BRAD V3.0: an upgraded Brassicaceae database.

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation.

Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.

Origin and Evolution of Diploid and Allopolyploid Camelina Genomes Were Accompanied by Chromosome Shattering.

Complexes of diploid and polyploid species have formed frequently during the evolution of land plants. In false flax (Camelina sativa), an important hexaploid oilseed crop closely related to Arabidopsis (Arabidopsis thaliana), the putative parental species as well as the origin of other Camelina species remained unknown. By using bacterial artificial chromosome-based chromosome painting, genomic in situ hybridization, and multi-gene phylogenetics, we aimed to elucidate the origin and evolution of the polyploid complex. Genomes of diploid camelinas (Camelina hispida, n = 7; Camelina laxa, n = 6; and Camelina neglecta, n = 6) originated from an ancestral n = 7 genome. The allotetraploid genome of Camelina rumelica (n = 13, N6H) arose from hybridization between diploids related to C. neglecta (n = 6, N6) and C. hispida (n = 7, H), and the N subgenome has undergone a substantial post-polyploid fractionation. The allohexaploid genomes of C. sativa and Camelina microcarpa (n = 20, N6N7H) originated through hybridization between an auto-allotetraploid C. neglecta-like genome (n = 13, N6N7) and C. hispida (n = 7, H), and the three subgenomes have remained stable overall since the genome merger. Remarkably, the ancestral and diploid Camelina genomes were shaped by complex chromosomal rearrangements, resembling those associated with human disorders and resulting in the origin of genome-specific shattered chromosomes.plantcell;31/11/2596/FX1F1fx1.

Successive duplication-divergence mechanisms at the RCO locus contributed to leaf shape diversity in the Brassicaceae.

Gene duplication is a major driver for the increase of biological complexity. The divergence of newly duplicated paralogs may allow novel functions to evolve, while maintaining the ancestral one. Alternatively, partitioning the ancestral function among paralogs may allow parts of that role to follow independent evolutionary trajectories. We studied the REDUCED COMPLEXITY (RCO) locus, which contains three paralogs that have evolved through two independent events of gene duplication, and which underlies repeated events of leaf shape evolution within the Brassicaceae. In particular, we took advantage of the presence of three potentially functional paralogs in Capsella to investigate the extent of functional divergence among them. We demonstrate that the RCO copies control growth in different areas of the leaf. Consequently, the copies that are retained active in the different Brassicaceae lineages contribute to define the leaf dissection pattern. Our results further illustrate how successive gene duplication events and subsequent functional divergence can increase trait evolvability by providing independent evolutionary trajectories to specialized functions that have an additive effect on a given trait.

Beyond the thale: comparative genomics and genetics of Arabidopsis relatives.

For decades a small number of model species have rightly occupied a privileged position in laboratory experiments, but it is becoming increasingly clear that our knowledge of biology is greatly improved when informed by a broader diversity of species and evolutionary context. Arabidopsis thaliana has been the primary model organism for plants, benefiting from a high-quality reference genome sequence and resources for reverse genetics. However, recent studies have made a group of species also in the Brassicaceae family and closely related to A. thaliana a focal point for comparative molecular, genomic, phenotypic and evolutionary studies. In this Review, we emphasize how such studies complement continued study of the model plant itself, provide an evolutionary perspective and summarize our current understanding of genetic and phenotypic diversity in plants.

Accumulation of potentially toxic elements by plants of North Caucasian Alyssum species and their molecular phylogenetic analysis.

Accumulations of potentially toxic metals were investigated in soils and five North Caucasian Alyssum species from metalliferous areas and non-metalliferous areas in Karachay-Cherkessia, Kabardino-Balkaria, Dagestan and the Krasnodar region. Analyses of field samples showed that chemical features of the soils significantly affected the concentrations of Ni, Co, Zn, but had less effect on Cu and Pb concentrations in the shoots of Alyssum. Variations in the degree of accumulating ability were found in the studied species, including hyperaccumulation of Ni in Alyssum murale (up to 12,100 mg kg-1), and significant accumulation of Zn in A. gehamense (up to 1700 mg kg-1). A comparative molecular genetic analysis of two A. murale populations, both Ni-hyperaccumulating population from Karachay-Cherkessia and non-hyperaccumulating population from Dagestan, indicated considerable genetic difference between them. This result supports the hypothesis that the selection of metal hyperaccumulator species with enhanced phytoremediation efficiency should be considered at the population level.

An updated explanation of ancestral karyotype changes and reconstruction of evolutionary trajectories to form Camelina sativa chromosomes.

BACKGROUND: Belonging to lineage I of Brassicaceae, Camelina sativa is formed by two hybridizations of three species (three sub-genomes). The three sub-genomes were diverged from a common ancestor, likely derived from lineage I (Ancestral Crucifer karyotype, ACK). The karyotype evolutionary trajectories of the C. sativa chromosomes are currently unknown. Here, we managed to adopt a telomere-centric theory proposed previously to explain the karyotype evolution in C. sativa. RESULTS: By characterizing the homology between A. lyrata and C. sativa chromosomes, we inferred ancestral diploid karyotype of C. sativa (ADK), including 7 ancestral chromosomes, and reconstructed the evolutionary trajectories leading to the formation of extant C. sativa genome. The process involved 2 chromosome fusions. We found that sub-genomes Cs-G1 and Cs-G2 may share a closer common ancestor than Cs-G3. Together with other lines of evidence from Arabidopsis, we propose that the Brassicaceae plants, even the eudicots, follow a chromosome fusion mechanism favoring end-end joining of different chromosomes, rather than a mechanism favoring the formation circular chromosomes and nested chromosome fusion preferred by the monocots. CONCLUSIONS: The present work will contribute to understanding the formation of C. sativa chromosomes, providing insight into Brassicaceae karyotype evolution.

Life-History Plasticity and Water-Use Trade-Offs Associated with Drought Resistance in a Clade of California Jewelflowers.

Water limitation is a primary driver of plant geographic distributions and individual plant fitness. Drought resistance is the ability to survive and reproduce despite limited water, and numerous studies have explored its physiological basis in plants. However, it is unclear how drought resistance and trade-offs associated with drought resistance evolve within plant clades. We quantified the relationship between water availability and fitness for 13 short-lived plant taxa in the Streptanthus clade that vary in their phenology and the availability of water in the environments where they occur. We derived two parameters from these relationships: plant fitness when water is not limiting and the water inflection point (WIF), the watering level at which additional water is most efficiently turned into fitness. We used phylogenetic comparative methods to explore trade-offs related to drought resistance and trait plasticity and the degree to which water relationship parameters are conserved. Taxa from drier climates produced fruits at the lowest water levels, had a lower WIF, flowered earlier, had shorter life spans, had greater plastic water-use efficiency (WUE), and had lower fitness at nonlimiting water. In contrast, later-flowering Streptanthus taxa from less xeric climates experienced high fitness at nonlimiting water but had no fitness at the lowest water levels. Across the clade, we found a trade-off between drought resistance and fitness at high water, though a single ruderal species was an outlier in this relationship. Our results suggest that drought escape trades off with maximal fitness under nonlimiting water, and both are tied to phenology. We also found that variation in trait plasticity determines how different plant species produce fitness over a water gradient.

Phylogeny of Euclidieae (Brassicaceae) based on plastome and nuclear ribosomal DNA data.

Euclidieae, a morphologically diverse tribe in the family Brassicaceae (Cruciferae), consists of 29 genera and more than 150 species distributed mainly in Asia. Prior phylogenetic analyses on Euclidieae are inadequate. In this study, sequence data from the plastid genome and nuclear ribosomal DNA of 72 species in 27 genera of Euclidieae were used to infer the inter- and intra-generic relationships within. The well-resolved and strongly supported plastome phylogenies revealed that Euclidieae could be divided into five clades. Both Cymatocarpus and Neotorularia are polyphyletic in nuclear and plastome phylogenies. Besides, the conflicts of systematic positions of three species of Braya and two species of Solms-laubachia s.l. indicated that hybridization and or introgression might have happened during the evolutionary history of the tribe. Results from divergence-time analyses suggested an early Miocene origin of Euclidieae, and it probably originated from the Central Asia, Pamir Plateau and West Himalaya. In addition, multiple ndh genes loss and pseudogenization were detected in eight species based on comparative genomic study.

Diversification of Biscutella ser. Biscutella (Brassicaceae) followed post-Miocene geologic and climatic changes in the Mediterranean basin.

Biscutella ser. Biscutella (= ser. Lyratae Malin.) is a group of mostly annual or short-lived perennial plants, with petals gradually tapering at the base and lateral intrastaminal nectaries, endemic to the Mediterranean basin and the Middle East. Recent taxonomic work has revealed that a relative morphological homogeneity occurs in Europe and Asia, but a high plasticity is found in N Africa for most of the characters traditionally used for taxonomic arrangements. This fact had generally led to overestimation of the number of taxa, which currently is reduced to ten (namely 7 species and 3 additional varieties), some of them being narrow endemics. In the present contribution, on the basis of a previous detailed morphological study carried out by the authors, the first comprehensive phylogeny based on 47 DNA sequence data including concatenation of two plastid (rpl32-trnL and trnV) and one nuclear (ITS) regions, together with the first time-calibrated phylogenetic tree, allows reappraisal of evolutionary and biogeographic relationships among the accepted taxa in the series. According to all evidence gathered in the present study, the current distribution of B. ser. Biscutella, mostly centred in the southern parts of the Mediterranean basin and the Middle East, suggests that it evolved in relation with the major geological and climatic events occurred in the Mediterranean basin and Eurasia within the last 20 million years. The origin of Biscutella is dated ca 18.75 Mya, and the radiation of the series triggered ca 5.87 Mya with the Messinian Salinity Crisis. Rapid diversification occurred coetaneously to the Intensification of Northern Hemisphere Glaciation (ca 2.86 Mya) onwards, with parallel large-amplitude aridity cycles in Africa and southwestern Asia. In recent times, the divergence of lineages became faster in the W Mediterranean (ca 1.54 to 0.43 Mya), mostly related to geographical and ecological patterns of specialisation. In many cases, the distribution of the current species is apparently linked to ancient glacial refuges in S Mediterranean basin.

Mutation Accumulation in an Asexual Relative of Arabidopsis.

Asexual populations experience weaker responses to natural selection, which causes deleterious mutations to accumulate over time. Additionally, stochastic loss of individuals free of deleterious mutations can lead to an irreversible increase in mutational load in asexuals (the "click" in Muller's Ratchet). Here we report on the genomic divergence and distribution of mutations across eight sympatric pairs of sexual and apomictic (asexual) Boechera (Brassicaceae) genotypes. We show that apomicts harbor a greater number of derived mutations than sympatric sexual genotypes. Furthermore, in phylogenetically constrained sites that are subject to contemporary purifying selection, the ancestral, conserved allele is more likely to be retained in sexuals than apomicts. These results indicate that apomictic lineages accumulate mutations at otherwise conserved sites more often than sexuals, and support the conclusion that deleterious mutation accumulation can be a powerful force in the evolution of asexual higher plants.

Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species.

BACKGROUND: Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated. RESULTS: We developed the software easy-to-annotate Helitron (EAHelitron), a Unix-like command line, and used it to identify Helitrons in a wide range of 53 plant genomes (including 13 Brassicaceae species). We determined Helitron density (abundance/Mb) and visualized and examined Helitron distribution patterns. We identified more than 104,653 Helitrons, including many new Helitrons not predicted by other software. Whole genome Helitron density is independent from genome size and shows stability at the species level. Using linear discriminant analysis, de novo genomes (next-generation sequencing) were successfully classified into Arabidopsis thaliana groups. For most Brassicaceae species, Helitron density negatively correlated with gene density, and Helitron distribution patterns were similar to those of A. thaliana. They preferentially inserted into sequence around the centromere and intergenic region. We also associated 13 Helitron polymorphism loci with flowering-time phenotypes in 18 A. thaliana ecotypes. CONCLUSION: EAHelitron is a fast and efficient tool to identify new Helitrons. Whole genome Helitron density can be an informative character for plant classification. Helitron insertion polymorphism could be used in association analysis.

Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years.

The small genus Ricotia (nine species, Brassicaceae) is confined to the eastern Mediterranean. By comparative chromosome painting and a dated multi-gene chloroplast phylogeny, we reconstructed the origin and subsequent evolution of Ricotia. The ancestral Ricotia genome originated through hybridization between two older genomes with n = 7 and n = 8 chromosomes, respectively, on the Turkish mainland during the Early Miocene (c. 17.8 million years ago, Ma). Since then, the allotetraploid (n = 15) genome has been altered by two independent descending dysploidies (DD) to n = 14 in Ricotia aucheri and the Tenuifolia clade (2 spp.). By the Late Miocene (c. 10 Ma), the latter clade started to evolve in the most diverse Ricotia core clade (6 spp.), the process preceded by a DD event to n = 13. It is noteworthy that this dysploidy was mediated by a unique chromosomal rearrangement, merging together the same two chromosomes as were merged during the origin of a fusion chromosome within the paternal n = 7 genome c. 20 Ma. This shows that within a time period of c. 8 Myr genome evolution can repeat itself and that structurally very similar chromosomes may originate repeatedly from the same ancestral chromosomes by different pathways (end-to-end translocation versus nested chromosome insertion).

Comparative genomics reveals origin of MIR159A-MIR159B paralogy, and complexities of PTGS interaction between miR159 and target GA-MYBs in Brassicaceae.

Whole-genome and segmental duplications coupled with sequence and functional diversification are responsible for gene family expansion, and morphological and adaptive diversity. Although broad contours of such processes are understood, detailed investigations on regulatory elements, such as miRNA-transcription factor modules, especially in non-model crop plants with complex genomes, are few. The present study was performed to understand evolutionary history of MIR159 family, and changes in the miRNA-binding site (MBS) of the targets MYB33, MYB65, and MYB101 that may affect post-transcriptional gene silencing. We established orthology and paralogy between members of MIR159 family by reconstructing the phylogeny based on 240 precursor sequences sampled across green plants. An unambiguous paralogous relationship between MIR159A and MIR159B was observed only in Brassicaceae which prompted us to analyze the origin of this paralogy. Comparative micro-synteny of ca. 100 kb genomic segments surrounding MIR159A, MIR159B, and MIR159C loci across 15 genomes of Brassicaceae revealed segmental duplication that occurred in the common ancestor of Brassicaceae to be responsible for origin of MIR159A-MIR159B paralogy; extensive gene loss and rearrangements were also encountered. The impact of polyploidy was revealed when the three sub-genomes-least fractionated (LF), moderately fractionated (MF1), and most fractionated (MF2) sub-genomes of Brassica and Camelina sativa-were analyzed. Extensive gene loss was observed among sub-genomes of Brassica, whereas those in Camelina were largely conserved. Analysis of the target MYBs revealed the complete loss of MYB33 homologs in a Brassica lineage-specific manner. Our findings suggest that mature miR159a/b /c are capable of targeting MYB65 across Brassicaceae, MYB33 in all species except Brassica, and MYB101 only in Arabidopsis thaliana. Comparative analysis of the mature miRNA sequence and the miRNA-binding site (MBS) in MYB33, MYB65, and MYB101 showed the complexity of regulatory network that is dependent on strict sequence complementarity potentially leading to regulatory diversity.

Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity.

The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome-wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher-level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.

A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq.

Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.

Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower).

Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.

Viruses infecting cool season crops in the northern Turkey.

Virus diseases of cool season vegetable crops (mainly cabbage, white and red head cabbage, broccoli, kale, radish, rocket salad, garden cress, and turnip) were surveyed in Bafra Plain, Turkey during winter 2017, and 2018. Leaf samples were collected from different species of the Brassicaceae family showing mosaic, mottling, necrotic spots, malformation, and chlorosis symptoms. These samples were tested for the presence of Cauliflower mosaic virus (CaMV), Cucumber mosaic virus (CMV), Beet western yellows virus (BWYV), Radish mosaic virus (RaMV), Turnip mosaic virus (TuMV), Turnip yellow mosaic virus (TYMV), and Turnip yellows virus (TuYV) by biological and serological methods. A total of 455 samples were collected from cole crop fields and tested for the seven viruses by double-antibody sandwich ELISA using specific polyclonal antibodies. According to the results, out of these, 7 % of the samples were infected by at least one of these viruses. TuMV was the most prevalent virus detected in cole crops. TuMV, CaMV, and CMV were detected in 3 %, 2 %, and 2 % of infected samples, respectively, and the infection rate of these three viruses changed significantly among Brassica species.

Phylogenetics of Camelina Crantz. (Brassicaceae) and insights on the origin of gold-of-pleasure (Camelina sativa).

Camelina sativa (false flax or gold-of-pleasure) is an Old World oilseed crop that fell out of use in the mid 20th Century but has recently gained renewed interest as a biofuel source. The crop is hexaploid, and its relationship to its diploid and polyploid congeners has remained unresolved. Using 54 accessions representing five species sampled across Camelina's center of diversity in Turkey and the Caucasus, we performed phylogenetic and genetic diversity analyses using RADseq genotyping and ITS sequencing. Flow cytometry was performed to assess relationships between genome size and phylogenetic groupings. Accessions fell into distinct, highly-supported clades that accord with named species, indicating that morphological characters can reliably distinguish members of the genus. A phylogenetically distinct lineage from Turkey may represent a currently unrecognized diploid species. In most analyses, C. sativa accessions nest within those of C. microcarpa, suggesting that the crop is descended from this wild hexaploid species. This inference is further supported by their similar genome size, and by lower genetic diversity in C. sativa, which is consistent with a domestication bottleneck. These analyses provide the first definitive phylogeny of C. sativa and its wild relatives, and they point to C. microcarpa as the crop's wild ancestor.

Natural Variation in Freezing Tolerance and Cold Acclimation Response in Arabidopsis thaliana and Related Species.

During low-temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. The molecular mechanisms involved in cold acclimation have been mostly investigated in Arabidopsis thaliana. In addition, other Brassicaceae species related to A. thaliana have been employed in recent years to study plant stress responses on a phylogenetically broader basis and in some cases with extremophile species with a much higher stress tolerance. In this paper, we briefly summarize cold acclimation responses in A. thaliana and current knowledge about cold acclimation in A. thaliana relatives with special emphasis on Eutrema salsugineum and two closely related Thellungiella species. We then present a transcriptomic and metabolomic analysis of cold acclimation in five A. thaliana and two E. salsugineum accessions that differ widely in their freezing tolerance. Differences in the cold responses of the two species are discussed.