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Background: The allo-octoploid Fragaria x ananassa follows disomic inheritance, yet the high sequence similarity among its subgenomes can lead to misalignment of short sequencing reads (150 bp). This misalignment results in an increased number of erroneous variants during variant calling. To accurately associate traits with the appropriate subgenome, it is essential to filter out these erroneous variants. By classifying variants into correct (type 1) and erroneous types (homoeologous variants-type 2, and multi-locus variants-type 3), we can improve the reliability of downstream analyses., Results: Our analysis reveals that while erroneous variant types often display skewed average allele balances (AAB) for heterozygous calls, this measure alone is insufficient. To mitigate the erroneous variants further, we employed a Linkage Disequilibrium (LD) based filtering method that correlates highly (99%) with an approach that utilizes a genetic map from a biparental population. This combined filtering strategy-using both LD-based and average allele balance methods-resulted in the lowest switch error rate (0.037). Notably, our best filtering approach decreased phasing switch error rates by 44% and preserved 72% of the original dataset., Conclusions: The results indicate that identifying erroneous variants due to subgenome similarity can be effectively achieved without extensive genotyping of mapping populations. By implementing the LD-based filtering method, the phasing accuracy improved which improves the tracability of important alleles in the germplasm, paving the way for better understanding of trait associations in F. x ananassa., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2024 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.)

Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution., Competing Interests: Conflict of Interest The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Premise: A complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). Homoeologous gene conversion was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly consider other evolutionary scenarios that may give rise to similar SNP patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events., Methods: Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploid Gossypium species (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange., Results: We found little evidence for homoeologous gene conversion in allopolyploid cottons, and that only two of the 40 best-supported events were shared by more than one species. We did, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species., Conclusions: Overall, our analyses demonstrated that homoeologous gene conversion and homoeologous exchanges are uncommon in Gossypium, affecting between zero and 24 genes per subgenome (0.0-0.065%) across the seven species. More generally, we highlighted the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids., (© 2024 The Author(s). American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants., (© 2024 Botanical Society of America.)

Whole-genome duplications (WGDs) are widespread genomic events in eukaryotes that are hypothesized to contribute to the evolutionary success of many lineages, including flowering plants, Saccharomyces yeast, and vertebrates. WGDs generally can be classified into autopolyploids (ploidy increase descended from one species) or allopolyploids (ploidy increase descended from multiple species). Assignment of allopolyploid progenitor species (called subgenomes in the polyploid) is important to understanding the biology and evolution of polyploids, including the asymmetric subgenome evolution following hybridization (biased fractionation). Here, I review the different methodologies used to identify the ancestors of allopolyploid subgenomes, discuss the advantages and disadvantages of these methods, and outline the implications of how these methods affect the subsequent evolutionary analysis of these genomes., Competing Interests: Declaration of interests The author declares no conflicts of interest., (Copyright © 2024 The Author. Published by Elsevier Ltd.. All rights reserved.)

Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review., (© 2022. The Author(s).)

Polyploidization influences the genetic composition and gene expression of an organism. This multi-level genetic change allows the formation of new regulatory pathways leading to increased adaptability. Although both forms of polyploidization provide advantages, autopolyploids were long thought to have little impact on plant divergence compared to allopolyploids due to their formation through genome duplication only, rather than in combination with hybridization. Recent advances have begun to clarify the molecular regulatory mechanisms such as microRNAs, alternative splicing, RNA-binding proteins, histone modifications, chromatin remodelling, DNA methylation, and N 6 -methyladenosine (m6A) RNA methylation underlying the evolutionary success of polyploids. Such research is expanding our understanding of the evolutionary adaptability of polyploids and the regulatory pathways that allow adaptive plasticity in a variety of plant species. Herein we review the roles of individual molecular regulatory mechanisms and their potential synergistic pathways underlying plant evolution and adaptation. Notably, increasing interest in m6A methylation has provided a new component in potential mechanistic coordination that is still predominantly unexplored. Future research should attempt to identify and functionally characterize the evolutionary impact of both individual and synergistic pathways in polyploid plant species., (© 2020 Cambridge Philosophical Society.)

Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, EAGLE-RC and GSNAP-PolyCat outperform other quantification pipelines tested, and their derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an overestimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids., (© The Author(s) 2020. Published by Oxford University Press.)

Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid Cucumis hytivus (S 14 ), its diploid parents, and the F 1 hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in C. hytivus , 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S 14 , which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.

Background: The Chinese Isoetes L. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploid I. sinensis and its diploid parents I. yunguiensis and I. taiwanensis is an ideal system with which to investigate the relationships between polyploid speciation and the ecological niches preferences., Results: There were two major clades in the nuclear phylogenetic tree, all of the populations of polyploid were simultaneously located in both clades. The chloroplast phylogenetic tree included two clades with different populations of the polyploid clustered with the diploids separately: I. yunguiensis with partial populations of the I. sinensis and I. taiwanensis with the rest populations of the I. sinensis. The crow node of the I. sinensis allopolyploid system was 4.43 Ma (95% HPD: 2.77-6.97 Ma). The divergence time between I. sinensis and I. taiwanensis was estimated to 0.65 Ma (95% HPD: 0.26-1.91 Ma). The narrower niche breadth in I.sinensis than those of its diploid progenitors and less niche overlap in the pairwise comparisons between the polyploid and its progenitors., Conclusions: Our results elucidate that I. yunguinensis and I. taiwanensis contribute to the speciation of I. sinensis, the diploid parents are the female parents of different populations. The change of altitude might have played an important role in allopolyploid speciation and the pattern of distribution of I. sinensis. Additionally, niche novelty of the allopolyploid population of I. sinensis has been detected, in accordance with the hypothesis that niche shift between the polyploids and its diploid progenitors is important for the establishment and persistence of the polyploids.

Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers ( Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages., (© 2020 The Authors.)

Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and plants, and is especially common in crop plants. There is an increasing interest in the study of allopolyploids because of advances in polyploid genome assembly; however, the high level of sequence similarity in duplicated gene copies (homeologs) poses many challenges. Here we compared standard RNA-seq expression quantification approaches used currently for diploid species against subgenome-classification approaches which maps reads to each subgenome separately. We examined mapping error using our previous and new RNA-seq data in which a subgenome is experimentally added (synthetic allotetraploid Arabidopsis kamchatica) or reduced (allohexaploid wheat Triticum aestivum versus extracted allotetraploid) as ground truth. The error rates in the two species were very similar. The standard approaches showed higher error rates (>10% using pseudo-alignment with Kallisto) while subgenome-classification approaches showed much lower error rates (<1% using EAGLE-RC, <2% using HomeoRoq). Although downstream analysis may partly mitigate mapping errors, the difference in methods was substantial in hexaploid wheat, where Kallisto appeared to have systematic differences relative to other methods. Only approximately half of the differentially expressed homeologs detected using Kallisto overlapped with those by any other method in wheat. In general, disagreement in low-expression genes was responsible for most of the discordance between methods, which is consistent with known biases in Kallisto. We also observed that there exist uncertainties in genome sequences and annotation which can affect each method differently. Overall, subgenome-classification approaches tend to perform better than standard approaches with EAGLE-RC having the highest precision., (© The Author(s) 2018. Published by Oxford University Press.)

Allopolyploids are often faced with the challenge of maintaining well-coordination between nuclear and cytoplasmic genes inherited from different species. The synthetic allotetraploid Cucumis × hytivus is a useful model to explore cytonuclear coevolution. In this study, the sequences and expression of cytonuclear enzyme complex RuBisCO as well as its content and activity in C. × hytivus were compared to its parents to explore plastid-nuclear coevolution. The plastome-coded rbcL gene sequence was confirmed to be stable maternal inheritance, and parental copy of nuclear rbcS genes were both preserved in C. × hytivus. Thus, the maternal plastid may interact with the biparentally inherited rbcS alleles. The expression of the rbcS gene of C-homoeologs (paternal) was significantly higher than that of H-homoeologs (maternal) in C. × hytivus (HHCC). Protein interaction prediction analysis showed that the rbcL protein has stronger binding affinity to the paternal copy of rbcS protein than that of maternal copy in C. × hytivus , which might explain the transcriptional bias of the rbcS homoeologs. Moreover, both the activity and content of RuBisCO in C. × hytivus showed mid-parent heterosis. In summary, our results indicate a paternal transcriptional bias of the rbcS genes in C. × hytivus , and we found new nuclear-cytoplasmic combination may be one of the reasons for allopolyploids heterosis.

Background: Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extensive prior knowledge like high resolution genetic maps or genome sequences of diploid progenitors. In theory, existing methods for assigning sequences to individual species from metagenome samples could be used to separate subgenomes in polyploid organisms, however, these methods rely on differences in coarse genome properties like GC content or sequences from related species. Thus, these approaches do not work for subgenomes where gross features are indistinguishable and related genomes are lacking. Here we describe a method that uses rapidly evolving repetitive DNA to circumvent these limitations., Results: By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes from test datasets and subgenomes from two polyploid plants, tobacco and wheat, without any prior knowledge., Conclusion: This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

Polyploid organisms have more than two sets of chromosomes, including autopolyploid via intraspecific genome doubling, and allopolyploid via merging genomes of distinct species by hybridization. Polyploid organisms are widespread in plants, indicating that polyploidy has some evolutionary advantages over its diploid ancestor. Actually, polyploidy is always tightly associated with hybrid vigor and adaptation to adverse environmental conditions. However, why polyploidy can develop such advantages is poorly known. MicroRNAs (miRNAs) are endogenous ∼21 nt small RNAs which can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. MicroRNAs are essential for cell development, differentiation, signal transduction, and show an adaptive response to biotic and abiotic stresses. Environmental stresses cause plants to over- or under-express certain miRNAs or synthesize new miRNAs to cope with stress. We have here reviewed our current knowledge on the molecular mechanisms, which can account for the evolutionary advantages of polyploidy over its diploid ancestor from genome-wide gene expression and microRNAs expression perspectives.

Polyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids arise from hybridization between species and possess duplicated gene copies (homeologs) that serve redundant roles immediately after polyploidization. Although polyploidization is a major contributor to plant evolution, it remains poorly understood. We describe an analytical approach for assessing homeolog-specific expression that begins with de novo assembly of parental transcriptomes and effectively (i) reduces redundancy in de novo assemblies, (ii) identifies putative orthologs, (iii) isolates common regions between orthologs, and (iv) assesses homeolog-specific expression using a robust Bayesian Poisson-Gamma model to account for sequence bias when mapping polyploid reads back to parental references. Using this novel methodology, we examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogon mirus and T. miscellus (Compositae). Notably, we assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, we find in both allopolyploids largely balanced expression with no strong parental bias. These new methods can be used to examine homeolog expression in any tetrapolyploid system without requiring a reference genome., (Copyright © 2018 by the Genetics Society of America.)

Premise of the Study: Recurrent formation of polyploid taxa is a common observation in many plant groups. Haploid, cytoplasmic genomes like the plastid genome can be used to overcome the problem of homeologous genes and recombination in polyploid taxa. Fragaria (Rosaceae) contains several octo- and decaploid species. We use plastome sequences to infer the plastid ancestry of these taxa with special focus on the decaploid Fragaria cascadensis., Methods: We used genome skimming of 96 polyploid Fragaria samples on a single Illumina HiSeq 3000 lane to obtain whole plastome sequences. These sequences were used for phylogenetic reconstructions and dating analyses. Ploidy of all samples was inferred with flow cytometry, and plastid inheritance was examined in a controlled cross of F. cascadensis., Key Results: The plastid genome phylogeny shows that only the octoploid F. chiloensis is monophyletic, all other polyploid taxa were supported to be para- or polyphyletic. The decaploid Fragaria cascadensis has biparental plastid inheritance and four different plastid donors. Diversification of the F. cascadensis clades occurred in the last 230,000 years. The southern part of its distribution range harbors considerably higher genetic diversity, suggestive of a potential refugium., Conclusions: Fragaria cascadensis had at least four independent origins from parents with different plastomes. In contrast, para- and polyphyletic taxa of the octoploid Fragaria species are best explained by incomplete lineage sorting and/or hybridization. Biogeographic patterns in F. cascadensis are probably a result of range shift during the last glacial maximum., (© 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.)

Polyploidization has played an important role in the speciation and diversification of plant species. However, genetic analyses of polyploids are challenging because the vast majority of the model species are diploids. The allotetraploid Arabidopsis kamchatica, which originated through the hybridization of the diploid Arabidopsis halleri and Arabidopsis lyrata, is an emerging model system for studying various aspects of polyploidy. However, a transgenic method that allows the insertion of a gene of interest into A. kamchatica is still lacking. In this study, we investigated the early development of pistils in A. kamchatica and confirmed the formation of open pistils in young flower buds (stages 8-9), which is important for allowing Agrobacterium to access female reproductive tissues. We established a simple Agrobacterium-mediated floral dip transformation method to transform a gene of interest into A. kamchatica by dipping A. kamchatica inflorescences bearing many young flower buds into a 5% sucrose solution containing 0.05% Silwet L-77 and Agrobacterium harboring the gene of interest. We showed that a screenable marker comprising fluorescence-accumulating seed technology with green fluorescent protein was useful for screening the transgenic seeds of two accessions of A. kamchatica subsp. kamchatica and an accession of A. kamchatica subsp. kawasakiana.

As the dynamic nature of progenitor genomes accompanies the speciation by interspecific hybridization, the extraction of the constituent subgenome(s) from a natural allopolyploid species of long history and then restitution of the progenitor(s) provides the unique opportunity to study the genome evolution and interplay. Herein, the A subgenome from the allotetraploid oilseed rape (Brassica napus L., AACC) was extracted through inducing the preferential elimination of C-subgenome chromosomes in intertribal crosses and the progenitor B. rapa was restituted (RBR). Then by crossing and backcrossing RBR with B. napus donor, the C subgenome was in situ dissected by adding each of its nine chromosomes to the extracted A subgenome and establishing the whole set of monosonic alien addition lines (MAALs). RBR from spring-type B. napus genotype "Oro" expressed a phenotype resembling some type of B. rapa never observed before, but showed a winter-type flowering habit. This RBR had weaker growth vigor and suffered more seriously from biotic and abiotic stresses compared with Oro. The phenotypes specific for these MAALs showed the location of the related genes on the particular C-subgenome chromosomes. These MAALs exhibited obviously different frequencies in homeologous pairing and transmission of additional C-subgenome chromosomes, which were associated with the distinct degrees of their relatedness, and even with the possible genetic regulation for meiotic pairing evolved in B. napus Finally, large scaffolds undetermined for sequence assembly of B. napus were anchored to specific C-subgenome chromosomes using MAALs., (Copyright © 2016 by the Genetics Society of America.)

Premise of the Study: The growth and spread of new polyploid populations have been explained in terms of fitness advantages over their diploid progenitors. However, a fitness advantage is not sufficient to insure the establishment of a polyploid; it must also overcome the obstacles of demographic stochasticity and minority disadvantage. Several studies have addressed the population dynamics of autopolyploids, but the present study is the first to consider allopolyploids, which are affected by more factors than autopolyploids., Methods: We constructed a population dynamic model of four types of plants (two parent species, hybrids, allopolyploids) that also included an explicit breeding system., Key Results: The numbers of plants of each type were the most important factors determining whether the new allopolyploid would become established. More polyploid plants greatly increased the likelihood of polyploid persistence. More plants of the parent species and more hybrids resulted in more polyploids being produced. The model parameters with the most effect on polyploid establishment were potential population size (K), individual plant fecundity, and niche separation (α). The most important breeding system parameters were selfing rates, which mitigated minority disadvantage imposed by pollen limitation., Conclusions: The importance of population sizes, and the parameters that controlled them, in overcoming demographic stochasticity parallels the well-recognized role of propagule pressure in determining the success of invasive species. We modeled the establishment of a new allopolyploid; analogous considerations would affect the establishment of a new autopolyploid. The critical role of population sizes in polyploid establishment should be more widely recognized., (© 2016 Botanical Society of America.)

The formation of allopolyploid cotton precipitated a rapid diversification and colonization of dry coastal American tropical and subtropical regions. Previous phylogenetic analyses, combined with molecular divergence analyses, have offered a temporal framework for this radiation, but provide only weak support for some of the resolved branches. Moreover, these earlier analyses did not include the recently recognized sixth polyploid species, G. ekmanianum Wittmack. Here we use targeted sequence capture of multiple loci in conjunction with both concatenated and Bayesian concordance analyses to reevaluate the phylogeny of allopolyploid cotton species. Although phylogenetic resolution afforded by individual genes is often low, sufficient signal was attained both through the concatenated and concordance analyses to provide robust support for the Gossypium polyploid clade, which is reported here., (Copyright © 2015 Elsevier Inc. All rights reserved.)

A new contact zone between Centaurea aspera and Centaurea seridis was found in Morocco. Chromosome counts and flow cytometry showed that both taxa were tetraploid (4x = 44). A literature review and morphometric analysis established that C. aspera corresponds to the autopolyploid C. aspera subsp. gentilii and C. seridis corresponds to the allopolyploid C. seridis var. auriculata. This contact area was compared with the homologous contact zones in Spain formed by the diploid C. aspera subsp. stenophylla and the tetraploid C. seridis subsp. maritima. Natural hybrids between parental species were frequent in both areas. In Spain, hybrids were triploid (from reduced gametes A and gamete AB), highly sterile and exerted a 'triploid block'. In Morocco, cytometry showed that hybrids were tetraploid and, therefore, probably fertile, but all the capitula lacked achenes. It is likely that the resulting genome of the new tetraploid hybrid (AAAB), through the fusion of reduced gametes AA (from subsp. gentilii) and AB (from var. auriculata), could explain irregularities in meiosis through formation of aneuploid gametes and, therefore, infertility of the hybrid. Moroccan sterile tetraploid hybrids develop, but have the identical irregularities to Spanish triploids, probably due to the odd number of homologous chromosomes. The new hybrid is first described as C. x subdecurrens nothosubsp. paucispinus. In addition, distribution and ecological traits are analysed., (© 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.)

• The semi-aquatic legumes belonging to the genus Aeschynomene constitute a premium system for investigating the origin and evolution of unusual symbiotic features such as stem nodulation and the presence of a Nod-independent infection process. This latter apparently arose in a single Aeschynomene lineage. But how this unique Nod-independent group then radiated is not yet known. • We have investigated the role of polyploidy in Aeschynomene speciation via a case study of the pantropical A. indica and then extended the analysis to the other Nod-independent species. For this, we combined SSR genotyping, genome characterization through flow cytometry, chromosome counting, FISH and GISH experiments, molecular phylogenies using ITS and single nuclear gene sequences, and artificial hybridizations. • These analyses demonstrate the existence of an A. indica polyploid species complex comprising A. evenia (C. Wright) (2n = 2x = 20), A. indica L. s.s. (2n = 4x = 40) and a new hexaploid form (2n = 6x = 60). This latter contains the two genomes present in the tetraploid (A. evenia and A. scabra) and another unidentified genome. Two other species, A. pratensis and A. virginica, are also shown to be of allopolyploid origin. • This work reveals multiple hybridization/polyploidization events, thus highlighting a prominent role of allopolyploidy in the radiation of the Nod-independent Aeschynomene., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We conducted a comparative analysis using deep re-sequencing of multiple accessions of each diploid species and identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index is widely applicable for read mapping efforts of other diploid and allopolyploid Gossypium accessions. Further analysis also revealed locations of putative duplications and deletions in the A-genome relative to the D-genome reference sequence. The approximately 25,400 deleted regions included more than 50% deletion of 978 genes, including many involved with starch synthesis. In the polyploid genome, we also detected 1,472 conversion events between homoeologous chromosomes, including events that overlapped 113 genes. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton.

Polyploidy is a major factor in the evolution of plants, yet we know little about the origin and evolution of polyploidy in intertidal species. This study aimed to identify the evolutionary transitions in three true-mangrove species of the genus Acanthus distributed in the Indo–West Pacific region. For this purpose, we took an integrative approach that combined data on morphology, cytology, climatic niche, phylogeny, and biogeography of 493 samples from 42 geographic sites. Our results show that the Acanthus ilicifolius lineage distributed east of the Thai–Malay Peninsula possesses a tetraploid karyotype, which is morphologically distinct from that of the lineage on the west side. The haplotype networks and phylogenetic trees for the chloroplast genome and eight nuclear genes reveal that the tetraploid species has two sub-genomes, one each from A. ilicifolius and A. ebracteatus, the paternal and maternal parents, respectively. Population structure analysis also supports the hybrid speciation history of the new tetraploid species. The two sub-genomes of the tetraploid species diverged from their diploid progenitors during the Pleistocene. Environmental niche models revealed that the tetraploid species not only occupied the near-entire niche space of the diploids, but also expanded into novel environments. Our findings suggest that A. ilicifolius species distributed on the east side of the Thai–Malay Peninsula should be regarded as a new species, A. tetraploideus, which originated from hybridization between A. ilicifolius and A. ebracteatus, followed by chromosome doubling. This is the first report of a true-mangrove allopolyploid species that can reproduce sexually and clonally reproduction, which explains the long-term adaptive potential of the species.

Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole‐genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid‐rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long‐read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids. [ABSTRACT FROM AUTHOR]

Background: Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. Results: We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance—both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. Conclusions: C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella. [ABSTRACT FROM AUTHOR]

Summary: Combining two or more related homoeologous genomes in a single nucleus, newly formed allopolyploids must rapidly adapt meiosis to restore balanced chromosome segregation, production of euploid gametes and fertility. The poor fertility of such neo‐allopolyploids thus strongly selects for the limitation or avoidance of genetic crossover formation between homoeologous chromosomes.In this study, we have reproduced the interspecific hybridization between Arabidopsis thaliana and Arabidopsis arenosa leading to the allotetraploid Arabidopsis suecica and have characterized the first allopolyploid meioses.First‐generation neo‐allopolyploid siblings vary considerably in fertility, meiotic behavior and levels of homoeologous recombination. We show that centromere dynamics at early meiosis is altered in synthetic neo‐allopolyploids compared with evolved A. suecica, with a significant increase in homoeologous centromere interactions at zygotene. At metaphase I, the presence of multivalents involving homoeologous chromosomes confirms that homoeologous recombination occurs in the first‐generation synthetic allopolyploid plants and this is associated with a significant reduction in homologous recombination, compared to evolved A. suecica.Together, these data strongly suggest that the fidelity of recombination partner choice, likely during the DNA invasion step, is strongly impaired during the first meiosis of neo‐allopolyploids and requires subsequent adaptation. [ABSTRACT FROM AUTHOR]

Abstract Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole‐genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid‐rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long‐read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.

Many recent studies have provided significant insights into polyploid breeding, but limited research has been carried out on trees. The genomic information needed to understand growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to forests imposed by climate change. Populus alba 'Berolinensis,' also known "Yinzhong poplar," is a triploid poplar from northeast China. This hybrid triploid poplar is widely used as a landscape ornamental and in urban forestry owing to its adaptation to adverse environments and faster growth than its parental diploid. It is an artificially synthesized male allotriploid hybrid, with three haploid genomes of P. alba 'Berolinensis' originating from different poplar species, so it is attractive for studying polyploidy genomic mechanisms in heterosis. In this study, we focused on the allelic genomic interactions in P. alba 'Berolinensis,' and generated a high‐quality chromosome‐level genome assembly consisting of 19 allelic chromosomes. Its three haploid chromosome sets are polymorphic with an average of 25.73 nucleotide polymorphism sites per kilobase. We found that some stress‐related genes such as RD22 and LEA7 exhibited sequence differences between different haploid genomes. The genome assembly has been deposited in our polyploid genome online analysis website TreeGenomes (https://www.treegenomes.com). These polyploid genome‐related resources will provide a critical foundation for the molecular breeding of P. alba 'Berolinensis' and help us uncover the allopolyploidization effects of heterosis and abiotic stress resistance and traits of polyploidy species in the future. [ABSTRACT FROM AUTHOR]

Premise: Recently formed allopolyploids Tragopogon mirus and T. miscellus and their diploid parental species, T. dubius, T. porrifolius, and T. pratensis, offer a rare opportunity to study the earliest stages of allopolyploidy. The allopolyploid species have also been resynthesized, allowing comparisons between the youngest possible allopolyploid lineages and their natural, established counterparts. For the first time, we compared phenotypic traits on a large scale in Tragopogon diploids, natural allopolyploids, and three generations of synthetic allopolyploids. Methods: Our large common‐garden experiment measured traits in growth, development, physiology, and reproductive fitness. We analyzed trait differences between allopolyploids and their parental species, and between synthetic and natural allopolyploids. Results: As in many polyploids, the allopolyploid species had some larger physical traits and a higher capacity for photosynthesis than diploid species. Reproductive fitness traits were variable and inconsistent. Allopolyploids had intermediate phenotypes compared to their diploid parents in several traits, but patterns of variation often varied between allopolyploid complexes. Resynthesized and natural allopolyploid lines generally showed minor to nonexistent trait differences. Conclusions: In Tragopogon, allopolyploidy results in some typical phenotypic changes, including gigas effects and increased photosynthetic capacity. Being polyploid did not produce a significant reproductive advantage. Comparisons between natural and synthetic T. mirus and T. miscellus are consistent with very limited, idiosyncratic phenotypic evolution following allopolyploidization. [ABSTRACT FROM AUTHOR]

Distant hybridization is an effective strategy for creating polyploids in fish genetic breeding. In this study, the cross of common carp (Cyprinus carpio , 2n = 100, COC, ♀) and topmouth culter (Culter alburnus , 2n = 48, TC, ♂), which belonged to different subfamilies, was conducted and obtained surviving hybrid offspring (CT hybrids). Based on the measurement of DNA content and chromosomal numbers, three ploidy levels of CT hybrids were identified: diploid hybrids (2n = 74, 2nCT), triploid hybrids (3n = 124, 3nCT), and tetraploid hybrids (4n = 148, 4nCT). Analyses of countable traits and measurable traits indicated a significant similarity between CT hybrids and COC in comparison to TC. The genetic variation analysis of 5S rDNA and HoxD10a gene in CT hybrids revealed the retention of all COC genotypes and the partial elimination of TC genotypes, as well as the generation of novel variant genotypes (derived from TC genotypes) and recombinant genotypes (derived from parental genotypes), which suggested that in CT hybrids, the paternal subgenome exhibited greater instability than the maternal subgenome. In addition, the droplet digital PCR (ddPCR) method, combining allele-specific probes targeting the EPHX2 gene, was employed for the first time to investigate the genome composition of hybrids. The results showed that the ratios of COC-allele number to TC-allele number were approximately 1 in 2nCT, 2 in 3nCT, and 1.5 in 4nCT, respectively, which confirmed the hybridization origins for each type and effectively distinguished between the three CT hybrids. The obtainment of CT hybrids harbors potential benefits and application in aquaculture and provides an ideal model for understanding the influence of hybridization and polyploidization on the genomic composition of fish species. • 2nCT, 3nCT, and 4nCT hybrids were obtained from the cross of female COC × male TC. • The appearance of CT hybrids resembled COC more than TC. • The paternal subgenome exhibited greater instability than the maternal subgenome. • Three CT hybrids could be effectively distinguished by ddPCR with specific probes. [ABSTRACT FROM AUTHOR]

Allopolyploids are believed to inherit the genetic characteristics of its progenitors and exhibit stronger adaptability and vigor. The allotetraploid Isoetes sinensis was formed by the natural hybridization and polyploidization of two diploid progenitors, Isoetes taiwanensis and Isoetes yunguiensis, and was believed to have the potential to adapt to plateau environments. To explore the expression pattern of homoeologous genes and their contributions to altitude adaptation, we transplanted natural allotetraploid I. sinensis (TnTnYnYn) along the altitude gradient for a long‐term, and harvested them in summer and winter, respectively. One year after transplanting, it still lived well, even in the extreme environment of the Qinghai‐Tibet Plateau. Then, we performed high‐throughput RNA sequencing to measure their gene expression level. A total of 7801 homoeologous genes were expressed, among which 5786 were identified as shared expression in different altitudes and seasons. We further found that altitude variations could change the subgenome bias trend of I. sinensis, but season could not. Moreover, the functions of uniquely expressed genes indicated that temperature might be an important restrictive factor during the adaptation process. Through the analysis of DEGs and uniquely expressed genes, we found that Y subgenome provided more contributions to high altitude adaptation than T subgenome. These adaptive traits to high altitude may be inherited from its plateau progenitor I. yunguiensis. Through weighted gene co‐expression network analysis, pentatricopeptide repeats gene family and glycerophospholipid metabolism pathway were considered to play important roles in high‐altitude adaptation. Totally, this study will enrich our understanding of allopolyploid in environmental adaptation. [ABSTRACT FROM AUTHOR]

Summary: Allopolyploid Brassica juncea crops in Brassicaceae are becoming increasingly revitalized as vegetables and oilseeds owing to wide adaptability and significant economic values. However, the genomic differentiation of diversified vegetables and oilseed B. juncea and the genetic basis underlying glucosinolates accumulation have yet to be elucidated. To address this knowledge gap, we report the sequencing of pairwise genomes of vegetable and oilseed B. juncea at chromosome scale. Comparative genomics analysis unveils panoramic structural variation footprints, particularly the genetic loci of HSP20 and TGA1 associated with abiotic and biotic stresses responses between oilseed and vegetable subgroups. We anchored two major loci of MYB28 (HAG1) orthologues caused by copy number variations on A02 and A09 chromosomes using scored genomic SNPs‐based GWAS that are responsible for seed oil quality‐determining glucosinolates biosynthesis. These findings will provide valuable repertories of polyploidy genomic information enabling polyploidy genome evolution studies and precise genomic selections for crucial traits like functional components of glucosinolates in B. juncea crops and beyond. [ABSTRACT FROM AUTHOR]

Lineage recombination is an important source of genetic and morphological variation in species-rich groups of plants. Tetraploids that are intermediate in morphology and ecology with respect to sympatric diploids are regularly hypothesized to be the products of hybridization. Arctostaphylos mewukka is one such intermediate tetraploid long regarded as the result of hybridization and genome duplication among divergent and geographically overlapping diploids widely distributed across the western slope of the Sierra Nevada. Here we set out to test this hypothesis leveraging the notion that allopolyploids arise repetitively and may show signs of reciprocal organellar exchange among species between maternal and paternal progenitors. We compared nuclear ribosomal and plastid sequence data acquired from samples within and outside this target species complex. Molecular sequence data show striking patterns indicative of widespread reticulation and chloroplast capture events across the genus Arctostaphylos. Results support the notion that outcrossing, long-lived woody plant species such as members of the genus Arctostaphylos can retain a secured morphological identity despite ongoing influence of interspecific gene flow that would otherwise render species boundaries vulnerable to dissolution. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Summary: Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine‐scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing.We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally.These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats. [ABSTRACT FROM AUTHOR]

Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America. [ABSTRACT FROM AUTHOR]

Genome polyploidy has been revealed to result in evolutionary advantages and novelties, and therefore, polyploid aquatic animals may possess excellent traits of economic interest including rapid growth, extensive adaptability and disease resistance. For this reason, numerous species of natural polyploid fishes, such as common carp, gibel carp, crucian carp, salmon, and sturgeon, were chosen as important target species for aquaculture. Many artificial polyploids have been commercially utilized for aquaculture and most of them were created from natural polyploid fishes of the Cyprinidae and Salmonidae. Thanks to the easy mass production and better economic traits in growth and flesh quality, the synthetized autopolyploids or allopolyploids from natural polyploid species in cyprinid fishes have been extensively applied to aquaculture throughout China. This review outlines polyploidy advantages and innovative opportunities, lists natural polyploid species used in aquaculture, and summarizes artificial polyploids that have been induced or synthetized, and used in aquaculture. Moreover, some main research trends on polyploid utilization and ploidy manipulation of aquaculture animals are also introduced and discussed in the review.

How polyploids become established is a long-debated question, especially for autopolyploids that seem to have no evolutionary advantage over their progenitors. The Centaurea aspera polyploid complex includes diploid C. aspera and two related tetraploids C. seridis and C. gentilii. Our purpose was to study the mating system among these three taxa and to analyze its influence on polyploid establishment. The distribution and ploidy level of the Moroccan populations, and forced intra- and inter-specific crosses were assessed. Allotetraploid C. seridis produced more cypselae per capitulum in the intra-specific crosses. It is a bigger plant and autogamous, and previous studies indicated that selfing forces the asymmetric formation of sterile hybrids. All these characteristics help C. seridis to avoid the minority-cytotype-exclusion effect and become established. Inter-specific hybridization was possible between C. aspera and C. gentilii, and with the symmetric formation of hybrids. However, 49% of the hybrid cypselae were empty, which probably reveals postzygotic barriers. Autotetraploid C. gentilii produced the same number of cypselae per capitulum as those of the diploid parental, has an indistinguishable field phenotype, is allogamous, and symmetrically produces hybrids. Therefore, C. gentilii does not seem to have the same competitive advantages as those of C. seridis.

Polyploidy is one of the most important events in plant evolution: the evidence suggests that more than 70% of the angiosperms underwent some event of genomic duplication during their diversification. In potato, the third more important crop worldwide, the effects of autopolyploidization at morphological, physiological and molecular levels have been explored and no evident phenotypic superiority of polyploid lines respect to the parental diploid lines has been found. On the other hand, the consequences of allopolyploidization have not been analysed so far in potato from a molecular point of view. In this work we study the variability induced by whole genome duplication in potato auto and allotetraploids obtained by chromosomal duplication of a S. kurtzianum genotype (autopolyploid model) and by chromosomal duplication of a diploid interspecific hybrid between S. tuberosum and S. kurtzianum (allopolyploid model). Polyploid lines in both models showed a tendency to increase the vigor in phenotypic characters compared with diploid parent they derived from. AFLP analysis showed no polymorphism between parental diploid and derived polyploids lines. However, there were DNA methylation changes between diploids and polyploids, indicating that polyploidization alters the epigenetic patterns in potato. It is possible that the superiority of the tetraploid can be explained as a heterotic response dependent on the presence of heterozygous loci and epistatic interactions inducing alterations in the gene regulation of the polyploid genomes. [ABSTRACT FROM AUTHOR]

There is a close association between parthenogenesis and polyploidy. For this reason, we undertook a karyological analysis to test whether the parthenogenetic Marmorkrebs, Procambarus fallax forma virginalis, possesses an enlarged set of chromosomes. For this purpose, we karyotyped the Marmorkrebs, the sexual form of P. fallax (together called P. fallax complex), and the closely related species P. alleni. The latter shows 94 chromosomes in the haploid condition. In contrast to this, we found a haploid set of 92 chromosomes in individuals of the P. fallax complex. However, in mitotic metaphases the sexual form shows 184 chromosomes, whereas the Marmorkrebs possesses 276 chromosomes. Hence, the parthenogenetic Marmorkrebs reveals a triple amount of the haploid chromosome number. In addition, we detected a strikingly large subtelocentric chromosome which appears once in haploid and twice in diploid cells of sexual individuals of the P. fallax complex. In the parthenogenetic Marmorkrebs, this prominent chromosome occurs thrice. All this clearly reveals that the Marmorkrebs is a triploid organism. The applicability of the used methods, the significance of polyploidy in evolution of Decapoda, putative pathways to parthenogenetic triploidy, a possible hybrid origin and the scientific and ecological consequences of an increased chromosome set in Marmorkrebs are discussed. [ABSTRACT FROM AUTHOR]

Allopolyploidization plays the special role in the evolution of many crops. Moreover, the evolution in early stage of some allopolyploidization events is predicted to be effected by nuclear-cytoplasmic interactions. Maize and teosintes are well model system for study of genetic recombination in allopolyploidization. In order to investigate the effects of genome organization and cytoplasm on genome evolution in newly synthesized allopolyploids (neoallopolyploids), a series of neoallopolyploids were produced by reciprocal crosses of maize and Zea perennis. By using dual-color genomic in situ hybridization, intra- and intergenomic meiosis pairing of these polyploids were quantified and compared with regard to its genome organization and cytoplasm background. In the four neoallopolyploids, the stability of maize genome is consistently lower than that of Z. perennis genome. Additional, the stability of maize genome is affected by genome ploidy. The cytoplasm, genome composition and their interaction do have the special role in chromosome paring and the meiosis behaviors in Zea allopolyploids vary significantly and showed non-diploidization. Z. perennis cytoplasm may give a relatively relaxed environment for maize genome. [ABSTRACT FROM AUTHOR]

Background: Forming a new species through the merger of two or more divergent parent species is increasingly seen as a key phenomenon in the evolution ofmany biological systems. However, little is known about how expression of parental gene copies (homeologs) responds following genome merger. High throughput RNA sequencing now makes this analysis technically feasible, but tools to determine homeolog expression are still in their infancy. Results: Here we present HyLiTE -- a single-step analysis to obtain tables of homeolog expression in a hybrid or allopolyploid and its parent species directly from raw mRNA sequence files. By implementing on-the-fly detection of diagnostic parental polymorphisms, HyLiTE can perform SNP calling and read classification simultaneously, thus allowing HyLiTE to be run as parallelized code. HyLiTE accommodates any number of parent species, multiple data sources (including genomic DNA reads to improve SNP detection), and implements a statistical framework optimized for genes with low to moderate expression. Conclusions: HyLiTE is a flexible and easy-to-use program designed for bench biologists to explore patterns of gene expression following genome merger. HyLiTE offers practical advantages over manual methods and existing programs, has been designed to accommodate a wide range of genome merger systems, can identify SNPs that arose following genome merger, and offers accurate performance on non-model organisms. [ABSTRACT FROM AUTHOR]

Background: Rubus is a large and taxonomically complex genus exhibiting agamospermy, polyploidy and frequent hybridization. The objective of this work was to elucidate rDNA disrtibution pattern and investigate genomic composition of polyploids in 16 Rubus taxa (2n = 2x, 3x, 4x, 8x) of two subgenera Idaeobatus and Malachobatus by ISH method. Results: The basic Rubus genome had one 45S rDNA locus, and all the polyploids (except R. setchuenensis) had the expected multiples of this number. Diploid and tetraploid Rubus taxa carried two 5S rDNA, whereas the triploid and octoploid species only had three. The duplicated 45S rDNA sites tended to be conserved, whereas those of 5S rDNA tended to be eliminated after polyploidization. The accession R03-20 was an autotriploid R. parvifolius, while R03-27 and R03-57 were naturally-occurred triploid hybrids between R. parvifolius and R. coreanus. GISH results suggested that R. parvifolius had close relationship with polyploids from Malachobatus. Conclusions: The polyploids from Malachobatus were probable allopolyploid. In addition, Rubus parvifolius might be involved in hybridization, polyploidization and speciation of some Idaeobatus and Malachobatus species. [ABSTRACT FROM AUTHOR]