The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana

Chromosome-level reference genome of Tetrastigma hemsleyanum (Vitaceae) provides insights into genomic evolution and the biosynthesis of phenylpropanoids and flavonoids

Here, we present a high-quality chromosome-scale genome assembly (2.19 Gb) and annotation of Tetrastigma hemsleyanum, a perennial herbaceous liana native to subtropical China with diverse medicinal applications. Approximately 73% of the genome was comprised of transposable elements (TEs), of which long terminal repeat retrotransposons (LTR-RTs) were a predominant group (69% of the genome). The genome size increase of T. hemsleyanum (relative to Vitis species) was mostly due to the proliferation of LTR-RTs. Of the different modes of gene duplication identified, transposed duplication (TRD) and dispersed duplication (DSD) were the predominant ones. Genes, particularly those involved in the phenylpropanoid-flavonoid (PF) pathway and those associated with therapeutic properties and environmental stress resistance, were significantly amplified through recent tandem duplications. We dated the divergence of two intraspecific lineages in Southwest (SW) versus Central-South-East (CSE) China to the late Miocene (approximately 5.2 million years ago). Of those, the former showed more upregulated genes and metabolites. Based on resequencing data of 38 individuals representing both lineages, we identified various candidate genes related to 'response to stimulus' and 'biosynthetic process', including ThFLS11, which is putatively involved in flavonoid accumulation. Overall, this study provides abundant genomic resources for future evolutionary, ecological, and functional genomics studies in T. hemsleyanum and related species.

Multiple Introductions and Distinct Genetic Groups of Canada Goldenrod (Solidago canadensis) in China Revealed by Genomic Single-Nucleotide Polymorphisms

Despite numerous studies reported in the context of ecology, the introduction history of the infamous invasive plant Canada goldenrod (Solidago canadensis L.) remains elusive. In the present study, we explored the sources and the number of introduction events of this species from its native areas into China. Using the genotyping-by-sequencing approach, we identified 34,035 selectively neutral single-nucleotide polymorphism (SNP) markers to infer the evolutionary trajectories of 77 S. canadensis individuals. Both the principal component analysis and the ADMIXTURE analysis revealed two genetic groups that are sympatric to each other in China and suggested the absence of genetic admixtures. The phylogenetic analysis indicated three feasible introduction routes and multiple introduction events of Canada goldenrod into China. Specifically, the one from the USA directly into China, the other from the USA into China through Japan, and the third from the USA into China through Europe. Based on the site frequency spectrum of these identified SNPs, we inferred strong bottleneck events for both genetic groups, and that the multiple introductions did not rescue the decline of genetic diversity. To conclude, multiple introduction events, genetic bottlenecks, and potential human-mediated spread characterize the introduction history of Canada goldenrod in China. The present study harnesses the power of SNP data in deciphering the evolutionary trajectory of invasive plants and paves the way for future studies concerning the invasion mechanism of Canada goldenrod.

Recent genome-wide replication promoted expansion and functional differentiation of the JAZs in soybeans

Jasmonate Zim-domain (JAZ) protein is an inhibitor of the jasmonate (JA) signal transduction pathway, and plays an important role in regulating plant growth, development, and defense. However, there have been few studies on its function under environmental stress in soybeans. In this study, a total of 275 JAZs protein-coding genes were identified in 29 soybean genomes. SoyC13 contained the least JAZ family members (26 JAZs), which was twice as high as AtJAZs. The genes are mainly generated by recent genome-wide replication (WGD), which replicated during the Late Cenozoic Ice Age. In addition, transcriptome analysis showed that the differences in gene expression patterns in the roots, stems, and leaves of the 29 cultivars at the V1 stage were not significant, but there was a significant difference among the three seed development stages. Finally, qRT-PCR results showed that GmJAZs responded the most strongly to heat stress, followed by drought and cold stress. This is consistent with the reason for their expansion and promoter analysis results. Therefore, we explored the significant role of conserved, duplicated, and neofunctionalized JAZs in the evolution of soybeans, which will contribute to the functional characterization of GmJAZ and the improvement of crops.

An evolutionary epigenetic clock in plants

Molecular clocks are the basis for dating the divergence between lineages over macro-evolutionary timescales (~10 5 -10 8 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes possess a clock-like behavior. This 'epimutation-clock' is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation-clocks recapitulate known topologies and branching times of intra-species phylogenetic trees in the selfing plant A. thaliana and the clonal seagrass Z. marina , which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.

A chromosome-scale genome sequence of sudangrass (Sorghum sudanense) highlights the genome evolution and regulation of dhurrin biosynthesis

Sudangrass is more similar to US commercial sorghums than to cultivated sorghums from Africa sequence-wise and contain significantly lower dhurrin than sorghums. CYP79A1 is linked to dhurrin content in sorghum. Sudangrass [Sorghum sudanense (Piper) Stapf] is a hybrid between grain sorghum and its wild relative S. bicolor ssp. verticilliflorum and is grown as a forage crop due to its high biomass production and low dhurrin content compared to sorghum. In this study, we sequenced the sudangrass genome and showed that the assembled genome was 715.95 Mb with 35,243 protein-coding genes. Phylogenetic analysis with whole genome proteomes demonstrated that the sudangrass genome was more similar to US commercial sorghums than to its wild relatives and cultivated sorghums from Africa. We confirmed that at seedling stage, sudangrass accessions contained significantly lower dhurrin as measured by hydrocyanic acid potential (HCN-p) than cultivated sorghum accessions. Genome-wide association study identified a QTL most tightly associated with HCN-p and the linked SNPs were located in the 3' UTR of Sobic.001G012300 which encodes CYP79A1, the enzyme that catalyzes the first step of dhurrin biosynthesis. As in other grasses such as maize and rice, we also found that copia/gypsy long terminal repeat (LTR) retrotransposons were more abundant in cultivated than in wild sorghums, implying that crop domestication in the grasses was accompanied by increased copia/gypsy LTR retrotransposon insertions in the genomes.

Evolution of woody plants to the land-sea interface - The atypical genomic features of mangroves with atypical phenotypic adaptation

How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt-secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species Lumnitzera littorea and Lumnitzera racemosa provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species Combretum micranthum. While most mangroves have small genomes, the genomes of both Lumnitzera species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, Lumnitzera species have not undergone post-gamma whole-genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, Lumnitzera genomes have reduced transposable elements by constraining the proliferation of new LTR-RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower colour differentiation between the Lumnitzera species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution.

Population genomics unravels the Holocene history of bread wheat and its relatives

Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.

Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.

Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton

Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LET_max of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were "hotspot" mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone

Understanding the phenotypic and genetic architecture of reproductive isolation is a long-standing goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine "top-down" and "bottom-up" approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of Mimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline-based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few "islands of speciation." Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.

High level of somatic mutations detected in a diploid banana wild relative Musa basjoo

Plants are thought to lack an early segregating germline and often retain both asexual and sexual reproduction, both of which may allow somatic mutations to enter the gametes or clonal progeny, and thereby impact plant evolution. It is yet unclear how often these somatic mutations occur during plant development and what proportion is transmitted to their sexual or cloned offspring. Asexual "seedless" propagation has contributed greatly to the breeding in many fruit crops, such as citrus, grapes and bananas. Whether plants in these lineages experience substantial somatic mutation accumulation is unknown. To estimate the somatic mutation accumulation and inheritance among a clonal population of plant, here we assess somatic mutation accumulation in Musa basjoo, a diploid banana wild relative, using 30 whole-genome resequenced samples collected from five structures, including leaves, sheaths, panicle, roots and underground rhizome connecting three clonal individuals. We observed 18.5 high proportion de novo somatic mutations on average between each two adjacent clonal suckers, equivalent to ~ 2.48 × 10^-8 per site per asexual generation, higher than the per site per sexual generation rates (< 1 × 10^-8) reported in Arabidopsis and peach. Interestingly, most of these inter-ramet somatic mutations were shared simultaneously in different tissues of the same individual with a high level of variant allele fractions, suggesting that these somatic mutations arise early in ramet development and that each individual may develop only from a few apical stem cells. These results thus suggest substantial mutation accumulation in a wild relative of banana. Our work reveals the significance of somatic mutation in Musa basjoo genetics variations and contribute to the trait improvement breeding of bananas and other asexual clonal crops.

Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis

The molecular nature of mutations induced by ionizing radiation and chemical mutagens in plants is becoming clearer owing to the availability of high-throughput DNA sequencing technology. However, few studies have compared the induced mutations between different radiation qualities and between different irradiated materials with the same analysis method. To compare mutation induction between dry-seeds and seedlings irradiated with carbon ions and gamma rays in Arabidopsis, in this study we detected the mutations induced by seedling irradiation with gamma rays and analyzed the data together with data previously obtained for the other irradiation treatments. Mutation frequency at the equivalent dose for survival reduction was higher with gamma rays than with carbon ions, and was higher with dry-seed irradiation than with seedling irradiation. Carbon ions induced a higher frequency of deletions (2-99 bp) than gamma rays in the case of dry-seed irradiation, but this difference was less evident in the case of seedling irradiation. This result supported the inference that dry-seed irradiation under a lower water content more clearly reflects the difference in radiation quality. However, the ratio of rearrangements (inversions, translocations, and deletions larger than 100 bp), which are considered to be derived from the rejoining of two distantly located DNA breaks, was significantly higher with carbon ions than gamma rays irrespective of the irradiated material. This finding suggested that high-linear energy transfer radiation induced closely located DNA damage, irrespective of the water content of the material, that could lead to the generation of rearrangements. Taken together, the results provide an overall picture of radiation-induced mutation in Arabidopsis and will be useful for selection of a suitable radiation treatment for mutagenesis.

Out of the Qinghai-Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)

Numerous high-elevation alpine plants of the Qinghai-Tibet Plateau (QTP) also have disjunct distribution in adjacent low-altitude mountains. The out-of-QTP versus into-the-QTP hypothesis of alpine plants provide strong evidence for the highly disputed assumption of the massive ice sheet developed in the central plateau during the Last Glacial Maximum (LGM). In this study, we sequenced the genomes of most known populations of Megadenia, a monospecific alpine genus of Brassicaceae distributed primarily in the QTP, though rarely found in adjacent low-elevation mountains of north China and Russia (NC-R). All sequenced samples clustered into four geographic genetic groups: one pair was in the QTP and another was in NC-R. The latter pair is nested within the former, and these findings support the out-of-QTP hypothesis. Dating the four genetic groups and niche distribution suggested that Megadenia migrated out of the QTP to adjacent regions during the LGM. The NC-R group showed a decrease in the effective population sizes. In addition, the genes with high genetic divergences in the QTP group were mainly involved in habitat adaptations during low-altitude colonization. These findings reject the hypothesis of development massive ice sheets, and support glacial survival of alpine plants within, as well as further migration out of, the QTP.

Japanese Regulatory Framework and Approach for Genome-edited Foods Based on Latest Scientific Findings

The food supply system is facing important challenges and its sustainability has to be considered. Genome-editing technology, which accelerates the development of new variety, could be used to achieve sustainable development goals, thereby protecting the environment and ensuring the stable production of food for an increasing global population. The most widely used genome-editing tool, CRISPR/Cas9, is easy to use, affordable, and versatile. Foods produced by genome-editing technologies have been developed worldwide to create novel traits. In the first half of the review, the latest scientific findings on genome-editing technologies are summarized, and the technical challenge in genome sequence analysis are clarified. CRISPR/Cas9 has versatile alternative techniques, such as base editor and prime editor. Genome sequencing technology has developed rapidly in recent years. However, it is still difficult to detect large deletions and structural variations. Long-read sequencing technology would solve this challenge. In the second part, regulatory framework and approach for genome-edited foods is introduced. The four government ministries, including the Ministry of Environment, the Ministry of Agriculture, Forestry and Fisheries, and the Ministry of Health, Labour and Welfare (MHLW), started to discuss how the regulation should be implemented in 2019. The SDN-1 technique is excluded from the current genetically modified organism (GMO) regulation. The Japanese regulatory framework includes pre-submission consultation and submission of notification form. In the last part of this review, transparency of regulatory framework and consumer confidence were described. Since maintaining consumer trust is vital, transparency of regulatory framework is a key to consumers. The information of notification process on approved genome-edited foods is made public immediately. This review will help regulators build regulatory frameworks, and lead to harmonization of the framework between the countries.

CRISPR/Cas9-Based Knock-Out of the PMR4 Gene Reduces Susceptibility to Late Blight in Two Tomato Cultivars

Phytophthora infestans, the causal agent of late blight (LB) in tomato (Solanum lycopersicum L.), is a devastating disease and a serious concern for plant productivity. The presence of susceptibility (S) genes in plants facilitates pathogen proliferation; thus, disabling these genes may help provide a broad-spectrum and durable type of tolerance/resistance. Previous studies on Arabidopsis and tomato have highlighted that knock-out mutants of the PMR4 susceptibility gene are tolerant to powdery mildew. Moreover, PMR4 knock-down in potato has been shown to confer tolerance to LB. To verify the same effect in tomato in the present study, a CRISPR-Cas9 vector containing four single guide RNAs (sgRNAs: sgRNA1, sgRNA6, sgRNA7, and sgRNA8), targeting as many SlPMR4 regions, was introduced via Agrobacterium-tumefaciens-mediated transformation into two widely grown Italian tomato cultivars: 'San Marzano' (SM) and 'Oxheart' (OX). Thirty-five plants (twenty-six SM and nine OX) were selected and screened to identify the CRISPR/Cas9-induced mutations. The different sgRNAs caused mutation frequencies ranging from 22.1 to 100% and alternatively precise insertions (sgRNA6) or deletions (sgRNA7, sgRNA1, and sgRNA8). Notably, sgRNA7 induced in seven SM genotypes a -7 bp deletion in the homozygous status, whereas sgRNA8 led to the production of fifteen SM genotypes with a biallelic mutation (-7 bp and -2 bp). Selected edited lines were inoculated with P. infestans, and four of them, fully knocked out at the PMR4 locus, showed reduced disease symptoms (reduction in susceptibility from 55 to 80%) compared to control plants. The four SM lines were sequenced using Illumina whole-genome sequencing for deeper characterization without exhibiting any evidence of mutations in the candidate off-target regions. Our results showed, for the first time, a reduced susceptibility to Phytophtora infestans in pmr4 tomato mutants confirming the role of KO PMR4 in providing broad-spectrum protection against pathogens.

Transposable elements maintain genome-wide heterozygosity in inbred populations

Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.

Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades

Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a Marasmius oreades fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.

Mutagenesis alters sperm swimming velocity in Astyanax cave fish

We investigated the hypothesis that intra ejaculate sperm competition screens against the transmission of deleterious alleles, including new mutants, from male parent to offspring. Recent investigations have established that sperm haploid genotypes can have major effects on sperm traits such as cellular robustness, longevity, and fertilization success. However, there is no evidence that new mutations can meaningfully affect sperm phenotypes. We tested this directly by comparing sperm from mutagenized and non-mutagenized control males in Astyanax fish. We used N-ethyl-N-nitrosourea (ENU) to induce single base substitutions in spermatogonial stem cells. We looked at swimming velocity, an important factor contributing to fertilization success, and flagellar length. Variability in swimming velocity was significantly higher in sperm from mutagenized males than in control sperm, reflecting their increased allelic diversity. In contrast, flagellar length, which is fixed during diploid stages of spermatogenesis, was unaffected by ENU treatment. We briefly discuss the implications of intra-ejaculate screening for maintenance of anisogamy and for outcomes of assisted reproductive technology.

Convergent evolution of AP2/ERF III and IX subfamilies through recurrent polyploidization and tandem duplication during eudicot adaptation to paleoenvironmental changes

Whole-genome duplication (WGD or polyploidization) has been suggested as a genetic contributor to angiosperm adaptation to environmental changes. However, many eudicot lineages did not undergo recent WGD (R-WGD) around and/or after the Cretaceous-Paleogene (K-Pg) boundary, times of severe environmental changes; how those plants survived has been largely ignored. Here, we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD: 12 R-WGD-containing plants (R-WGD-Y) and 10 R-WGD-lacking plants (R-WGD-N). Subsequently, we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation. The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF III and IX subfamilies through recurrent independent WGDs and tandem duplications (TDs) after the radiation of the plants. The expansions showed coincident enrichments in- times around and/or after the K-Pg boundary, when global cooling was a major environmental stressor. Consequently, convergent expansions and co-retentions of AP2/ERF III C-repeat binding factor (CBF) duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks. Moreover, promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code (G-box: CACGTG). We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF III and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes, and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.

Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme

Thyme has medicinal and aromatic value because of its potent antimicrobial and antioxidant properties. However, the absence of a fully sequenced thyme genome limits functional genomic studies of Chinese native thymes. Thymus quinquecostatus Čelak., which contains large amounts of bioactive monoterpenes such as thymol and carvacrol, is an important wild medicinal and aromatic plant in China. Monoterpenoids are abundant in glandular secretory trichomes. Here, high-fidelity and chromatin conformation capture technologies were used to assemble and annotate the T. quinquecostatus genome at the chromosome level. The 13 chromosomes of T. quinquecostatus had a total length of 528.66 Mb, a contig N50 of 8.06 Mb, and a BUSCO score of 97.34%. We found that T. quinquecostatus had experienced two whole-genome duplications, with the most recent event occurring ∼4.34 million years ago. Deep analyses of the genome, in conjunction with comparative genomic, phylogenetic, transcriptomic, and metabonomic studies, uncovered many regulatory factors and genes related to monoterpenoids and glandular secretory trichome development. Genes encoding terpene synthase (TPS), cytochrome P450 monooxygenases (CYPs), short-chain dehydrogenase/reductase (SDR), R2R3-MYB, and homeodomain-leucine zipper (HD-ZIP) IV were among those present in the T. quinquecostatus genome. Notably, Tq02G002290.1 (TqTPS1) was shown to encode the terpene synthase responsible for catalyzing production of the main monoterpene product γ-terpinene from geranyl diphosphate (GPP). Our study provides significant insight into the mechanisms of glandular secretory trichome formation and monoterpenoid biosynthesis in thyme. This work will facilitate the development of molecular breeding tools to enhance the production of bioactive secondary metabolites in Lamiaceae.

Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.

The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

BACKGROUND

The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome.

FINDINGS

We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28%, and transposable element sequences accounted for 43.98%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago.

CONCLUSIONS

This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.

Chromosome-scale genome assembly provides insights into the molecular mechanisms of tissue development of Populus wilsonii

Populus wilsonii is an important species of section Leucoides, and the natural populations mainly grow in southwest China. In this study, a single genotype of wild P. wilsonii was sequenced and assembled at genome size of 477.35 Mb in 19 chromosomes with contig N50 of 16.3 Mb. A total of 38,054 genes were annotated, and 49.95% of the genome was annotated as repetitive elements. Phylogenetic analysis identified that the divergence between P. wilsonii and the ancestor of P. deltoides and P. trichocarpa was 12 (3–23) Mya. 4DTv and Ks distributions supported the occurrence of the salicoid WGD event (~65 Mya). The highly conserved collinearity supports the close evolutionary relationship among these species. Some key enzyme-encoding gene families related to the biosynthesis of lignin and flavonoids were expanded and highly expressed in the stems or leaves, which probably resist the damage of the natural environment. In addition, some key gene families related to cellulose biosynthesis were highly expressed in stems, accounting for the high cellulose content of P. wilsonii variety. Our findings provided deep insights into the genetic evolution of P. wilsonii and will contribute to further biological research and breeding as well as for other poplars in Salicaceae.

A genome assembly for the Chinese poplar tree, Populus wilsonii, provides a unique resource to guide research into poplar development and breeding efforts.

The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice

The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.

Alteration of synonymous codon usage bias accompanies polyploidization in wheat

The diploidization of polyploid genomes is accompanied by genomic variation, including synonymous nucleotide substitutions that may lead to synonymous codon usage bias (SCUB). SCUB can mirror the evolutionary specialization of plants, but its effect on the formation of polyploidies is not well documented. We explored this issue here with hexaploid wheat and its progenitors. Synonymous codons (SCs) ending in either cytosine (NNC) or guanidine (NNG) were more frequent than those ending in either adenosine (NNA) or thymine (NNT), and the preference for NNC/G codons followed the increase in genome ploidy. The ratios between NNC/G and NNA/T codons gradually decreased in genes with more introns, and the difference in these ratios between wheat and its progenitors diminished with increasing ploidy. SCUB frequencies were heterogeneous among exons, and the bias preferred to NNA/T in more internal exons, especially for genes with more exons; while the preference did not appear to associate with ploidy. The SCUB alteration of the progenitors was different during the formation of hexaploid wheat, so that SCUB was the homogeneous among A, B and D subgenomes. DNA methylation-mediated conversion from cytosine to thymine weakened following the increase of genome ploidy, coinciding with the stronger bias for NNC/G SCs in the genome as a function of ploidy, suggesting that SCUB contribute to the epigenetic variation in hexaploid wheat. The patterns in SCUB mirrored the formation of hexaploid wheat, which provides new insight into genome shock-induced genetic variation during polyploidization. SCs representing non-neutral synonymous mutations can be used for genetic dissection and improvement of agricultural traits of wheat and other polyploidies.

Limited accumulation of high-frequency somatic mutations in a 1700-year-old Osmanthus fragrans tree

Lifespan varies greatly between and within species. Mutation accumulation is considered an important factor explaining this life-history trait. However, direct assessment of somatic mutations in long-lived species is still rare. In this study, we sequenced a 1700-year-old sweet olive tree and analysed the high-frequency somatic mutations accumulated in its six primary branches. We found the lowest per-year mutation accumulation rate in this oldest tree among those studied via the whole-genome sequencing approach. Investigation of mutation profiles suggests that this low rate of high-frequency mutation was unlikely to result from strong purifying selection. More intriguingly, on a per-branching scale, the high-frequency mutation accumulation rate was similar among the long-lived individuals such as oak, wild peach and sweet olive investigated here. We therefore suggest the possibility that the accumulation of high-frequency somatic mutations in very long-lived trees might have an upper boundary due to both the possible limited number of stem cell divisions and the early segregation of the stem cell lineage.

Postglacial range expansion of high-elevation plants is restricted by dispersal ability and habitat specialization

Aim

Species' ecological traits influence their spatial genetic patterns. Bedrock preference strongly shapes the phylogeography of alpine plants, but its interactions with other ecological traits have rarely been disentangled. Here, we explore whether dispersal ability and degree of habitat specialization account for divergent postglacial expansion patterns of high-elevation plants in spite of similar bedrock preference.

Location

The Pyrenees, southwestern Europe.

Taxon

Cirsium glabrum (Asteraceae), Salix pyrenaica (Salicaceae) and Silene borderei (Caryophyllaceae).

Methods

Phylogenetic, genetic structure and demographic modelling analyses based on restriction-site-associated DNA sequencing (RADseq) data from a range-wide populational sampling were conducted. Occurrence data and environmental variables were used to construct species distribution models, which were projected under current and Last Glacial Maximum conditions, and were combined with RADseq data to reconstruct the postglacial history of the study species. The degree of habitat specialization of each species was estimated based on the plant communities within which they occur, and their climatic niche breadth.

Results

Salix pyrenaica, which occupies a broad range of habitats, shows a high level of range filling, a blurred genetic structure and an admixture cline between the two main genetic groups, congruent with rapid postglacial expansion. The microsite specialists C. glabrum and S. borderei exhibit a strong genetic structure and low levels of range filling, indicative of slow postglacial expansion. The good disperser C. glabrum shows higher levels of admixture between genetic groups and weaker population differentiation than the poor disperser S. borderei.

Main Conclusions

Factors other than bedrock preference have a strong impact on the postglacial range dynamics of high-elevation species. Habitat specialization plays an important role, allowing species occupying a broad range of habitats to more rapidly expand their ranges after environmental change. The effect of dispersal ability is lower than expected for the study species.

Will epigenetics be a key player in crop breeding?

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.

Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations

Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. In this review, we aim to bring together natural animal population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. We first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. Second, we discuss DNA methylation dynamics which create observed epigenetic population structures by including basic population genetics processes. Then, we highlight the relevance of DNA methylation variation as an evolutionary mechanism in the extended evolutionary synthesis. Finally, we suggest new research directions by highlighting gaps in the knowledge of the population epigenetics field. As for our results, DNA methylation diversity was found to reveal parameters that can be used to characterize natural animal populations. Some concepts of population genetics dynamics can be applied to explain the observed epigenetic structure in natural animal populations. The set of recent advancements in ecological epigenetics, especially in transgenerational epigenetic inheritance in wild animal population, might reshape the way ecologists generate predictive models of the capacity of organisms to adapt to changing environments.

Selection in a growing colony biases results of mutation accumulation experiments

Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 108). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.

Mutational effects of chronic gamma radiation throughout the life cycle of Arabidopsis thaliana: Insight into radiosensitivity in the reproductive stage

Organisms living on Earth have always been exposed to natural sources of ionizing radiation, but following recent nuclear disasters, these background levels have often increased regionally due to the addition of man-made sources of radiation. To assess the mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life cycle of Arabidopsis thaliana grown under controlled conditions. We obtained resequencing data from 36 second generation post-mutagenesis (M₂) progeny derived from 12 first generation (M₁) lines grown under gamma-irradiation conditions, ranging from 0.0 to 2.0 Gray per day (Gy/day), to identify de novo mutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship between de novo mutation frequency and radiation dose rate from 0.0 to 2.0 Gy/day was assessed by statistical modeling. The increase in de novo mutations in response to irradiation dose fit the negative binomial model, which accounted for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, and deletions were more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation were greater during the reproductive stage. These results will provide valuable insights into practical strategies for analyzing mutational effects in wild plants growing in environments with various mutagens.

Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing

Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of "foreign" recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.

Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects

Foxtail millet (Setaria italica), which was domesticated from the wild species green foxtail (Setaria viridis), is a rich source of phytonutrients for humans. To evaluate how breeding changed the metabolome of foxtail millet grains, we generated and analyzed the datasets encompassing the genomes, transcriptomes, metabolomes, and anti-inflammatory indices from 398 foxtail millet accessions. We identified hundreds of common variants that influence numerous secondary metabolites. We observed tremendous differences in natural variations of the metabolites and their underlying genetic architectures between distinct sub-groups of foxtail millet. Furthermore, we found that the selection of the gene alleles associated with yellow grains led to altered profiles of metabolites such as carotenoids and endogenous phytohormones. Using CRISPR-mediated genome editing we validated the function of PHYTOENE SYNTHASE 1 (PSY1) gene in affecting millet grain color and quality. Interestingly, our in vitro cell inflammation assays showed that 83 metabolites in millet grains have anti-inflammatory effects. Taken together, our multi-omics study illustrates how the breeding history of foxtail millet has shaped its metabolite profile. The datasets we generated in this study also provide important resources for further understanding how millet grain quality is affected by different metabolites, laying the foundations for future millet genetic research and metabolome-assisted improvement.

Is the mutation rate lower in genomic regions of stronger selective constraints?

A study of the plant Arabidopsis thaliana detected lower mutation rates in genomic regions where mutations are more likely to be deleterious, challenging the principle that mutagenesis is blind to its consequence. To examine the generality of this finding, we analyze large mutational data from baker's yeast and humans. The yeast data do not exhibit this trend, whereas the human data show an opposite trend that disappears upon the control of potential confounders. We find that the Arabidopsis study identified substantially more mutations than reported in the original data-generating studies and expected from Arabidopsis' mutation rate. These extra mutations are enriched in polynucleotide tracts and have relatively low sequencing qualities so are likely sequencing errors. Furthermore, the polynucleotide “mutations” can produce the purported mutational trend in Arabidopsis. Together, our results do not support lower mutagenesis of genomic regions of stronger selective constraints in the plant, fungal, and animal models examined.

Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA

Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the 3 bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, among the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions: transversion bias. The data are consistent with a CpG effect, and it is shown that both the A + T content and the arrangement of purines/pyrimidines along the same DNA strand are correlated with rate variation. Expected equilibrium A + T content ranges from 36.4% to 82.8% across contexts, while G–C skew ranges from −77.4 to 72.2 and A–T skew ranges from −63.9 to 68.2. The predicted equilibria are associated with specific features of the content of the hexanucleotide context, and also show close agreement with the observed context-dependent compositions. Finally, by controlling for the content of nucleotides closer to the substitution site, it is shown that both the third and fourth nucleotide removed on each side of the substitution directly influence substitution dynamics at that site. Overall, the results demonstrate that noncoding sites in different contexts are evolving along very different evolutionary trajectories and that substitution dynamics are far more complex than typically assumed. This has important implications for a number of types of sequence analysis, particularly analyses of natural selection, and the context-dependent substitution matrices developed here can be applied in future analyses.

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L

WD40 proteins serve as crucial regulators in a broad spectrum of plant developmental and physiological processes, including anthocyanin biosynthesis. However, in fig (Ficus carica L.), neither the WD40 family nor any member involved in anthocyanin biosynthesis has been elucidated. In the present study, 204 WD40 genes were identified from the fig genome and phylogenetically classified into 5 clusters and 12 subfamilies. Bioinformatics analysis prediction localized 109, 69, and 26 FcWD40 proteins to the cytoplasm, nucleus and other cellular compartments, respectively. RNA-seq data mining revealed 127 FcWD40s expressed at FPKM > 10 in fig fruit. Most of these genes demonstrated higher expression in the early stages of fruit development. FcWD40-97 was recruited according to three criteria: high expression in fig fruit, predicted nuclear localization, and closest clustering with TTG1s identified in other plants. FcWD40-97, encoding 339 amino acids including 5 WD-repeat motifs, showed 88.01 and 87.94% amino acid sequence similarity to apple and peach TTG1, respectively. The gene is located on fig chromosome 4, and is composed of 1 intron and 2 exons. Promoter analysis revealed multiple light-responsive elements, one salicylic acid-responsive element, three methyl jasmonate-responsive elements, and one MYB-binding site involved in flavonoid biosynthesis gene regulation. FcWD40-97 was in the FPKM > 100 expression level group in fig fruit, and higher expression was consistently found in the peel compared to the flesh at the same development stages. Expression level did not change significantly under light deprivation, whereas in leaves and roots, its expression was relatively low. Transient expression verified FcWD40-97's localization to the nucleus. Yeast two-hybrid (Y2H) and biomolecular fluorescence complementation (BiFC) assays revealed that FcWD40-97 interacts with FcMYB114, FcMYB123, and FcbHLH42 proteins in vitro and in vivo, showing that FcWD40-97 functions as a member of the MYB-bHLH-WD40 (MBW) complex in anthocyanin-biosynthesis regulation in fig. We therefore renamed FcWD40-97 as FcTTG1. Our results provide the first systematic analysis of the FcWD40 family and identification of FcTTG1 in fig pigmentation.

Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness

Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of ∼ 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant-pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat gene family, which may be linked to the defence response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.

Hard versus soft selective sweeps during domestication and improvement in soybean

Genome scans for selection can provide an efficient way to dissect the genetic basis of domestication traits and understand mechanisms of adaptation during crop evolution. Selection involving soft sweeps (simultaneous selection for multiple alleles) is probably common in plant genomes but is under-studied, and few if any studies have systematically scanned for soft sweeps in the context of crop domestication. Using genome resequencing data from 302 wild and domesticated soybean accessions, we conducted selection scans using five widely employed statistics to identify selection candidates under classical (hard) and soft sweeps. Across the genome, inferred hard sweeps are predominant in domesticated soybean landraces and improved varieties, whereas soft sweeps are more prevalent in a representative subpopulation of the wild ancestor. Six domestication-related genes, representing both hard and soft sweeps and different stages of domestication, were used as positive controls to assess the detectability of domestication-associated sweeps. Performance of various test statistics suggests that differentiation-based (FST ) methods are robust for detecting complete hard sweeps, and that LD-based strategies perform well for identifying recent/ongoing sweeps; however, none of the test statistics detected a known soft sweep we previously documented at the domestication gene Dt1. Genome scans yielded a set of 66 candidate loci that were identified by both differentiation-based and LD-based (iHH) methods; notably, this shared set overlaps with many previously identified QTLs for soybean domestication/improvement traits. Collectively, our results will help to advance genetic characterizations of soybean domestication traits and shed light on selection modes involved in adaptation in domesticated plant species.

A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment

Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.

Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations.

Globally Relaxed Selection and Local Adaptation in Boechera stricta

The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.

Congruent evolutionary responses of European steppe biota to late Quaternary climate change

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level.

Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines

Rice (Oryza sativa) production is seriously affected by the root-knot nematode Meloidogyne graminicola, which has emerged as a menace in upland and irrigated rice cultivation systems. Previously, activation tagging in rice was utilized to identify candidate gene(s) conferring resistance against M. graminicola. T-DNA insertional mutants were developed in a rice landrace (acc. JBT 36/14), and four mutant lines showed nematode resistance. Whole-genome sequencing of JBT 36/14 was done along with the four nematode resistance mutant lines to identify the structural genetic variations that might be contributing to M. graminicola resistance. Sequencing on Illumina NovaSeq 6000 platform identified 482,234 genetic variations in JBT 36/14 including 448,989 SNPs and 33,245 InDels compared to reference indica genome. In addition, 293,238-553,648 unique SNPs and 32,395-65,572 unique InDels were found in the four mutant lines compared to their JBT 36/14 background, of which 93,224 SNPs and 8,170 InDels were common between all the mutant lines. Functional annotation of genes containing these structural variations showed that the majority of them were involved in metabolism and growth. Trait analysis revealed that most of these genes were involved in morphological traits, physiological traits and stress resistance. Additionally, several families of transcription factors, such as FAR1, bHLH, and NAC, and putative susceptibility (S) genes, showed the presence of SNPs and InDels. Our results indicate that subject to further genetic validations, these structural genetic variations may be involved in conferring nematode resistance to the rice mutant lines.

Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change is mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue.

Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.

Gene-body methylation in plants: mechanisms, functions and important implications for understanding evolutionary processes

Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). CG methylation is transmitted transgenerationally in plants, opening the possibility that gbM may be shaped by adaptation. This presupposes, however, that gbM has a function that affects phenotype, which has been a topic of debate in the literature. Here, we review our current knowledge of gbM in plants. We start by presenting the well-elucidated mechanisms of plant gbM establishment and maintenance. We then review more controversial topics: the evolution of gbM and the potential selective pressures that act on it. Finally, we discuss the potential functions of gbM that may affect organismal phenotypes: gene expression stabilization and upregulation, inhibition of aberrant transcription (reverse and internal), prevention of aberrant intron retention, and protection against TE insertions. To bolster the review of these topics, we include novel analyses to assess the effect of gbM on transcripts. Overall, a growing body of literature finds that gbM correlates with levels and patterns of gene expression. It is not clear, however, if this is a causal relationship. Altogether, functional work suggests that the effects of gbM, if any, must be relatively small, but there is nonetheless evidence that it is shaped by natural selection. We conclude by discussing the potential adaptive character of gbM and its implications for an updated view of the mechanisms of adaptation in plants.

Single-nucleotide mosaicism in citrus: Estimations of somatic mutation rates and total number of variants

Most of the hundreds of citrus varieties are derived from spontaneous mutations. We characterized the dynamics of single-nucleotide mosaicism in a 36-yr-old clementine (Citrus ×clementina hort. ex Tanaka) tree, a commercial citrus whose vegetative behavior is known in detail. Whole-genome sequencing identified 73 reliable somatic mutations, 48% of which were transitions from G/C to A/T, suggesting ultraviolet (UV) exposure as mutagen. The mutations accumulated in sectorized areas of the tree in a nested hierarchy determined by the branching pattern, although some variants detected in the basal parts were also found in the new growth and were fixed in some branches and leaves of much younger age. The estimate of mutation rates in our tree was 4.4 × 10^-10 bp^-1 yr^-1 , a rate in the range reported in other perennials. Assuming a perfect configuration and taking advantage of previous counts on the number of total leaves of typical clementine trees, these mutation determinations allowed to estimate for the first time the total number of variants present in a standard adult tree (1,500-5,000) and the somatic mutations generated in a typical leaf flush (0.92-1.19). From an evolutionary standpoint, the sectoral distribution of somatic mutations and the habit of periodic foliar renewal of long-lived plants appear to increase genetic heterogeneity and, therefore, the adaptive role of somatic mutations reducing the mutational load and providing fitness benefits.