Contrasting evolutionary dynamics between angiosperm and mammalian genomes

Cavity architecture based modulation of ligand binding tunnels in plant START domains

The Steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain represents an evolutionarily conserved superfamily of lipid transfer proteins widely distributed across the tree of life. Despite significant expansion in plants, knowledge about this domain remains inadequate in plants. In this work, we explore the role of cavity architectural modulations in START protein evolution and functional diversity. We use deep-learning approaches to generate plant START domain models, followed by surface accessibility studies and a comprehensive structural investigation of the rice START family. We validate 28 rice START domain models, delineate binding cavities, measure pocket volumes, and compare these with mammalian counterparts to understand evolution of binding preferences. Overall, plant START domains retain the ancestral α/β helix-grip signature, but we find subtle variation in cavity architectures, resulting in significantly smaller ligand-binding tunnels in the plant kingdom. We identify cavity lining residues (CLRs) responsible for reduction in ancestral tunnel space, and these appear to be class specific, and unique to plants, providing a mechanism for the observed shift in domain function. For instance, mammalian cavity lining residues A135, G181 and A192 have evolved to larger CLRs across the plant kingdom, contributing to smaller sizes, minimal STARTs being the largest, while members of type-IV HD-Zip family show almost complete obliteration of lipid binding cavities, consistent with their present-day DNA binding functions. In summary, this work quantifies plant START structural & functional divergence, bridging current knowledge gaps.

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.

Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing

Understanding the evolutionary conservation of complex eukaryotic transcriptomes significantly illuminates the physiological relevance of alternative splicing (AS). Examining the evolutionary depth of a given AS event with ordinary homology searches is generally challenging and time-consuming. Here, we present Catsnap, an algorithmic pipeline for assessing the conservation of putative protein isoforms generated by AS. It employs a machine learning approach following a database search with the provided pair of protein sequences. We used the Catsnap algorithm for analyzing the conservation of emerging experimentally characterized alternative proteins from plants and animals. Indeed, most of them are conserved among other species. Catsnap can detect the conserved functional protein isoforms regardless of the AS type by which they are generated. Notably, we found that while the primary amino acid sequence is maintained, the type of AS determining the inclusion or exclusion of protein regions varies throughout plant phylogenetic lineages in these proteins. We also document that this phenomenon is less seen among animals. In sum, our algorithm highlights the presence of unexpectedly frequent hotspots where protein isoforms recurrently arise to carry physiologically relevant functions. The user web interface is available at https://catsnap.cesnet.cz/.

Phylogenetic analysis and expression profiles of jasmonate ZIM-domain gene family provide insight into abiotic stress resistance in sunflower

Jasmonate ZIM-domain (JAZ) proteins act as inhibitory factors of the jasmonic acid (JA) pathway, which is involved in regulating plant development and defense responses. However, there are no extensive studies available on JAZ genes in sunflower (Helianthus annuus L.). In this study, the phylogenetic analysis of 139 putative JAZ genes from eight plants demonstrated that these JAZs could be divided into five groups (Groups I-V), and the 27 sunflower JAZs (HaJAZs) were classified into these five groups. All groups contained genes from both monocotyledons and dicotyledons, indicating that the emergence of JAZ genes predates the differentiation of monocotyledons and dicotyledons. Both segmental and tandem duplications contributed greatly to this gene family's expansion in sunflower, especially in Group II. Moreover, the expression profiles of HaJAZ genes under normal conditions, hormone treatments or abiotic stresses were analyzed based on RNA-seq data. HaJAZ2 may be undergoing pseudogenization as a nonfunctional gene because it was not expressed in any tissue. Many HaJAZ genes in roots upregulated their expression when involved in responding to exogenous hormones, especially methyl-jasmonate. The abiotic stress treatments of sunflower showed that HaJAZ5, HaJAZ15, HaJAZ17, HaJAZ20, and HaJAZ21 tend to be sensitive to certain abiotic stresses. HaJAZs from different groups may share similar functions but also exercise their unique functions when responding to abiotic stresses. We speculated that this gene family was conserved in sequence but varied in its expression among duplicated HaJAZ genes, which implies that they may confer neofunctionalization in the adaptation to abiotic stresses; this work provides insight into the resistance of sunflowers and their adaptation to diverse environmental conditions.

Evolution of complex genome architecture in gymnosperms

Gymnosperms represent an ancient lineage that diverged from early spermatophytes during the Devonian. The long fossil records and low diversity in living species prove their complex evolutionary history, which included ancient radiations and massive extinctions. Due to their ultra-large genome size, the whole-genome assembly of gymnosperms has only generated in the past 10 years and is now being further expanded into more taxonomic representations. Here, we provide an overview of the publicly available gymnosperm genome resources and discuss their assembly quality and recent findings in large genome architectures. In particular, we describe the genomic features most related to changes affecting the whole genome. We also highlight new realizations relative to repetitive sequence dynamics, paleopolyploidy, and long introns. Based on the results of relevant genomic studies of gymnosperms, we suggest additional efforts should be made toward exploring the genomes of medium-sized (5–15 gigabases) species. Lastly, more comparative analyses among high-quality assemblies are needed to understand the genomic shifts and the early species diversification of seed plants.

Specificities and Dynamics of Transposable Elements in Land Plants

Simple Summary

Transposable elements are dynamic components of plant genomes, and display a high diversity of lineages and distribution as the result of evolutionary driving forces and overlapping mechanisms of genetic and epigenetic regulation. They are now regarded as main contributors for genome evolution and function, and important regulators of endogenous gene expression. In this review, we survey recent progress and current challenges in the identification and classification of transposon lineages in complex plant genomes, highlighting the molecular specificities that may explain the expansion and diversification of mobile genetic elements in land plants.

Abstract

Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.

Nucleic acids movement and its relation to genome dynamics of repetitive DNA: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?

There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments.

Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery

Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.

Genome-wide expression analysis of phospholipase A1 (PLA1) gene family suggests phospholipase A1-32 gene responding to abiotic stresses in cotton

Cotton is the most important crop for the production of natural fibres used in the textile industry. High salinity, drought, cold and high temperature represent serious abiotic stresses, which seriously threaten cotton production. Phospholipase A_S has an irreplaceable role in lipid signal transmission, growth and development and stress events. Phospholipase A can be divided into three families: PLA1, PLA2 and pPLA. Among them, the PLA1 family is rarely studied in plants. In order to study the potential functions of the PLA1 family in cotton, the bioinformatics analysis of the PLA1 family was correlated with cotton adversity, and tissue-specific analysis was performed. Explore the structure-function relationship of PLA1 members. It is found that the expression of GbPLA1-32 gene is affected by a variety of environmental stimuli, indicating that it plays a very important role in stress and hormone response, and closely associates the cotton adversity with this family. Through further functional verification, we found that virus-induced GbPLA1-32 gene silencing (VIGS) caused Gossypium barbadense to be sensitive to salt stress. This research provides an important basis for further research on the molecular mechanism of cotton resistance to abiotic stress.

Exploring environmental selection on genome size in angiosperms

Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO₂-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.

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.

A prescient evolutionary model for genesis, duplication and differentiation of MIR160 homologs in Brassicaceae

MicroRNA160 is a class of nitrogen-starvation responsive genes which governs establishment of root system architecture by down-regulating AUXIN RESPONSE FACTOR genes (ARF10, ARF16 and ARF17) in plants. The high copy number of MIR160 variants discovered by us from land plants, especially polyploid crop Brassicas, posed questions regarding genesis, duplication, evolution and function. Absence of studies on impact of whole genome and segmental duplication on retention and evolution of MIR160 homologs in descendent plant lineages prompted us to undertake the current study. Herein, we describe ancestry and fate of MIR160 homologs in Brassicaceae in context of polyploidy driven genome re-organization, copy number and differentiation. Paralogy amongst Brassicaceae MIR160a, MIR160b and MIR160c was inferred using phylogenetic analysis of 468 MIR160 homologs from land plants. The evolutionarily distinct MIR160a was found to represent ancestral form and progenitor of MIR160b and MIR160c. Chronology of evolutionary events resulting in origin and diversification of genomic loci containing MIR160 homologs was delineated using derivatives of comparative synteny. A prescient model for causality of segmental duplications in establishment of paralogy in Brassicaceae MIR160, with whole genome duplication accentuating the copy number increase, is being posited in which post-segmental duplication events viz. differential gene fractionation, gene duplications and inversions are shown to drive divergence of chromosome segments. While mutations caused the diversification of MIR160a, MIR160b and MIR160c, duplicated segments containing these diversified genes suffered gene rearrangements via gene loss, duplications and inversions. Yet the topology of phylogenetic and phenetic trees were found congruent suggesting similar evolutionary trajectory. Over 80% of Brassicaceae genomes and subgenomes showed a preferential retention of single copy each of MIR160a, MIR160b and MIR160c suggesting functional relevance. Thus, our study provides a blue-print for reconstructing ancestry and phylogeny of MIRNA gene families at genomics level and analyzing the impact of polyploidy on organismal complexity. Such studies are critical for understanding the molecular basis of agronomic traits and deploying appropriate candidates for crop improvement.

Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR-RT) families in the 272-Mb genome of the Mediterranean grass Brachypodium distachyon. We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half-life as low as 66 kyr, the latter are the most dynamic part of the genome and an important source of within-species polymorphisms. Second, GC-rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains > 20% of the genome-wide variation in GC content and is associated with higher methylation levels. Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?

LTR retrotransposons constitute a significant part of plant genomes and their evolutionary dynamics play an important role in genome size changes. Current methods of LTR retrotransposon age estimation are based only on LTR (long terminal repeat) divergence. This has prompted us to analyze sequence similarity of LTRs in 25,144 LTR retrotransposons from fifteen plant species as well as formation of solo LTRs. We found that approximately one fourth of nested retrotransposons showed a higher LTR divergence than the pre-existing retrotransposons into which they had been inserted. Moreover, LTR similarity was correlated with LTR length. We propose that gene conversion can contribute to this phenomenon. Gene conversion prediction in LTRs showed potential converted regions in 25% of LTR pairs. Gene conversion was higher in species with smaller genomes while the proportion of solo LTRs did not change with genome size in analyzed species. The negative correlation between the extent of gene conversion and the abundance of solo LTRs suggests interference between gene conversion and ectopic recombination. Since such phenomena limit the traditional methods of LTR retrotransposon age estimation, we recommend an improved approach based on the exclusion of regions affected by gene conversion.

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Background

Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.

Results

We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family ("autoinsertions"). Nested LTR retrotransposons were preferentially located in the 3'UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons.

Conclusions

We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.

The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing

BACKGROUND AND AIMS

Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing.

METHODS

Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes.

KEY RESULTS

Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species.

CONCLUSIONS

The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.

Meiosis, the master driver of gene duplication in higher plants?

Meiosis is a critical biological process for reproduction and genetic variation in higher plants. Gene duplication is a prominent feature of plant genomic architecture. Meiosis and gene duplication are of fundamental importance in unraveling the nature of genetics and evolution. The ideas and findings in this letter demonstrate a highly significant connection between meiosis and gene duplication, bring together these two disparate fields of study and highlight the importance of meiosis for understanding the evolutionary success of flowering plants. These insights and opinions open a new area of investigation and point to a significant way to illustrate the impact of duplicated genes on meiosis and fitness in higher plants, as well as their ultimate evolutionary, ecological, and agronomic impacts in light of challenges that have arisen due to global climate change. This study addresses novel ideas and viewpoints in plant developmental genomics and evolution.

Genomic and evolutionary aspects of chloroplast tRNA in monocot plants

BACKGROUND

Chloroplasts are one of the most indispensable organelles that make life forms on the earth possible by their capacity to photosynthesize. These organelles possess a circular genome with a number of coding genes responsible for self-regulation. tRNAs are an important evolutionary-conserved gene family that are responsible for protein translation. However, within the chloroplast genome, tRNA machinery are poorly understood.

RESULTS

In the present study, the chloroplast genome of six monocot plants, Oryza nivara (NC_005973), Oryza sativa (NC_001320), Sachharum officinarum (NC_006084), Sorghum bicolor (NC_008602), Triticum aestivum (NC_002762), and Zea mays (NC_001666) were downloaded and analyzed to identify tRNA sequences. Further analysis of the tRNA sequences in the chloroplast genomes of the monocot plants resulted in the identification of several novel features. The length of tRNAs in the chloroplast genome of the monocot plants ranged from 59 to 155 nucleotides. Pair-wise sequence alignment revealed the presence of a conserved A-C-x-U-A-x-U-A-x-U-x5-U-A-A nucleotide consensus sequence. In addition, the tRNAs in chloroplast genomes of the monocot plants also contain 21-28 anti-codons against 61 sense codons in the genome. They also contain a group I intron and a C-A-U anti-codon for tRNAIle, which is a common anti-codon of tRNAMet. Evolutionary analysis indicates that tRNAs in the chloroplast genome have evolved from multiple common ancestors, and tRNAMet appears to be the ancestral tRNA that underwent duplication and diversification to give rise to other tRNAs.

CONCLUSION

The results obtained from the study of chloroplast tRNA will greatly help to increase our understanding of tRNA biology at a new level. Functional studies of the reported novel aspects of the chloroplast tRNA of the monocot plants will greatly help to decipher their roles in diverse cellular processes.

Impact of Repetitive Elements on the Y Chromosome Formation in Plants

In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.

Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms

Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.

From Mendel's discovery on pea to today's plant genetics and breeding : Commemorating the 150th anniversary of the reading of Mendel's discovery

KEY MESSAGE

This work discusses several selected topics of plant genetics and breeding in relation to the 150th anniversary of the seminal work of Gregor Johann Mendel. In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin's theory of evolution was based on differential survival and differential reproductive success, Mendel's theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin's concepts were continuous variation and "soft" heredity; Mendel espoused discontinuous variation and "hard" heredity. Thus, the combination of Mendelian genetics with Darwin's theory of natural selection was the process that resulted in the modern synthesis of evolutionary biology. Although biology, genetics, and genomics have been revolutionized in recent years, modern genetics will forever rely on simple principles founded on pea breeding using seven single gene characters. Purposeful use of mutants to study gene function is one of the essential tools of modern genetics. Today, over 100 plant species genomes have been sequenced. Mapping populations and their use in segregation of molecular markers and marker-trait association to map and isolate genes, were developed on the basis of Mendel's work. Genome-wide or genomic selection is a recent approach for the development of improved breeding lines. The analysis of complex traits has been enhanced by high-throughput phenotyping and developments in statistical and modeling methods for the analysis of phenotypic data. Introgression of novel alleles from landraces and wild relatives widens genetic diversity and improves traits; transgenic methodologies allow for the introduction of novel genes from diverse sources, and gene editing approaches offer possibilities to manipulate gene in a precise manner.

Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.

Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.

Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation

Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation.

Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression

There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5′ and 3′ UTRs) between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex

Long terminal repeat retrotransposons (LTR-RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR-RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR-RTs and/or genetic redundancy supports the accumulation of active LTR-RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR-RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR-RT families revealed contrasted dynamics during species diversification. Quiescent LTR-RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR-RT families in autopolyploids further supported that genome shock and redundancy are non-mutually exclusive triggers of LTR-RT proliferation. Although reputed stable, autopolyploid genomes show LTR-RT fractions presenting analogies with polyploids between widely divergent genomes.

Structurally Complex Organization of Repetitive DNAs in the Genome of Cobia (Rachycentron canadum)

Repetitive DNAs comprise the largest fraction of the eukaryotic genome. They include microsatellites or simple sequence repeats (SSRs), which play an important role in the chromosome differentiation among fishes. Rachycentron canadum is the only representative of the family Rachycentridae. This species has been focused on several multidisciplinary studies in view of its important potential for marine fish farming. In the present study, distinct classes of repetitive DNAs, with emphasis on SSRs, were mapped in the chromosomes of this species to improve the knowledge of its genome organization. Microsatellites exhibited a diversified distribution, both dispersed in euchromatin and clustered in the heterochromatin. The multilocus location of SSRs strengthened the heterochromatin heterogeneity in this species, as suggested by some previous studies. The colocalization of SSRs with retrotransposons and transposons pointed to a close evolutionary relationship between these repetitive sequences. A number of heterochromatic regions highlighted a greater complex organization than previously supposed, harboring a diversity of repetitive elements. In this sense, there was also evidence of colocalization of active genetic regions and different classes of repetitive DNAs in a common heterochromatic region, which offers a potential opportunity for further researches regarding the interaction of these distinct fractions in fish genomes.

Genomic repeat abundances contain phylogenetic signal

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.

Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.

Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades

A large fraction of eukaryotic genomes is made up of long interspersed nuclear elements (LINEs). Due to their capability to create novel copies via error-prone reverse transcription, they generate multiple families and reach high copy numbers. Although mammalian LINEs have been well described, plant LINEs have been only poorly investigated. Here, we present a systematic cross-species survey of LINEs in higher plant genomes shedding light on plant LINE evolution as well as diversity, and facilitating their annotation in genome projects. Applying a Hidden Markov Model (HMM)-based analysis, 59 390 intact LINE reverse transcriptases (RTs) were extracted from 23 plant genomes. These fall in only two out of 28 LINE clades (L1 and RTE) known in eukaryotes. While plant RTE LINEs are highly homogenous and mostly constitute only a single family per genome, plant L1 LINEs are extremely diverse and form numerous families. Despite their heterogeneity, all members across the 23 species fall into only seven L1 subclades, some of them defined here. Exemplarily focusing on the L1 LINEs of a basal reference plant genome (Beta vulgaris), we show that the subclade classification level does not only reflect RT sequence similarity, but also mirrors structural aspects of complete LINE retrotransposons, like element size, position and type of encoded enzymatic domains. Our comprehensive catalogue of plant LINE RTs serves the classification of highly diverse plant LINEs, while the provided subclade-specific HMMs facilitate their annotation.

GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis

In angiosperms (as in other species), GC content varies along and between genes, within a genome, and between genomes of different species, but the reason for this distribution is still an open question. Grass genomes are particularly intriguing because they exhibit a strong bimodal distribution of genic GC content and a sharp 5'-3' decreasing GC content gradient along most genes. Here, we propose a unifying model to explain the main patterns of GC content variation at the gene and genome scale. We argue that GC content patterns could be mainly determined by the interactions between gene structure, recombination patterns, and GC-biased gene conversion. Recent studies on fine-scale recombination maps in angiosperms support this hypothesis and previous results also fit this model. We propose that our model could be used as a null hypothesis to search for additional forces that affect GC content in angiosperms.

Impact of recurrent gene duplication on adaptation of plant genomes

BACKGROUND

Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale.

RESULTS

We studied available sequenced angiosperm genomes to assess the frequency of positive selection footprints in lineage specific expanded (LSE) gene families compared to single-copy genes using a dN/dS-based test in a phylogenetic framework. We found 5.38% of alignments in LSE genes with codons under positive selection. In contrast, we found no evidence for codons under positive selection in the single-copy reference set. An analysis at the branch level shows that purifying selection acted more strongly on single-copy genes than on LSE gene clusters. Moreover we detect significantly more branches indicating evolution under positive selection and/or relaxed constraint in LSE genes than in single-copy genes.

CONCLUSIONS

In this - to our knowledge -first genome-scale study we provide strong empirical support for the hypothesis that LSE genes fuel adaptation in angiosperms. Our conservative approach for detecting selection footprints as well as our results can be of interest for further studies on (plant) gene family evolution.

Transposable elements: powerful contributors to angiosperm evolution and diversity

Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's "abominable mystery": the spectacular success of the angiosperms.

Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats

Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions. TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.

Deep genetic divergence between disjunct Refugia in the Arctic-Alpine King's Crown, Rhodiola integrifolia (Crassulaceae)

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King's Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome.

Quadruplex-forming sequences occupy discrete regions inside plant LTR retrotransposons

Retrotransposons with long terminal repeats (LTR) form a significant proportion of eukaryotic genomes, especially in plants. They have gag and pol genes and several regulatory regions necessary for transcription and reverse transcription. We searched for potential quadruplex-forming sequences (PQSs) and potential triplex-forming sequences (PTSs) in 18 377 full-length LTR retrotransposons collected from 21 plant species. We found that PQSs were often located in LTRs, both upstream and downstream of promoters from which the whole retrotransposon is transcribed. Upstream-located guanine PQSs were dominant in the minus DNA strand, whereas downstream-located guanine PQSs prevailed in the plus strand, indicating their role both at transcriptional and post-transcriptional levels. Our circular dichroism spectroscopy measurements confirmed that these PQSs readily adopted guanine quadruplex structures-some of them were paralell-stranded, while others were anti-parallel-stranded. The PQS often formed doublets at a mutual distance of up to 400 bp. PTSs were most abundant in 3'UTR (but were also present in 5'UTR). We discuss the potential role of quadruplexes and triplexes as the regulators of various processes participating in LTR retrotransposon life cycle and as potential recombination sites during post-insertional retrotransposon-based genome rearrangements.

Evolutionary consequences, constraints and potential of polyploidy in plants

Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.

Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences

Recent advances have highlighted the ubiquity of whole-genome duplication (polyploidy) in angiosperms, although subsequent genome size change and diploidization (returning to a diploid-like condition) are poorly understood. An excellent system to assess these processes is provided by Nicotiana section Repandae, which arose via allopolyploidy (approximately 5 million years ago) involving relatives of Nicotiana sylvestris and Nicotiana obtusifolia. Subsequent speciation in Repandae has resulted in allotetraploids with divergent genome sizes, including Nicotiana repanda and Nicotiana nudicaulis studied here, which have an estimated 23.6% genome expansion and 19.2% genome contraction from the early polyploid, respectively. Graph-based clustering of next-generation sequence data enabled assessment of the global genome composition of these allotetraploids and their diploid progenitors. Unexpectedly, in both allotetraploids, over 85% of sequence clusters (repetitive DNA families) had a lower abundance than predicted from their diploid relatives; a trend seen particularly in low-copy repeats. The loss of high-copy sequences predominantly accounts for the genome downsizing in N. nudicaulis. In contrast, N. repanda shows expansion of clusters already inherited in high copy number (mostly chromovirus-like Ty3/Gypsy retroelements and some low-complexity sequences), leading to much of the genome upsizing predicted. We suggest that the differential dynamics of low- and high-copy sequences reveal two genomic processes that occur subsequent to allopolyploidy. The loss of low-copy sequences, common to both allopolyploids, may reflect genome diploidization, a process that also involves loss of duplicate copies of genes and upstream regulators. In contrast, genome size divergence between allopolyploids is manifested through differential accumulation and/or deletion of high-copy-number sequences.

Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization

We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.

Contrasting patterns of transposable element and satellite distribution on sex chromosomes (XY1Y2) in the dioecious plant Rumex acetosa

Rumex acetosa is a dioecious plant with the XY1Y2 sex chromosome system. Both Y chromosomes are heterochromatic and are thought to be degenerated. We performed low-pass 454 sequencing and similarity-based clustering of male and female genomic 454 reads to identify and characterize major groups of R. acetosa repetitive DNA. We found that Copia and Gypsy retrotransposons dominated, followed by DNA transposons and nonlong terminal repeat retrotransposons. CRM and Tat/Ogre retrotransposons dominated the Gypsy superfamily, whereas Maximus/Sireviruses were most abundant among Copia retrotransposons. Only one Gypsy subfamily had accumulated on Y1 and Y2 chromosomes, whereas many retrotransposons were ubiquitous on autosomes and the X chromosome, but absent on Y1 and Y2 chromosomes, and others were depleted from the X chromosome. One group of CRM Gypsy was specifically localized to centromeres. We also found that majority of previously described satellites (RAYSI, RAYSII, RAYSIII, and RAE180) are accumulated on the Y chromosomes where we identified Y chromosome-specific variant of RAE180. We discovered two novel satellites-RA160 satellite dominating on the X chromosome and RA690 localized mostly on the Y1 chromosome. The expression pattern obtained from Illumina RNA sequencing showed that the expression of transposable elements is similar in leaves of both sexes and that satellites are also expressed. Contrasting patterns of transposable elements (TEs) and satellite localization on sex chromosomes in R. acetosa, where not only accumulation but also depletion of repetitive DNA was observed, suggest that a plethora of evolutionary processes can shape sex chromosomes.

Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat

Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes.

Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes

Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allow inferring the evolutionary history of entire plant and animal genomes. Based on the comparison of the plant and animal genome paleohistory, major differences are unveiled in 1) evolutionary mechanisms (i.e., polyploidization versus diploidization processes), 2) genome conservation (i.e., coding versus noncoding sequence maintenance), and 3) modern genome architecture (i.e., genome organization including repeats expansion versus contraction phenomena). This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes.

Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris)

Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

The large-scale replacement of gymnosperms by angiosperms in many ecological niches over time and the huge disparity in species numbers have led scientists to explore factors (e.g. polyploidy, developmental systems, floral evolution) that may have contributed to the astonishing rise of angiosperm diversity. Here, we explore genomic and ecological factors influencing seed plant genomes. This is timely given the recent surge in genomic data. We compare and contrast the genomic structure and evolution of angiosperms and gymnosperms and find that angiosperm genomes are more dynamic and diverse, particularly amongst the herbaceous species. Gymnosperms typically have reduced frequencies of a number of processes (e.g. polyploidy) that have shaped the genomes of other vascular plants and have alternative mechanisms to suppress genome dynamism (e.g. epigenetics and activity of transposable elements). Furthermore, the presence of several characters in angiosperms (e.g. herbaceous habit, short minimum generation time) has enabled them to exploit new niches and to be viable with small population sizes, where the power of genetic drift can outweigh that of selection. Together these processes have led to increased rates of genetic divergence and faster fixation times of variation in many angiosperms compared with gymnosperms.

Next-generation hybridization and introgression

Hybridization has a major role in evolution-from the introgression of important phenotypic traits between species, to the creation of new species through hybrid speciation. Molecular studies of hybridization aim to understand the class of hybrids and the frequency of introgression, detect the signature of ancient hybridization, and understand the behaviour of introgressed loci in their new genomic background. This often involves a large investment in the design and application of molecular markers, leading to a compromise between the depth and breadth of genomic data. New techniques designed to assay a large sub-section of the genome, in association with next-generation sequencing (NGS) technologies, will allow genome-wide hybridization and introgression studies in organisms with no prior sequence data. These detailed genotypic data will unite the breadth of sampling of loci characteristic of population genetics with the depth of sequence information associated with molecular phylogenetics. In this review, we assess the theoretical and methodological constraints that limit our understanding of natural hybridization, and promote the use of NGS for detecting hybridization and introgression between non-model organisms. We also make recommendations for the ways in which emerging techniques, such as pooled barcoded amplicon sequencing and restriction site-associated DNA tags, should be used to overcome current limitations, and enhance our understanding of this evolutionary significant process.

Genomic diversity in two related plant species with and without sex chromosomes--Silene latifolia and S. vulgaris

Background

Genome size evolution is a complex process influenced by polyploidization, satellite DNA accumulation, and expansion of retroelements. How this process could be affected by different reproductive strategies is still poorly understood.

Methodology/Principal Findings

We analyzed differences in the number and distribution of major repetitive DNA elements in two closely related species, Silene latifolia and S. vulgaris. Both species are diploid and possess the same chromosome number (2n = 24), but differ in their genome size and mode of reproduction. The dioecious S. latifolia (1C = 2.70 pg DNA) possesses sex chromosomes and its genome is 2.5× larger than that of the gynodioecious S. vulgaris (1C = 1.13 pg DNA), which does not possess sex chromosomes. We discovered that the genome of S. latifolia is larger mainly due to the expansion of Ogre retrotransposons. Surprisingly, the centromeric STAR-C and TR1 tandem repeats were found to be more abundant in S. vulgaris, the species with the smaller genome. We further examined the distribution of major repetitive sequences in related species in the Caryophyllaceae family. The results of FISH (fluorescence in situ hybridization) on mitotic chromosomes with the Retand element indicate that large rearrangements occurred during the evolution of the Caryophyllaceae family.

Conclusions/Significance

Our data demonstrate that the evolution of genome size in the genus Silene is accompanied by the expansion of different repetitive elements with specific patterns in the dioecious species possessing the sex chromosomes.

Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution

Plant genomes are generally very large, mostly paleopolyploid, and have numerous gene duplicates and complex genomic features such as repeats and transposable elements. Many of these features have been hypothesized to enable plants, which cannot easily escape environmental challenges, to rapidly adapt. Another mechanism, which has recently been well described as a major facilitator of rapid adaptation in bacteria, animals, and fungi but not yet for plants, is modular rearrangement of protein-coding genes. Due to the high precision of profile-based methods, rearrangements can be well captured at the protein level by characterizing the emergence, loss, and rearrangements of protein domains, their structural, functional, and evolutionary building blocks. Here, we study the dynamics of domain rearrangements and explore their adaptive benefit in 27 plant and 3 algal genomes. We use a phylogenomic approach by which we can explain the formation of 88% of all arrangements by single-step events, such as fusion, fission, and terminal loss of domains. We find many domains are lost along every lineage, but at least 500 domains are novel, that is, they are unique to green plants and emerged more or less recently. These novel domains duplicate and rearrange more readily within their genomes than ancient domains and are overproportionally involved in stress response and developmental innovations. Novel domains more often affect regulatory proteins and show a higher degree of structural disorder than ancient domains. Whereas a relatively large and well-conserved core set of single-domain proteins exists, long multi-domain arrangements tend to be species-specific. We find that duplicated genes are more often involved in rearrangements. Although fission events typically impact metabolic proteins, fusion events often create new signaling proteins essential for environmental sensing. Taken together, the high volatility of single domains and complex arrangements in plant genomes demonstrate the importance of modularity for environmental adaptability of plants.