to three pairs of small metacentrics, the current karyotype of M. mirumnovem contains two pairs of large metacentric chromosomes, MMI1 and MMI2. The generation of microdissected DNA libraries enriched for DNA repeats followed by DNA probe preparation and fluorescent in situ hybridization (FISH) were performed. The DNA probes obtained marked chromosome regions enriched for different DNA repeats in the M. mirumnovem chromosomes. The size and localization of these regions varied in different copies of large chromosomes. They varied even in homologous chromosomes, suggesting their divergence due to genome re-diploidization after a WGD. Besides the newly formed chromosome regions enriched for DNA repeats, B chromosomes were found in the karyotypes of the studied specimens of M. mirumnovem. These B chromosomes varied in size and morphology. FISH with microdissected DNA probes revealed that some Bs had a distinct DNA content. FISH could paint differently B chromosomes in different worms and even in the same sample. B chromosomes could carry a bright specific fluorescent signal or could show no fluorescent signal at all. In latter cases, the specific FISH signal could be absent even in the pericentromeric region of the B chromosome. Possible mechanisms of B chromosome formation and their further evolution are discussed. The results obtained indicate an important role that repetitive DNAs play in genome re-diploidization initiating a rapid differentiation of large chromosome copies. Taking together, karyotype peculiarities (a high level of intraspecific karyotypic diversity associated with chromosome number variation, structural chromosomal rearrangements, and the formation of new regions enriched for DNA repeats) and some phenotypic features of M. mirumnovem (small body size, short lifecycle, easy maintenance in the laboratory) make this species a perspective model in the studies of genomic and karyotypic evolution in species passed through a recent WGD event.

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids

Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.

Preferential Disomic Segregation and C. micrantha/C. medica Interspecific Recombination in Tetraploid 'Giant Key' Lime; Outlook for Triploid Lime Breeding

The triploid 'Tahiti' lime (C. x latifolia (Yu. Tanaka) Tanaka) naturally originated from a merger between a haploid ovule of lemon (C. x limon (L.) Burm) and a diploid pollen from a 'Mexican' lime (C. x aurantiifolia (Christm.) Swing). The very limited natural inter-varietal diversity and gametic sterility of C. latifolia requires a phylogenomic based reconstruction breeding strategy to insure its diversification. We developed a strategy based on interploid hybridization between diploid lemon and the doubled diploid 'Giant Key' lime. This lime is a doubled diploid of 'Mexican' lime, itself a natural interspecific F1 hybrid between C. medica L. and C. micrantha Wester. For an optimized breeding program, we analyzed the meiotic behavior of the allotetraploid lime, the genetic structure of its diploid gametes, the interspecific recombination between C. medica and C. micrantha, and constructed its genetic map. A population of 272 triploid hybrids was generated using 'Giant Key' lime as pollinator. One hundred fifty-eight SNPs diagnostic of C. micrantha, regularly distributed throughout the citrus genome were successfully developed and applied. The genetic structure of the diploid gametes was examined based on C. micrantha doses along the genome. The diploid gametes transmitted in average 91.17% of the parental interspecific C. medica/C. micrantha heterozygosity. Three chromosomes (2, 8, and 9) showed disomic segregation with high preferential pairing values, while the remaining chromosomes showed an intermediate inheritance with a preferential disomic trend. A total of 131 SNPs were assigned to nine linkage groups to construct the genetic map. It spanned 272.8 cM with a low average recombination rate (0.99 cM Mb-1) and high synteny and colinearity with the reference clementine genome. Our results confirmed that an efficient reconstruction breeding strategy for 'Tahiti' lime is possible, based on interploid hybridization using a doubled diploid of C. aurantiifolia. The tetraploid parent should be selected for favorable agronomic traits and its genetic value should be efficiently inherited by the progeny thanks to transmission of the high level of parental heterozygosity. However, it would require developing numerous progeny to overcome the linkage drag caused by the limited interspecific recombination associated with the predominant disomic inheritance.

Adaptive strategy of allohexaploid wheat to long-term salinity stress

BACKGROUND

Most studies of crop salinity tolerance are conducted under short-term stress condition within one growth stage. Understanding of the mechanisms of crop response to long-term salinity stress (LSS) is valuable for achieving the improvement of crop salinity tolerance. In the current study, we exposed allohexaploid wheat seeds to LSS conditions from germination stage to young seedling stage for 30 days. To elucidate the adaptive strategy of allohexaploid wheat to LSS, we analyzed chloroplast ultrastructure, leaf anatomy, transcriptomic profiling and concentrations of plant hormones and organic compatible solutes, comparing stressed and control plants.

RESULTS

Transcriptomic profiling and biochemical analysis showed that energy partitioning between general metabolism maintenance and stress response may be crucial for survival of allohexaploid wheat under LSS. Under LSS, wheat appeared to shift energy from general maintenance to stress response through stimulating the abscisic acid (ABA) pathway and suppressing gibberellin and jasmonic acid pathways in the leaf. We further distinguished the expression status of the A, B, and D homeologs of any gene triad, and also surveyed the effects of LSS on homeolog expression bias for salinity-tolerant triads. We found that LSS had similar effects on expression of the three homeologs for most salinity-tolerant triads. However, in some of these triads, LSS induced different effects on the expression of the three homeologs.

CONCLUSIONS

The shift of the energy from general maintenance to stress response may be important for wheat LSS tolerance. LSS influences homeolog expression bias of salinity-tolerant triads.

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

Background

Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited.

Results

In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response.

Conclusions

These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

Molecular Organization and Chromosomal Localization Analysis of 5S rDNA Clusters in Autotetraploids Derived From Carassius auratus Red Var. (♀) × Megalobrama amblycephala (♂)

The autotetraploid fish (4n = 200, RRRR) (abbreviated as 4nRR) resulted from the whole genome duplication of red crucian carp (Carassius auratus red var., 2n = 100, RR) (abbreviated as RCC). During investigation of the influence of polyploidization on organization and evolution of the multigene family of 5S rDNA, molecular organization and chromosomal localization of the 5S rDNA were characterized in autotetraploid fish. By sequence analysis of the coding region (5S) and adjacent non-transcribed spacer (NTS), three distinct 5S rDNA units (type I: 203 bp; type II: 340 bp; and type III: 477bp) were identified and characterized in 4nRR. These 5S rDNA units were inherited from their female parent (RCC), in which obvious base variations in NTS and array recombination of repeat units were found. Using fluorescence in situ hybridization employing different 5S rDNA units as probes, these 5S rDNA clusters were localized in chromosomes of 4nRR, respectively, and showed obvious loss of chromosomal loci (type I and type II). Our data revealed genetic variation of the 5S rDNA multigene family in the genome of autopolyploid fish. Furthermore, results provided new insights into the evolutionary patterns of this vertebrate multigene family.

Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates

Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous–Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, Ceratopteris thalictroides, for the detection of WGDs. High-quality RNA-seq data was used to infer the number of synonymous substitutions per synonymous site (Ks) between paralogs; Ks age distribution and absolute dating approach were used to determine the age of WGD events. Evidence of an ancient WGD event with a Ks peak value of approximately 1.2 was obtained for both samples; however, the Ks frequency distributions varied significantly. Importantly, we dated the WGD event at 51–53 mya, which coincides with the Paleocene-Eocene Thermal Maximum (PETM), when the Earth became warmer and wetter than any other period during the Cenozoic. Duplicate genes were preferentially retained for specific functions, such as environment response, further support that the duplicates may have promoted quick adaption to environmental changes and potentially resulted in evolutionary success, especially for pantropical species, such as C. thalictroides, which exhibits higher temperature tolerance.

A Low Resolution Epistasis Mapping Approach To Identify Chromosome Arm Interactions in Allohexaploid Wheat

Epistasis is an important contributor to genetic variance. In inbred populations, pairwise epistasis is present as additive by additive interactions. Testing for epistasis presents a multiple testing problem as the pairwise search space for modest numbers of markers is large. Single markers do not necessarily track functional units of interacting chromatin as well as haplotype based methods do. To harness the power of multiple markers while minimizing the number of tests conducted, we present a low resolution test for epistatic interactions across whole chromosome arms. Epistasis covariance matrices were constructed from the additive covariances of individual chromosome arms. These covariances were subsequently used to estimate an epistatic variance parameter while correcting for background additive and epistatic effects. We find significant epistasis for 2% of the interactions tested for four agronomic traits in a winter wheat breeding population. Interactions across homeologous chromosome arms were identified, but were less abundant than other chromosome arm pair interactions. The homeologous chromosome arm pair 4BL/4DL showed a strong negative relationship between additive and interaction effects that may be indicative of functional redundancy. Several chromosome arms appeared to act as hubs in an interaction network, suggesting that they may contain important regulatory factors. The differential patterns of epistasis across different traits demonstrate that detection of epistatic interactions is robust when correcting for background additive and epistatic effects in the population. The low resolution epistasis mapping method presented here identifies important epistatic interactions with a limited number of statistical tests at the cost of low precision.

Homeologous Epistasis in Wheat: The Search for an Immortal Hybrid

Hybridization between related species results in the formation of an allopolyploid with multiple subgenomes. These subgenomes will each contain complete, yet evolutionarily divergent, sets of genes. Like a diploid hybrid, allopolyploids will have two versions, or homeoalleles, for every gene. Partial functional redundancy between homeologous genes should result in a deviation from additivity. These epistatic interactions between homeoalleles are analogous to dominance effects, but are fixed across subgenomes through self pollination. An allopolyploid can be viewed as an immortalized hybrid, with the opportunity to select and fix favorable homeoallelic interactions within inbred varieties. We present a subfunctionalization epistasis model to estimate the degree of functional redundancy between homeoallelic loci and a statistical framework to determine their importance within a population. We provide an example using the homeologous dwarfing genes of allohexaploid wheat, Rht-1, and search for genome-wide patterns indicative of homeoallelic subfunctionalization in a breeding population. Using the IWGSC RefSeq v1.0 sequence, 23,796 homeoallelic gene sets were identified and anchored to the nearest DNA marker to form 10,172 homeologous marker sets. Interaction predictors constructed from products of marker scores were used to fit the homeologous main and interaction effects, as well as estimate whole genome genetic values. Some traits displayed a pattern indicative of homeoallelic subfunctionalization, while other traits showed a less clear pattern or were not affected. Using genomic prediction accuracy to evaluate importance of marker interactions, we show that homeologous interactions explain a portion of the nonadditive genetic signal, but are less important than other epistatic interactions.

Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

A Novel Approach to Isolating Improved Industrial Interspecific Wine Yeasts Using Chromosomal Mutations as Potential Markers for Increased Fitness

Wine yeast breeding programs utilizing interspecific hybridization deliver cost-effective tools to winemakers looking to differentiate their wines through the development of new wine styles. The addition of a non-Saccharomyces cerevisiae genome to a commercial wine yeast can generate novel phenotypes ranging from wine flavor and aroma diversity to improvements in targeted fermentation traits. In the current study we utilized a novel approach to screen isolates from an evolving population for increased fitness in a S. cerevisiae × S. uvarum interspecific hybrid previously generated to incorporate the targeted phenotype of lower volatile acidity production. Sequential grape-juice fermentations provided a selective environment from which to screen isolates. Chromosomal markers were used in a novel approach to identify isolates with potential increased fitness. A strain with increased fitness relative to its parents was isolated from an early timepoint in the evolving population, thereby minimizing the risk of introducing collateral mutations and potentially undesirable phenotypes. The evolved strain retained the desirable fermentation trait of reduced volatile acidity production, along with other winemaking traits of importance while exhibiting improved fermentation kinetics.

Phenotypic and Comparative Transcriptome Analysis of Different Ploidy Plants in Dendrocalamus latiflorus Munro

Elucidating the differences in gene expression profiles of plants with different ploidy levels and how they affect phenotypic traits is vital to allow genetic improvement of plants such as Ma bamboo (Dendrocalamus latiflorus Munro). We previously obtained triploid (2n = 3X = 36), hexaploid (2n = 6X = 72), and dodecaploid (2n = 12X = 144) Ma bamboo plants from embryogenic callus by anther culturing. Phenotypic differences between these plants appeared to be correlated with differences in ploidy. Here, we performed transcriptome profiling and sequencing of anther-regenerated plants and F1 seedlings of different ploidy levels using RNA-Seq technology. Pair-wise comparisons of the four resulting libraries revealed 8,396 differentially expressed genes. These differentially expressed genes were annotated, functionally classified, and partially validated. We found that the chromosome doubling led to substantially up- or down-regulation of genes that were involved in cell growth and differentiation; the polyploidy levels altered the anatomical, physiological and growth characteristics, such as leaf thickness, fusoid cell and stomatal size, shoot number, photosynthesis and respiration rate and so on. Additionally, two candidate genes, EXPB3 and TCP with potenitial regulatory roles in cell division and differentiation, were identified through gene coexpresseion network analysis. These results highlight the significance of potential applications of polyploidy, and provide valuable information for the genetic breeding of bamboo species.

Genome-wide analysis suggests high level of microsynteny and purifying selection affect the evolution of EIN3/EIL family in Rosaceae

The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

γ-Aminobutyric acid (GABA) signalling in plants

The role of γ-aminobutyric acid (GABA) as a signal in animals has been documented for over 60 years. In contrast, evidence that GABA is a signal in plants has only emerged in the last 15 years, and it was not until last year that a mechanism by which this could occur was identified-a plant 'GABA receptor' that inhibits anion passage through the aluminium-activated malate transporter family of proteins (ALMTs). ALMTs are multigenic, expressed in different organs and present on different membranes. We propose GABA regulation of ALMT activity could function as a signal that modulates plant growth, development, and stress response. In this review, we compare and contrast the plant 'GABA receptor' with mammalian GABAA receptors in terms of their molecular identity, predicted topology, mode of action, and signalling roles. We also explore the implications of the discovery that GABA modulates anion flux in plants, its role in signal transduction for the regulation of plant physiology, and predict the possibility that there are other GABA interaction sites in the N termini of ALMT proteins through in silico evolutionary coupling analysis; we also explore the potential interactions between GABA and other signalling molecules.

Chromatin modification contributes to the expression divergence of three TaGS2 homoeologs in hexaploid wheat

Plastic glutamine synthetase (GS2) is responsible for ammonium assimilation. The reason that TaGS2 homoeologs in hexaploid wheat experience different selection pressures in the breeding process remains unclear. TaGS2 were minimally expressed in roots but predominantly expressed in leaves, and TaGS2-B had higher expression than TaGS2-A and TaGS2-D. ChIP assays revealed that the activation of TaGS2-B expression in leaves was correlated with increased H3K4 trimethylation. The transcriptional silencing of TaGS2 in roots was correlated with greater cytosine methylation and less H3K4 trimethylation. Micrococcal nuclease and DNase I accessibility experiments indicated that the promoter region was more resistant to digestion in roots than leaves, which indicated that the closed nucleosome conformation of the promoter region was important to the transcription initiation for the spatial-temporal expression of TaGS2. In contrast, the transcribed regions possess different nuclease accessibilities of three TaGS2 homoeologs in the same tissue, suggesting that nucleosome conformation of the transcribed region was part of the fine adjustment of TaGS2 homoeologs. This study provides evidence that histone modification, DNA methylation and nuclease accessibility coordinated the control of the transcription of TaGS2 homoeologs. Our results provided important evidence that TaGS2-B experienced the strongest selection pressures during the breeding process.

Inducing triploids and tetraploids with high temperatures in Populus sect. Tacamahaca

This study is the first to report that triploids and tetraploids have been successfully produced through embryo sac and zygotic embryo chromosome doubling with high temperatures in P. simonii Carr. and its hybrid. A new synthetic polyploid induced by hybridization with unreduced gametes and heterozygotic embryo chromosome doubling can effectively combine polyploidy and heterosis, which can provide two major breeding advantages. In Populus, successfully creating and cultivating new polyploid varieties have economic and ecological production value. This was the first successful study in which embryo sac and zygotic embryo chromosome doubling was induced using high temperatures to produce triploids and tetraploids in Populus simonii Carr. and its hybrid, P. simonii × P. nigra var. Italica, of Populus sect. Tacamahaca. The relationship between flower bud morphological characteristics (time after pollination) and female meiotic stage (embryo sac and zygotic embryo development) was established to guide the induction treatment period. In the resulting progeny, 37 triploids and 12 tetraploids were obtained and identified using flow cytometry. The optimal temperatures for embryo sac and zygotic embryo chromosome doubling were 38 and 41 °C, respectively. Cytogenetic analysis revealed that 66-72 h after pollination (HAP), a period characterized by a high proportion of one-nucleate and two-nucleate embryo sacs, was the optimal period for embryo sac chromosome doubling. For zygotic embryo chromosome doubling, 168 HAP was the optimal induction period, as there was a high proportion of two-cell and four-cell proembryos. The results indicate that inducing embryo sac and zygotic embryo chromosome doubling is an ideal method for producing polyploids. The methods for inducing polyploids and for evaluating ploidy and offspring with different ploidies and heterozygosity in this study will be useful for genetic research and Populus breeding programmes.

Genome-wide divergence, haplotype distribution and population demographic histories for Gossypium hirsutum and Gossypium barbadense as revealed by genome-anchored SNPs

Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we examined genetic diversity, haplotype distribution and linkage disequilibrium patterns in the G. hirsutum and G. barbadense genomes to clarify population demographic history. Diversity and identity-by-state analyses have revealed little sharing of alleles between the two cultivated allotetraploid genomes, with a few exceptions that indicated sporadic gene flow. We found a high number of new alleles, representing increased nucleotide diversity, on chromosomes 1 and 2 in cultivated G. hirsutum as compared with low nucleotide diversity on these chromosomes in landrace G. hirsutum. In contrast, G. barbadense chromosomes showed negative Tajima's D on several chromosomes for both cultivated and landrace types, which indicate that speciation of G. barbadense itself, might have occurred with relatively narrow genetic diversity. The presence of conserved linkage disequilibrium (LD) blocks and haplotypes between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our study illustrates the potential use of population genetic techniques to identify genomic regions for domestication.

Molecular phylogenetics, seed morphometrics, chromosome number evolution and systematics of European Elatine L. (Elatinaceae) species

The genus Elatine contains ca 25 species, all of which are small, herbaceous annuals distributed in ephemeral waters on both hemispheres. However, due to a high degree of morphological variability (as a consequence of their amphibious life-style), the taxonomy of this genus remains controversial. Thus, to fill this gap in knowledge, we present a detailed molecular phylogenetic study of this genus based on nuclear (rITS) and plastid (accD-psaI, psbJ-petA, ycf6-psbM-trnD) sequences using 27 samples from 13 species. On the basis of this phylogenetic analysis, we provide a solid phylogenetic background for the modern taxonomy of the European members of the genus. Traditionally accepted sections of this tree (i.e., Crypta and Elatinella) were found to be monophyletic; only E. borchoni—found to be a basal member of the genus—has to be excluded from the latter lineage to achieve monophyly. A number of taxonomic conclusions can also be drawn: E. hexandra, a high-ploid species, is most likely a stabilised hybrid between the main sections; E. campylosperma merits full species status based on both molecular and morphological evidence; E. gussonei is a more widespread and genetically diverse species with two main lineages; and the presence of the Asian E. ambigua in the European flora is questionable. The main lineages recovered in this analysis are also supported by a number of synapomorphic morphological characters as well as uniform chromosome counts. Based on all the evidence presented here, two new subsections within Elatinella are described: subsection Hydropipera consisting of the temperate species of the section, and subsection Macropodae including the Mediterranean species of the section.

TaTypA, a Ribosome-Binding GTPase Protein, Positively Regulates Wheat Resistance to the Stripe Rust Fungus

Tyrosine phosphorylation protein A (TypA/BipA) belongs to the ribosome-binding GTPase superfamily. In many bacterial species, TypA acts as a global stress and virulence regulator and also mediates resistance to the antimicrobial peptide bactericidal permeability-increasing protein. However, the function of TypA in plants under biotic stresses is not known. In this study, we isolated and functionally characterized a stress-responsive TypA gene (TaTypA) from wheat, with three copies located on chromosomes 6A, 6B, and 6D, respectively. Transient expression assays indicated chloroplast localization of TaTypA. The transcript levels of TaTypA were up-regulated in response to treatment with methyl viologen, which induces reactive oxygen species (ROS) in chloroplasts through photoreaction, cold stress, and infection by an avirulent strain of the stripe rust pathogen. Knock down of the expression of TaTypA through virus-induced gene silencing decreased the resistance of wheat to stripe rust accompanied by weakened ROS accumulation and hypersensitive response, an increase in TaCAT and TaSOD expression, and an increase in pathogen hyphal growth and branching. Our findings suggest that TaTypA contributes to resistance in an ROS-dependent manner.

Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses

BACKGROUND

The P1B-ATPase subfamily is an important group involved in transporting heavy metals and has been extensively studied in model plants, such as Arabidopsis thaliana and Oryza sativa. Emerging evidence indicates that one homolog in Glycine max is also involved in cadmium (Cd) stress, but the gene family has not been fully investigated in soybean.

RESULTS

Here, we identified 20 heavy metal ATPase (HMA) family members in the soybean genome, presented as 10 paralogous pairs, which is significantly greater than the number in Arabidopsis or rice, and was likely caused by the latest whole genome duplication event in soybean. A phylogenetic analysis divided the 20 members into six groups, each having conserved or divergent gene structures and protein motif patterns. The integration of RNA-sequencing and qRT-PCR data from multiple tissues provided an overall expression pattern for the HMA family in soybean. Further comparisons of expression patterns and the single nucleotide polymorphism distribution between paralogous pairs suggested functional conservation and the divergence of HMA genes during soybean evolution. Finally, analyses of the HMAs expressed in response to Cd stress provided evidence on how plants manage Cd tolerance, at least in the two contrasting soybean genotypes examined.

CONCLUSIONS

The genome-wide identification, chromosomal distribution, gene structures, and evolutionary and expression analyses of the 20 HMA genes in soybean provide an overall insight into their potential involvement in Cd responses. These results will facilitate further research on the HMA gene family, and their conserved and divergent biological functions in soybean.

Solidago altissima differs with respect to ploidy frequency and clinal variation across the prairie-forest biome border in Minnesota

PREMISE OF THE STUDY

Although our awareness of ploidy diversity has expanded with the application of flow cytometry, we still know little about the extent to which cytotypes within mixed-ploidy populations are genetically differentiated across environmental gradients.

METHODS

To address this issue, we reared 14 populations of Solidago altissima spanning the prairie-forest ecotone in Minnesota in a common garden with a watering treatment. We assessed ploidy frequencies and measured survival, flowering phenology, and plant architectural traits for 4 years.

KEY RESULTS

All populations harbored multiple cytotypes; prairie populations were dominated by tetraploids, forest populations by hexaploids. Diploids and polyploids differed significantly for 84% of the traits. Beyond average differences, the slope of trait values covaried with latitude and longitude, but this relationship was stronger for diploids than the other two polyploid cytotypes as indicated by numerous ploidy × latitude and ploidy × longitude interactions. For example, the timing of flowering of the cytotypes overlapped in populations sampled from the northeastern hemiboreal forest but differed significantly between cytotypes sampled from populations in the southwestern prairie. The watering treatments had weak effects, and there were no ploidy differences for phenotypic plasticity.

CONCLUSIONS

Our data show that diploids have diverged genetically to a greater extent than polyploids along the environmental clines sampled in this study. Moreover, different environments favor phenotypic convergence over divergence among cytotypes for some traits. Differences in ploidy frequency and phenotypic divergence among cytotypes across gradients of temperature and precipitation are important considerations for restoration in an age of climate change.

Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response to Fusarium graminearum

Fusarium head blight is a prevalent disease of bread wheat (Triticum aestivum L.), which leads to considerable losses in yield and quality. Quantitative resistance to the causative fungus Fusarium graminearum is poorly understood. We integrated transcriptomics and metabolomics data to dissect the molecular response to the fungus and its main virulence factor, the toxin deoxynivalenol in near-isogenic lines segregating for two resistance quantitative trait loci, Fhb1 and Qfhs.ifa-5A. The data sets portrait rearrangements in the primary metabolism and the translational machinery to counter the fungus and the effects of the toxin and highlight distinct changes in the metabolism of glutamate in lines carrying Qfhs.ifa-5A. These observations are possibly due to the activity of two amino acid permeases located in the quantitative trait locus confidence interval, which may contribute to increased pathogen endurance. Mapping to the highly resolved region of Fhb1 reduced the list of candidates to few genes that are specifically expressed in presence of the quantitative trait loci and in response to the pathogen, which include a receptor-like protein kinase, a protein kinase, and an E3 ubiquitin-protein ligase. On a genome-scale level, the individual subgenomes of hexaploid wheat contribute differentially to defense. In particular, the D subgenome exhibited a pronounced response to the pathogen and contributed significantly to the overall defense response.

WsMAGO2, a duplicated MAGO NASHI protein with fertility attributes interacts with MPF2-like MADS-box proteins

WsMAGO2 a duplicated protein in Withania through interactions with MPF2-like proteins affects male fertility by producing fewer flowers and aborted non-viable pollens/seeds regulated by anther-specific GAATTTGTGA motif. The MAGO NASHIs are highly conserved genes that encode proteins known to be involved in RNA physiology and many other developmental processes including germ cell differentiation in animals. However, their structural and functional implications in plants as fertility function proteins remained fragmented. MAGO (shorter name of MAGO NASHI) proteins form heterodimers with MPF2-like MADS-box proteins which are recruited in calyx identity and male fertility in Solanaceous plants. Four MAGO genes namely WsMAGO1 and WsMAGO2 and TaMAGO1 and TaMAGO2 were isolated from Withania somnifera and Tubocapsicum anomalum, respectively. These genes have duplicated probably due to whole genome duplication event. Dysfunction of WsMAGO2 through double-stranded RNAi in Withania revealed suppression of RNA transcripts, non-viable pollens, fewer flowers and aborted non-viable seeds in the developing berry suggesting a role of this protein in many traits particularly male fertility. WsMAGO2 flaunted stronger yeast 2-hybrid interactions with MPF2-like proteins WSA206, WSB206 and TAB201 than other MAGO counterparts. The native transcripts of WsMAGO2 culminated in stamens and seed-bearing berries though other MAGO orthologs also exhibited expression albeit at lower level. Coding sequences of the two orthologs are highly conserved, but they differ substantially in their upstream promoter regions. Remarkably, WsMAGO2 promoter is enriched with many anther-specific cis-motifs common in fertility function genes promoters. Among them, disruption of GAATTTGTGA abolished YFP/GUS gene expression in anthers alluding towards its involvement in regulating expression of MAGO in anther. Our findings support a possible recruitment of WsMAGO2 in fertility trait in Withania. These genes have practical application in hybrid production through cytoplasmic male sterility maintenance for enhancement in crops yield.

Comparative metabolic and transcriptional analysis of a doubled diploid and its diploid citrus rootstock (C. junos cv. Ziyang xiangcheng) suggests its potential value for stress resistance improvement

BACKGROUND

Polyploidy has often been considered to confer plants a better adaptation to environmental stresses. Tetraploid citrus rootstocks are expected to have stronger stress tolerance than diploid. Plenty of doubled diploid citrus plants were exploited from diploid species for citrus rootstock improvement. However, limited metabolic and molecular information related to tetraploidization is currently available at a systemic biological level. This study aimed to evaluate the occurrence and extent of metabolic and transcriptional changes induced by tetraploidization in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka), which is a special citrus germplasm native to China and widely used as an iron deficiency tolerant citrus rootstock.

RESULTS

Doubled diploid Ziyang xiangcheng has typical morphological and anatomical features such as shorter plant height, larger and thicker leaves, bigger stomata and lower stomatal density, compared to its diploid parent. GC-MS (Gas chromatography coupled to mass spectrometry) analysis revealed that tetraploidization has an activation effect on the accumulation of primary metabolites in leaves; many stress-related metabolites such as sucrose, proline and γ-aminobutyric acid (GABA) was remarkably up-regulated in doubled diploid. However, LC-QTOF-MS (Liquid chromatography quadrupole time-of-flight mass spectrometry) analysis demonstrated that tetraploidization has an inhibition effect on the accumulation of secondary metabolites in leaves; all the 33 flavones were down-regulated while all the 6 flavanones were up-regulated in 4x. By RNA-seq analysis, only 212 genes (0.8% of detected genes) are found significantly differentially expressed between 2x and 4x leaves. Notably, those genes were highly related to stress-response functions, including responses to salt stress, water and abscisic acid. Interestingly, the transcriptional divergence could not explain the metabolic changes, probably due to post-transcriptional regulation.

CONCLUSION

Taken together, tetraploidization induced considerable changes in leaf primary and secondary metabolite accumulation in Ziyang xiangcheng. However, the effect of tetraploidization on transcriptome is limited. Compared to diploid, higher expression level of stress related genes and higher content of stress related metabolites in doubled diploid could be beneficial for its stress tolerance.

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data

The narrow genetic base and limited genetic information on Arachis species have hindered the process of marker-assisted selection of peanut cultivars. However, recent developments in sequencing technologies have expanded opportunities to exploit genetic resources, and at lower cost. To use the genetic information for Arachis species available at the transcriptome level, it is important to have a good quality reference transcriptome. The available Tifrunner 454 FLEX transcriptome sequences have an assembly with 37,000 contigs and low N50 values of 500-751bp. Therefore, we generated de novo transcriptome assemblies, with about 38 million reads in the tetraploid cultivar OLin, and 16 million reads in each of the diploids, A. duranensis K38901 and A. ipaënsis KGBSPSc30076 using three different de novo assemblers, Trinity, SOAPdenovo-Trans and TransAByss. All these assemblers can use single kmer analysis, and the latter two also permit multiple kmer analysis. Assemblies generated for all three samples had N50 values ranging from 1278–1641 bp in Arachis hypogaea (AABB), 1401–1492 bp in Arachis duranensis (AA), and 1107–1342 bp in Arachis ipaënsis (BB). Comparison with legume ESTs and protein databases suggests that assemblies generated had more than 40% full length transcripts with good continuity. Also, on mapping the raw reads to each of the assemblies generated, Trinity had a high success rate in assembling sequences compared to both TransAByss and SOAPdenovo-Trans. De novo assembly of OLin had a greater number of contigs (67,098) and longer contig length (N50 = 1,641) compared to the Tifrunner TSA. Despite having shorter read length (2×50) than the Tifrunner 454FLEX TSA, de novo assembly of OLin proved superior in comparison. Assemblies generated to represent different genome combinations may serve as a valuable resource for the peanut research community.

Heat shock factors in carrot: genome-wide identification, classification, and expression profiles response to abiotic stress

Heat shock factors (HSFs) play key roles in the response to abiotic stress in eukaryotes. In this study, 35 DcHSFs were identified from carrot (Daucus carota L.) based on the carrot genome database. All 35 DcHSFs were divided into three classes (A, B, and C) according to the structure and phylogenetic relationships of four different plants, namely, Arabidopsis thaliana, Vitis vinifera, Brassica rapa, and Oryza sativa. Comparative analysis of algae, gymnosperms, and angiosperms indicated that the numbers of HSF transcription factors were related to the plant's evolution. The expression profiles of five DcHsf genes (DcHsf 01, DcHsf 02, DcHsf 09, DcHsf 10, and DcHsf 16), which selected from each subfamily (A, B, and C), were detected by quantitative real-time PCR under abiotic stresses (cold, heat, high salinity, and drought) in two carrot cultivars, D. carota L. cvs. Kurodagosun and Junchuanhong. The expression levels of DcHsfs were markedly increased by heat stress, except that of DcHsf 10, which was down regulated. The expression profiles of different DcHsfs in the same class also differed under various stress treatments. The expression profiles of these DcHsfs were also different in tissues of two carrot cultivars. This study is the first to identify and characterize the DcHSF family transcription factors in plants of Apiaceae using whole-genome analysis. The results of this study provide an in-depth understanding of the DcHSF family transcription factors' structure, function, and evolution in carrot.

Polyploidy and hybridization as main factors of speciation: complex reticulate evolution within the grass genus Helictochloa

To study the origin and evolution of naturally occurring polyploids, we performed phylogenetic analyses of nuclear ribosomal DNA spacers combined with molecular cytogenetics in 55 accessions of 27 taxa of the oat genus Helictochloa. A complex pattern of reticulate evolution was revealed with many diploid species and extensive polyploidy up to 20x. Altogether 11 groups of internal transcribed spacer (ITS) sequences can be distinguished. Sequences from 1-3 different ITS lineages were detected in polyploids. Cytogenetic data allow reconstruction of 8 basic monoploid chromosome sets. Six of these genomes occur in different combinations in the polyploid species. Two genomes are only found in diploids. Our sequence and karyological data highlight the occurrence of autopolyploidy and allopolyploidy, provide new information about the evolutionary history of taxa, and allow a more accurate systematic treatment of the concerned species. The geographical distribution of the 11 ITS lineages distinguished is highly structured and points to an origin of the genus in western Asia, presumably in grasslands like steppes or mountain steppes and meadows. The evolutionary basal lineages are of Asian, Minor Asian and east Mediterranean distribution and are present also in North America. The western and central parts of the Mediterranean and northern Europe harbor the modern lineages.

Natural pathways to polyploidy in plants and consequences for genome reorganization

The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative 'diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.