Brassicaceae phylogeny and trichome evolution

Brassicaceae flowers: diversity amid uniformity

The mustard family Brassicaceae, which includes the model plant Arabidopsis thaliana, exhibits morphological stasis and significant uniformity of floral plan. Nonetheless, there is untapped diversity in almost every aspect of floral morphology in the family that lends itself to comparative study, including organ number, shape, form, and color. Studies on the genetic basis of morphological diversity, enabled by extensive genetic tools and genomic resources and the close phylogenetic distance among mustards, have revealed a mosaic of conservation and divergence in numerous floral traits. Here I review the morphological diversity of the flowers of Brassicaceae and discuss studies addressing the underlying genetic and developmental mechanisms shaping floral diversity. To put flowers in the context of the floral display, I describe diversity in inflorescence morphology and the variation that exists in the structures preceding the floral organs. Reconstructing the floral morphospace in Brassicaceae coupled with next-generation sequencing data and unbiased approaches to interrogate gene function in species throughout the mustard phylogeny offers promising ways to understand how developmental mechanisms originate and diversify.

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.

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica's adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.

Taxonomy through the lens of neutral helium microscopy

The field of taxonomy is critically important for the identification, conservation, and ecology of biological species. Modern taxonomists increasingly need to employ advanced imaging techniques to classify organisms according to their observed morphological features. Moreover, the generation of three-dimensional datasets is of growing interest; moving beyond qualitative analysis to true quantitative classification. Unfortunately, biological samples are highly vulnerable to degradation under the energetic probes often used to generate these datasets. Neutral atom beam microscopes avoid such damage due to the gentle nature of their low energy probe, but to date have not been capable of producing three-dimensional data. Here we demonstrate a means to recover the height information for samples imaged in the scanning helium microscope (SHeM) via the process of stereophotogrammetry. The extended capabilities, namely sparse three-dimensional reconstructions of features, were showcased via taxonomic studies of both flora (Arabidopsis thaliana) and fauna (Heterodontus portusjacksoni). In concert with the delicate nature of neutral helium atom beam microscopy, the stereophotogrammetry technique provides the means to derive comprehensive taxonomical data without the risk of sample degradation due to the imaging process.

Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species

BACKGROUND

Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Our goals were: (1) produce a robust, time-dependent evolutionary framework for Plukenetia using BEAST; (2) reconstruct its biogeographical history with ancestral range estimation in BIOGEOBEARS; (3) define seed size categories; (4) identify patterns of seed size evolution using ancestral state estimation; and (5) conduct regression analyses with putative drivers of seed size using the threshold model.

RESULTS

Plukenetia was resolved into two major groups, which we refer to as the pinnately- and palmately-veined clades. Our analyses suggest Plukenetia originated in the Amazon or Atlantic Forest of Brazil during the Oligocene (28.7 Mya) and migrated/dispersed between those regions and Central America/Mexico throughout the Miocene. Trans-oceanic dispersals explain the pantropical distribution of Plukenetia, including from the Amazon to Africa in the Early Miocene (17.4 Mya), followed by Africa to Madagascar and Africa to Southeast Asia in the Late Miocene (9.4 Mya) and Pliocene (4.5 Mya), respectively. We infer a single origin of large seeds in the ancestor of Plukenetia. Seed size fits a Brownian motion model of trait evolution and is moderately to strongly associated with plant size, fruit type/dispersal syndrome, and seedling ecology. Biome shifts were not drivers of seed size, although there was a weak association with a transition to fire prone semi-arid savannas.

CONCLUSIONS

The major relationships among the species of Plukenetia are now well-resolved. Our biogeographical analyses support growing evidence that many pantropical distributions developed by periodic trans-oceanic dispersals throughout the Miocene and Pliocene. Selection on a combination of traits contributed to seed size variation, while movement between forest edge/light gap and canopy niches likely contributed to the seed size extremes in Plukenetia.

Plant evolution in alkaline magnesium-rich soils: A phylogenetic study of the Mediterranean genus Hormathophylla (Cruciferae: Alysseae) based on nuclear and plastid sequences

Habitats with alkaline edaphic substrates are often associated with plant speciation and diversification. The tribe Alysseae, in the family Brassicaceae, epitomizes this evolutionary trend. In this lineage, some genera, like Hormathophylla, can serve as a good case for testing the evolutionary framework. This genus is centered in the western Mediterranean. It grows on different substrates, but mostly on alkaline soils. It has been suggested that diversification in many lineages of the tribe Alysseae and in the genus Hormathophylla is linked to a tolerance for high levels of Mg+2 in xeric environments. In this study, we investigated the controversial phylogenetic placement of Hormathophylla in the tribe, the generic limits and the evolutionary relationships between the species using ribosomal and plastid DNA sequences. We also examined the putative association between the evolution of different ploidy levels, trichome morphology and the type of substrates. Our analyses demonstrated the monophyly of the genus Hormathophylla including all previously described species. Nuclear sequences revealed two lineages that differ in basic chromosome numbers (x = 7 and x = 8 or derived 11, 15) and in their trichome morphology. Contrasting results with plastid genes indicates more complex relationships between these two lineages involving recent hybridization processes. We also found an association between chloroplast haplotypes and substrate, especially in populations growing on dolomites. Finally, our dated phylogeny demonstrates that the origin of the genus took place in the mid-Miocene, during the establishment of temporal land bridges between the Tethys and Paratethys seas, with a later diversification during the upper Pliocene.

Genome-Wide Identification and Characterization of Pectin Methylesterase Inhibitor Genes in Brassica oleracea

The activities of pectin methylesterases (PMEs) are regulated by pectin methylesterase inhibitors (PMEIs), which consequently control the pectin methylesterification status. However, the role of PMEI genes in Brassica oleracea, an economically important vegetable crop, is poorly understood. In this study, 95 B. oleracea PMEI (BoPMEI) genes were identified. A total of 77 syntenic ortholog pairs and 10 tandemly duplicated clusters were detected, suggesting that the expansion of BoPMEI genes was mainly attributed to whole-genome triplication (WGT) and tandem duplication (TD). During diploidization after WGT, BoPMEI genes were preferentially retained in accordance with the gene balance hypothesis. Most homologous gene pairs experienced purifying selection with ω (Ka/Ks) ratios lower than 1 in evolution. Five stamen-specific BoPMEI genes were identified by expression pattern analysis. By combining the analyses of expression and evolution, we speculated that nonfunctionalization, subfunctionalization, neofunctionalization, and functional conservation can occur in the long evolutionary process. This work provides insights into the characterization of PMEI genes in B. oleracea and contributes to the further functional studies of BoPMEI genes.

BrFLC5: a weak regulator of flowering time in Brassica rapa

A splicing site mutation in BrFLC5, a non-syntenic paralogue of FLOWERING LOCUS C, was demonstrated to be related to flowering time variation in Brassica rapa. Flowering time regulation in Brassica rapa is more complex than in Arabidopsis, as there are multiple paralogues of flowering time genes in B. rapa. Brassica rapa contains four FLOWERING LOCUS C (FLC) genes, three of which are syntenic orthologues of AtFLC, while BrFLC5 is not. BrFLC1, BrFLC2, and BrFLC3 have been reported to be involved in flowering time regulation. However, BrFLC5 has thus far been deemed a pseudogene. We detected two alternative splicing patterns of BrFLC5 resulting from a nucleotide mutation (G/A) at the first nucleotide of intron 3 (named as Pi3+1(G/A)). Genotyping of BrFLC5Pi3 + 1(G/A) for 301 B. rapa accessions showed that this single nucleotide polymorphism was significantly related to flowering time variation (p < 0.001). In the collection, the frequency of the functional G allele (35.2%) was much lower than that of the nonfunctional A allele (59.1%); however, the frequency of the G allele was very high among the turnips (83.6%). An F2 population segregating at this locus was developed to analyze the genetic effect of BrFLC5. The result showed that the G allele individuals began to bolt two days later than the A allele individuals, indicating that BrFLC5 is a weak regulator of flowering time. BrFLC5 was expressed at the lowest level among the three analyzed BrFLCs. The late allele (G allele) was dominant to the early allele (A allele) at the BrFLC5 locus, which was in contrast to that of BrFLC1 and BrFLC2. This characteristic suggests that BrFLC5 would be more efficient for breeding premature bolting resistance in B. rapa.

Array of MADS-Box Genes: Facilitator for Rapid Adaptation?

In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.

New insights into the taxonomy of tribe Euclidieae (Brassicaceae), evidence from nrITS sequence data

As currently delimitated, the species-rich mustard tribe Euclidieae DC. (Brassicaceae) comprises 28 genera and 152 species distributed primarily in Asia. To date, no tribe-wide comprehensive phylogenetic analysis has been conducted. In this study, sequence data from the nuclear ribosomal internal transcribed spacer (nrITS) region of 82 species in all 28 genera of Euclidieae were used to test its monophyly and infer inter- and intra-generic relationships within. Phylogenetic analyses revealed that Rhammatophyllum and Sisymbriopsis are embedded within Solms-laubachia s.l., and Solms-laubachia lanuginosa (Eurycarpus lanuginosus) fell outside the tribe. Therefore, Solms-laubachia s.l. as currently recognized is not monophyletic and its generic delimitation needed further study. Besides, our results suggest that the genera Lepidostemon, Neotorularia, and Tetracme are polyphyletic.

Antioxidant and Hepatoprotective Effects of Methanolic Extracts of Zilla spinosa and Hammada elegans Against Carbon Tetrachlorideinduced Hepatotoxicity in Rats

The detoxification, metabolism, and excretion of various endogenous and exogenous materials occur mainly in the liver. Liver diseases are a global concern, and classified as chronic hepatitis, cirrhosis, and hepatosis. The development of safe hepatoprotective agents remains an unmet need. Therefore, we investigated the antioxidant effects of methanolic and n-hexane fractions of Zilla spinosa (ZSM and ZSH, respectively) and Hammada elegans (HEM and HEH, respectively) against carbon tetrachloride (CCl4)-induced liver toxicity in rats. Antioxidant activity was studied by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. The rats were divided into 11 groups (n=6)–group, 1 (control), group 2 (CCl4 only), group 3 (CCl4+silymarin 10 mg/kg), group 4 (CCl4+HEM 250 mg/kg), group 5 (CC14+HEM 500 mg/kg), group 6 (CCl4+HEH 250 mg/kg), group, 7 (CCl4+HEH 500 mg/kg), group, 8 (CCl4+ZSM 250 mg/kg), group 9 (CCl4+ZSM 500 mg/kg), group 10 (CCl4+ZSH 250 mg/kg), and group 11 (CCl4+ZSH 500 mg/kg). Serum levels of aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma glutamyl transferase, and total bilirubin were measured. The extent of hepatic injury was histopathologically assessed. Treatment with ZSM and ZSH at 250 and 500 mg/kg did not significantly affect biochemical results compared with the CCl4 only group. However, treatment with both HEM and HEH at 250 and 500 mg/kg provided significant (p<0.001) results compared with the CCl4 only group. These results were consistent with histological findings. HEM and HEH at 250 μg/mL significantly inhibited DPPH radical formation by 38.E6 and 35.65%, rerpectively. However antioxidant effects of ZSM and ZSH were insignificant.

Mutagenesis of the FAE1 genes significantly changes fatty acid composition in seeds of Camelina sativa

Camelina sativa is a re-emerging low-input oilseed crop that has great potentials. It is necessary to ameliorate camelina oils for optimized fatty acid composition that can meet different application requirements. Camelina seed contains significant amounts of C20-C24 very long-chain fatty acids (VLCFAs) that may not be desirable. We demonstrated that these VLCFAs can be effectively reduced by deactivating the Fatty Acid Elongase1 (FAE1) in camelina. The allohexaploid camelina contains three alleles of FAE1 genes. Ethyl methanesulfonate (EMS) induced mutation at the FAE1-B gene caused over 60% reduction of VLCFAs in seed. Homozygous knockout mutants were successfully created in a single generation by simultaneously targeting three FAE1 alleles using the CRISPR technology with an egg cell-specific Cas9 expression. VLCFAs were reduced to less than 2% of total fatty acids compared to over 22% in the wild type, and the C18 unsaturated fatty acids were concomitantly increased. The fae1 mutants were indistinguishable from wild type in seed physiology and plant growth. This study demonstrated that the CRISPR/Cas9 technology can be effectively applied to the polyploid crop camelina to rapidly obtain desired traits such as optimal fatty acid composition in its seed oil. Knocking out FAE1 also provides a means to increase the levels of oleic acid or α-linolenic acid in camelina oils that are desirable for industrial or food/feed uses.

Multispeed genome diploidization and diversification after an ancient allopolyploidization

Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of postpolyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an intertribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in northeastern Asia or western North America during the Late Miocene (c. 10.6-7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.) and 2.1-3.75-fold DD of n = 15 → n = 7-4 in the largely annual crown-group genera (42 spp. in 15 genera). These results are among the first to demonstrate multispeed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies and can be tentatively linked to life histories and the extent of taxonomic diversity.

Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus

Background

Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from diverse population in one map and utilizing it for comparison, but also as a basis for multiple analyses assure a stronger evidence to understand the genetic system related to a given phenotype.

Results

In this study, 439 genes involved in fatty acid (FA) and triacylglycerol (TAG) biosyntheses were identified in Brassica napus. B. napus genome showed mixed gene loss and insertion compared to B. rapa and B. oleracea, and C genome had more inserted genes. Identified QTLs for oil (OC-QTLs) and fatty acids (FA-QTLs) from nine reported populations were projected on the physical map of the reference genome “Darmor-bzh” to generate a map. Thus, 335 FA-QTLs and OC-QTLs could be highlighted and 82 QTLs were overlapping. Chromosome C3 contained 22 overlapping QTLs with all trait studied except for C18:3. In total, 218 candidate genes which were potentially involved in FA and TAG were identified in 162 QTLs confidence intervals and some of them might affect many traits. Also, 76 among these candidate genes were found inside 57 overlapping QTLs, and candidate genes for oil content were in majority (61/76 genes). Then, sixteen genes were found in overlapping QTLs involving three populations, and the remaining 60 genes were found in overlapping QTLs of two populations. Interaction network and pathway analysis of these candidate genes indicated ten genes that might have strong influence over the other genes that control fatty acids and oil formation.

Conclusion

The present results provided new information for genetic basis of FA and TAG formation in B. napus. A map including QTLs from numerous populations was built, which could serve as reference to study the genome profile of B. napus, and new potential genes emerged which might affect seed oil. New useful tracks were showed for the selection of population or/and selection of interesting genes for breeding improvement purpose.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4176-6) contains supplementary material, which is available to authorized users.

Understanding of MYB Transcription Factors Involved in Glucosinolate Biosynthesis in Brassicaceae

Glucosinolates (GSLs) are widely known secondary metabolites that have anticarcinogenic and antioxidative activities in humans and defense roles in plants of the Brassicaceae family. Some R2R3-type MYB (myeloblastosis) transcription factors (TFs) control GSL biosynthesis in Arabidopsis. However, studies on the MYB TFs involved in GSL biosynthesis in Brassica species are limited because of the complexity of the genome, which includes an increased number of paralog genes as a result of genome duplication. The recent completion of the genome sequencing of the Brassica species permits the identification of MYB TFs involved in GSL biosynthesis by comparative genome analysis with A. thaliana. In this review, we describe various findings on the regulation of GSL biosynthesis in Brassicaceae. Furthermore, we identify 63 orthologous copies corresponding to five MYB TFs from Arabidopsis, except MYB76 in Brassica species. Fifty-five MYB TFs from the Brassica species possess a conserved amino acid sequence in their R2R3 MYB DNA-binding domain, and share close evolutionary relationships. Our analysis will provide useful information on the 55 MYB TFs involved in the regulation of GSL biosynthesis in Brassica species, which have a polyploid genome.

Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica

It has been well documented that most nuclear protein-coding genes in organisms can be classified into two categories: positively selected genes (PSGs) and negatively selected genes (NSGs). The characteristics and evolutionary fates of different types of genes, however, have been poorly understood. In this study, the rates of nonsynonymous substitution (K_a ) and the rates of synonymous substitution (K_s ) were investigated by comparing the orthologs between the two sequenced Brassica species, Brassica rapa and Brassica oleracea, and the evolutionary rates, gene structures, expression patterns, and codon bias were compared between PSGs and NSGs. The resulting data show that PSGs have higher protein evolutionary rates, lower synonymous substitution rates, shorter gene length, fewer exons, higher functional specificity, lower expression level, higher tissue-specific expression and stronger codon bias than NSGs. Although the quantities and values are different, the relative features of PSGs and NSGs have been largely verified in the model species Arabidopsis. These data suggest that PSGs and NSGs differ not only under selective pressure (K_a /K_s ), but also in their evolutionary, structural and functional properties, indicating that selective modes may serve as a determinant factor for measuring evolutionary rates, gene compactness and expression patterns in Brassica.

Defense and signalling metabolites of the crucifer Erucastrum canariense: Synchronized abiotic induction of phytoalexins and galacto-oxylipins

Erucastrum canariense Webb & Berthel. (Brassicaceae) is a wild crucifer that grows in rocky soils, in salt and water stressed habitats, namely in the Canary Islands and similar environments. Abiotic stress induced by copper chloride triggered formation of a phytoalexin and galacto-oxylipins in E. canariense, whereas wounding induced galacto-oxylipins but not phytoalexins. Analysis of the metabolite profiles of leaves of E. canariense followed by isolation and structure determination afforded the phytoalexin erucalexin, the phytoanticipin indolyl-3-acetonitrile, the galacto-oxylipins arabidopsides A, C, and D, and the oxylipin 12-oxophytodienoic acid. In addition, arabidopsides A and D were also identified in extracts of leaves of Nasturtium officinale R. Br.

Plastome phylogeny and early diversification of Brassicaceae

Background

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.

Results

Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.

Conclusions

Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3555-3) contains supplementary material, which is available to authorized users.

Plastome phylogeny and early diversification of Brassicaceae

BACKGROUND

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.

RESULTS

Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.

CONCLUSIONS

Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.

The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism

Expansion of the cytochrome P450 gene family is often proposed to have a critical role in the evolution of metabolic complexity, in particular in microorganisms, insects and plants. However, the molecular mechanisms underlying the evolution of this complexity are poorly understood. Here we describe the evolutionary history of a plant P450 retrogene, which emerged and underwent fixation in the common ancestor of Brassicales, before undergoing tandem duplication in the ancestor of Brassicaceae. Duplication leads first to gain of dual functions in one of the copies. Both sister genes are retained through subsequent speciation but eventually return to a single copy in two of three diverging lineages. In the lineage in which both copies are maintained, the ancestral functions are split between paralogs and a novel function arises in the copy under relaxed selection. Our work illustrates how retrotransposition and gene duplication can favour the emergence of novel metabolic functions.

A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants

Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs). Recently, attention has focused on understanding the evolutionary dynamics of lincRNAs, particularly their conservation within genomes. Here, we take a comparative genomic and phylogenetic approach to uncover factors influencing lincRNA emergence and persistence in the plant family Brassicaceae, to which Arabidopsis thaliana belongs. We searched 10 genomes across the family for evidence of > 5000 lincRNA loci from A. thaliana. From loci conserved in the genomes of multiple species, we built alignments and inferred phylogeny. We then used gene tree/species tree reconciliation to examine the duplication history and timing of emergence of these loci. Emergence of lincRNA loci appears to be linked to local duplication events, but, surprisingly, not whole genome duplication events (WGD), or transposable elements. Interestingly, WGD events are associated with the loss of loci for species having undergone relatively recent polyploidy. Lastly, we identify 1180 loci of the 6480 previously annotated A. thaliana lincRNAs (18%) with elevated levels of conservation. These conserved lincRNAs show higher expression, and are enriched for stress-responsiveness and cis-regulatory motifs known as conserved noncoding sequences (CNSs). These data highlight potential functional pathways and suggest that CNSs may regulate neighboring genes at both the genomic and transcriptomic level. In sum, we provide insight into processes that may influence lincRNA diversification by providing an evolutionary context for previously annotated lincRNAs.

Molecular phylogeny reveals the non-monophyly of tribe Yinshanieae (Brassicaceae) and description of a new tribe, Hillielleae

The taxonomic treatment within the unigeneric tribe Yinshanieae (Brassicaceae) is controversial, owing to differences in generic delimitation applied to its species. In this study, sequences from nuclear ITS and chloroplast trnL-F regions were used to test the monophyly of Yinshanieae, while two nuclear markers (ITS, ETS) and four chloroplast markers (trnL-F, trnH-psbA, rps16, rpL32-trnL) were used to elucidate the phylogenetic relationships within the tribe. Using maximum parsimony, maximum likelihood, and Bayesian inference methods, we reconstructed the phylogeny of Brassicaceae and Yinshanieae. The results show that Yinshanieae is not a monophyletic group, with the taxa splitting into two distantly related clades: one clade contains four taxa and falls in Lineage I, whereas the other includes all species previously placed in Hilliella and is embedded in the Expanded Lineage II. The tribe Yinshanieae is redefined, and a new tribe, Hillielleae, is proposed based on combined evidence from molecular phylogeny, morphology, and cytology.

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes

This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

Suitability of Root and Rhizome Anatomy for Taxonomic Classification and Reconstruction of Phylogenetic Relationships in the Tribes Cardueae and Cichorieae (Asteraceae)

The value of root and rhizome anatomy for the taxonomic characterisation of 59 species classified into 34 genera and 12 subtribes from the Asteraceae tribes Cardueae and Cichorieae was assessed. In addition, the evolutionary history of anatomical characters was reconstructed using a nuclear ribosomal DNA sequence-based phylogeny of the Cichorieae. Taxa were selected with a focus on pharmaceutically relevant species. A binary decision tree was constructed and discriminant function analyses were performed to extract taxonomically relevant anatomical characters and to infer the separability of infratribal taxa, respectively. The binary decision tree distinguished 33 species and two subspecies, but only five of the genera (sampled for at least two species) by a unique combination of hierarchically arranged characters. Accessions were discriminated-except for one sample worthy of discussion-according to their subtribal affiliation in the discriminant function analyses (DFA). However, constantly expressed subtribe-specific characters were almost missing and even in combination, did not discriminate the subtribes. Most anatomical characters showed at least some degree of homoplasious evolution limiting their suitability as phylogenetically informative characters.

Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri

Two Brassicaceae species, Physaria fendleri and Camelina sativa, are genetically very closely related to each other and to Arabidopsis thaliana. Physaria fendleri seeds contain over 50% hydroxy fatty acids (HFAs), while Camelina sativa and Arabidopsis do not accumulate HFAs. To better understand how plants evolved new biochemical pathways with the capacity to accumulate high levels of unusual fatty acids, transcript expression and protein sequences of developing seeds of Physaria fendleri, wild-type Camelina sativa, and Camelina sativa expressing a castor bean (Ricinus communis) hydroxylase were analyzed. A number of potential evolutionary adaptations within lipid metabolism that probably enhance HFA production and accumulation in Physaria fendleri, and, in their absence, limit accumulation in transgenic tissues were revealed. These adaptations occurred in at least 20 genes within several lipid pathways from the onset of fatty acid synthesis and its regulation to the assembly of triacylglycerols. Lipid genes of Physaria fendleri appear to have co-evolved through modulation of transcriptional abundances and alterations within protein sequences. Only a handful of genes showed evidence for sequence adaptation through gene duplication. Collectively, these evolutionary changes probably occurred to minimize deleterious effects of high HFA amounts and/or to enhance accumulation for physiological advantage. These results shed light on the evolution of pathways for novel fatty acid production in seeds, help explain some of the current limitations to accumulation of HFAs in transgenic plants, and may provide improved strategies for future engineering of their production.

Comparative paleogenomics of crucifers: ancestral genomic blocks revisited

A decade ago the concept of the Ancestral Crucifer Karyotype (ACK) and the definition of 24 conserved genomic blocks was presented. Subsequently, 35 cytogenetic reconstructions and/or draft genome sequences of crucifer species (members of the Brassicaceae family) have been analyzed in the context of this system; placing crucifers at the forefront of plant phylogenomics. In this review, we highlight how the ACK and genomic blocks have facilitated and guided genomic analysis of crucifers in the last 10 years and provide an update of this robust model.

Clade-specific positive selection on a developmental gene: BRANCHLESS TRICHOME and the evolution of stellate trichomes in Physaria (Brassicaceae)

Positive selection is known to drive the evolution of genes involved in evolutionary arms races, but what role does it play in the evolution of genes involved in developmental processes? We used the single-celled epidermal trichomes of Brassicaceae as a model to uncover the molecular evolutionary processes that contributed to the transition from dendritic trichomes, as seen in most species of Brassicaceae, to the distinctive stellate trichomes of the genus Physaria. We explored the role of positive selection on the evolution of BRANCHLESS TRICHOME (BLT), a candidate gene for changes in trichome branching pattern. Maximum likelihood models of codon evolution point to a shift in selective pressure affecting the evolution of BLT across the entire Physaria clade, and we found strong evidence that positive selection has acted on a subset of Physaria BLT codons. Almost all of the 10 codon sites with the highest probability of having evolved under positive selection are clustered in a predicted coiled-coil domain, pointing to changes in protein-protein interactions. Thus, our findings suggest that selection acted on BLT to modify its interactions with other proteins. The fact that positive selection occurred throughout the radiation of Physaria could reflect selection to stabilize development in response to an abrupt switch from the dendritic form to the stellate form, divergent selection for diversification of the stellate form, or both. These results point to the need for evolutionary developmental studies of BLT and its interacting proteins in Physaria.

Biogeography and diversification of Brassicales: A 103million year tale

Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.

Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes

Background

There are three basic Brassica genomes (A, B, and C) and three parallel sets of subgenomes distinguished in the diploid Brassica (i.e.: B. rapa, A^rA^r; B. nigra, BⁿⁱBⁿⁱ; B. oleracea, C^oC^o) and the derived allotetraploid species (i.e.: B. juncea, A^jA^jB^jB^j; B. napus, AⁿAⁿCⁿCⁿ; B. carinata, B^cB^cC^cC^c). To understand subgenome differentiation in B. juncea in comparison to other A genome-carrying Brassica species (B. rapa and B. napus), we constructed a dense genetic linkage map of B. juncea, and conducted population genetic analysis on diverse lines of the three A-genome carrying Brassica species using a genotyping-by-sequencing approach (DArT-seq).

Results

A dense genetic linkage map of B. juncea was constructed using an F₂ population derived from Sichuan Yellow/Purple Mustard. The map included 3329 DArT-seq markers on 18 linkage groups and covered 1579 cM with an average density of two markers per cM. Based on this map and the alignment of the marker sequences with the physical genome of Arabidopsis thaliana, we observed strong co-linearity of the ancestral blocks among the different A subgenomes but also considerable block variation. Comparative analyses at the level of genome sequences of B. rapa and B. napus, and marker sequence anchored on the genetic map of B. juncea, revealed a total of 30 potential inversion events across large segments and 20 potential translocation events among the three A subgenomes. Population genetic analysis on 26 accessions of the three A genome-carrying Brassica species showed that the highest genetic distance were estimated when comparing A^j-Aⁿ than between Aⁿ-A^r and A^j-A^r subgenome pairs.

Conclusions

The development of the dense genetic linkage map of B. juncea with informative DArT-seq marker sequences and availability of the reference sequences of the A^r, and AⁿCⁿ genomes allowed us to compare the A subgenome structure of B. juncea (A^j) . Our results suggest that strong co-linearity exists among the three A Brassica genomes (A^r, Aⁿ and A^j) but with apparent subgenomic variation. Population genetic analysis on three A-genome carrying Brassica species support the idea that B. juncea has distinct genomic diversity, and/or evolved from a different A genome progenitor of B. napus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2343-1) contains supplementary material, which is available to authorized users.

Understanding Brassicaceae evolution through ancestral genome reconstruction

BACKGROUND

Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed.

RESULTS

We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula. The ancestral Brassicaceae karyotype (Brassicaceae lineages I and II) is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype (eight protochromosomes and 22,085 ordered protogenes) and the proto-Calepineae karyotype (seven protochromosomes and 21,035 ordered protogenes) genomes.

CONCLUSIONS

The three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. This new resource should accelerate research in comparative genomics and translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa

The glucosinolate biosynthetic gene AOP2 encodes an enzyme that plays a crucial role in catalysing the conversion of beneficial glucosinolates into anti-nutritional ones. In Brassica rapa, three copies of BrAOP2 have been identified, but their function in establishing the glucosinolate content of B. rapa is poorly understood. Here, we used phylogenetic and gene structure analyses to show that BrAOP2 proteins have evolved via a duplication process retaining two highly conserved domains at the N-terminal and C-terminal regions, while the middle part has experienced structural divergence. Heterologous expression and in vitro enzyme assays and Arabidopsis mutant complementation studies showed that all three BrAOP2 genes encode functional BrAOP2 proteins that convert the precursor methylsulfinyl alkyl glucosinolate to the alkenyl form. Site-directed mutagenesis showed that His356, Asp310, and Arg376 residues are required for the catalytic activity of one of the BrAOP2 proteins (BrAOP2.1). Promoter-β-glucuronidase lines revealed that the BrAOP2.3 gene displayed an overlapping but distinct tissue- and cell-specific expression profile compared with that of the BrAOP2.1 and BrAOP2.2 genes. Quantitative real-time reverse transcription-PCR assays demonstrated that BrAOP2.1 showed a slightly different pattern of expression in below-ground tissue at the seedling stage and in the silique at the reproductive stage compared with BrAOP2.2 and BrAOP2.3 genes in B. rapa. Taken together, our results revealed that all three BrAOP2 paralogues are active in B. rapa but have functionally diverged.

Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes

Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting (CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2n = 14) and aneuploid (2n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype (n = 8) of Brassicaceae lineage I. Whereas three chromosomes (BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1-BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentromere on chromosome BS5. In apomictic 2n = 14 plants, CCP identifies the largely heterochromatic chromosome (Het) being one of the BS1 homologues with the expansion of pericentromeric heterochromatin. In apomictic B. polyantha (2n = 15), the Het has undergone a centric fission resulting in two smaller chromosomes - the submetacentric Het' and telocentric Del. Here we show that new chromosomes can be formed by a centric fission and can be fixed in populations due to the apomictic mode of reproduction.

Dietary Sulforaphane in Cancer Chemoprevention: The Role of Epigenetic Regulation and HDAC Inhibition

SIGNIFICANCE

Sulforaphane, produced by the hydrolytic conversion of glucoraphanin after ingestion of cruciferous vegetables, particularly broccoli and broccoli sprouts, has been extensively studied due to its apparent health-promoting properties in disease and limited toxicity in normal tissue. Recent Studies: Recent identification of a sub-population of tumor cells with stem cell-like self-renewal capacity that may be responsible for relapse, metastasis, and resistance, as a potential target of the dietary compound, may be an important aspect of sulforaphane chemoprevention. Evidence also suggests that sulforaphane may target the epigenetic alterations observed in specific cancers, reversing aberrant changes in gene transcription through mechanisms of histone deacetylase inhibition, global demethylation, and microRNA modulation.

CRITICAL ISSUES

In this review, we discuss the biochemical and biological properties of sulforaphane with a particular emphasis on the anticancer properties of the dietary compound. Sulforaphane possesses the capacity to intervene in multistage carcinogenesis through the modulation and/or regulation of important cellular mechanisms. The inhibition of phase I enzymes that are responsible for the activation of pro-carcinogens, and the induction of phase II enzymes that are critical in mutagen elimination are well-characterized chemopreventive properties. Furthermore, sulforaphane mediates a number of anticancer pathways, including the activation of apoptosis, induction of cell cycle arrest, and inhibition of NFκB.

FUTURE DIRECTIONS

Further characterization of the chemopreventive properties of sulforaphane and its capacity to be selectively toxic to malignant cells are warranted to potentially establish the clinical utility of the dietary compound as an anti-cancer compound alone, and in combination with clinically relevant therapeutic and management strategies.

Lineage-specific evolution of Methylthioalkylmalate synthases (MAMs) involved in glucosinolates biosynthesis

Methylthioalkylmalate synthases (MAMs) encoded by MAM genes are central to the diversification of the glucosinolates, which are important secondary metabolites in Brassicaceae species. However, the evolutionary pathway of MAM genes is poorly understood. We analyzed the phylogenetic and synteny relationships of MAM genes from 13 sequenced Brassicaceae species. Based on these analyses, we propose that the syntenic loci of MAM genes, which underwent frequent tandem duplications, divided into two independent lineage-specific evolution routes and were driven by positive selection after the divergence from Aethionema arabicum. In the lineage I species Capsella rubella, Camelina sativa, Arabidopsis lyrata, and A. thaliana, the MAM loci evolved three tandem genes encoding enzymes responsible for the biosynthesis of aliphatic glucosinolates with different carbon chain-lengths. In lineage II species, the MAM loci encode enzymes responsible for the biosynthesis of short-chain aliphatic glucosinolates. Our proposed model of the evolutionary pathway of MAM genes will be useful for understanding the specific function of these genes in Brassicaceae species.

Diversified glucosinolate metabolism: biosynthesis of hydrogen cyanide and of the hydroxynitrile glucoside alliarinoside in relation to sinigrin metabolism in Alliaria petiolata

Alliaria petiolata (garlic mustard, Brassicaceae) contains the glucosinolate sinigrin as well as alliarinoside, a γ-hydroxynitrile glucoside structurally related to cyanogenic glucosides. Sinigrin may defend this plant against a broad range of enemies, while alliarinoside confers resistance to specialized (glucosinolate-adapted) herbivores. Hydroxynitrile glucosides and glucosinolates are two classes of specialized metabolites, which generally do not occur in the same plant species. Administration of [UL-(14)C]-methionine to excised leaves of A. petiolata showed that both alliarinoside and sinigrin were biosynthesized from methionine. The biosynthesis of alliarinoside was shown not to bifurcate from sinigrin biosynthesis at the oxime level in contrast to the general scheme for hydroxynitrile glucoside biosynthesis. Instead, the aglucon of alliarinoside was formed from metabolism of sinigrin in experiments with crude extracts, suggesting a possible biosynthetic pathway in intact cells. Hence, the alliarinoside pathway may represent a route to hydroxynitrile glucoside biosynthesis resulting from convergent evolution. Metabolite profiling by LC-MS showed no evidence of the presence of cyanogenic glucosides in A. petiolata. However, we detected hydrogen cyanide (HCN) release from sinigrin and added thiocyanate ion and benzyl thiocyanate in A. petiolata indicating an enzymatic pathway from glucosinolates via allyl thiocyanate and indole glucosinolate derived thiocyanate ion to HCN. Alliarinoside biosynthesis and HCN release from glucosinolate-derived metabolites expand the range of glucosinolate-related defenses and can be viewed as a third line of defense, with glucosinolates and thiocyanate forming protein being the first and second lines, respectively.

Variation in plant defences among populations of a range-expanding plant: consequences for trophic interactions

Although plant-herbivore-enemy interactions have been studied extensively in cross-continental plant invasions, little is known about intra-continental range expanders, despite their rapid spread globally. Using an ecological and metabolomics approach, we compared the insect performance of a generalist and specialist herbivore and a parasitoid, as well as plant defence traits, among native, exotic invasive and exotic non-invasive populations of the Turkish rocket, Bunias orientalis, a range-expanding species across parts of Eurasia. In the glasshouse, the generalist herbivore, Mamestra brassicae, and its parasitoid, Microplitis mediator, performed better on non-native than on native plant populations. Insect performance did not differ between the two non-native origins. By contrast, the specialist herbivore, Pieris brassicae, developed poorly on all populations. Differences in trichome densities and in the metabolome, particularly in the family-specific secondary metabolites (i.e. glucosinolates), may explain population-related variation in the performance of the generalist herbivore and its parasitoid. Total glucosinolate concentrations were significantly induced by herbivory, particularly in native populations. Native populations of B. orientalis are generally better defended than non-native populations. The role of insect herbivores and dietary specialization as a selection force on defence traits in the range-expanding B. orientalis is discussed.

Neofunctionalization of duplicated Tic40 genes caused a gain-of-function variation related to male fertility in Brassica oleracea lineages

Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes.

Molecular phylogenetics of tribe Eudemeae (Brassicaceae) and implications for its morphology and distribution

Tribe Eudemeae comprises a morphologically heterogeneous group of genera distributed along the Andes of South America from Colombia southward into southern Chile and Argentina. The tribe currently includes seven genera: Aschersoniodoxa, Brayopsis, Dactylocardamum, Delpinophytum, Eudema, Onuris, and Xerodraba, and exhibits a wide morphological diversification in growth habit, inflorescences, and fruits. However, little is known about the phylogenetic relationships and evolution of the tribe. We present here a molecular phylogeny of representative sampling of all genera, utilizing sequence data from the nuclear ribosomal ITS region and chloroplast regions trnL-F, trnH-psbA, and rps16. Additionally, climatic niches of the tribe and its main lineages, along with the evolution of diagnostic morphological characters, were studied. All analyses confirmed the monophyly of Eudemeae, with the exception of Delpinophytum that was included with genera of the lineage I of Brassicaceae. Eudemeae is divided into two main lineages differentiated by their geographical distribution and climatic niche: the primarily north-central Andean lineage included Aschersoniodoxa, Brayopsis, Dactylocardamum, and Eudema, and the Patagonian and southern Andean lineage included Onuris and Xerodraba. Finally, ancestral-state reconstructions in the tribe generally reveal multiple and independent gains or losses of diagnostic morphological characters, such as growth form, inflorescence reduction, and fruit type. Relevant taxonomic implications stemming from the results are also discussed.

The Camelina aquaporin CsPIP2;1 is regulated by phosphorylation at Ser273, but not at Ser277, of the C-terminus and is involved in salt- and drought-stress responses

Aquaporin (AQP) proteins are involved in water homeostasis in cells at all taxonomic levels of life. Phosphorylation of some AQPs has been proposed to regulate water permeability via gating of the channel itself. We analyzed plasma membrane intrinsic proteins (PIP) from Camelina and characterized their biological functions under both stressful and favorable conditions. A three-dimensional theoretical model of the Camelina AQP proteins was built by homology modeling which could prove useful in further functional characterization of AQPs. CsPIP2;1 was strongly and constitutively expressed in roots and leaves of Camelina, suggesting that this gene is related to maintenance of homeostasis during salt and drought stresses. CsPIP2s exhibited water channel activity in Xenopus oocytes. We then examined the roles of CsPIP2;1 phosphorylation at Ser273 and Ser277 in the regulation of water permeability using phosphorylation mutants. A single deletion strain of CsPIP2;1 was generated to serve as the primary host for testing AQP expression constructs. A Ser277 to alanine mutation (to prevent phosphorylation) did not change CsPIP2;1 water permeability while a Ser273 mutation to alanine did affect water permeability. Furthermore, a CsPIP2;1 point mutation when ectopically expressed in yeast resulted in lower growth in salt and drought conditions compared with controls, and confirmation of Ser273 as the phosphorylation site. Our results support the idea that post-translational modifications in the Ser273 regulatory domains of the C-terminus fine tune water flux through CsPIP2;1.

Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica

This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9-92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.

Development of a complete set of monosomic alien addition lines between Brassica napus and Isatis indigotica (Chinese woad)

A complete set of monosomic alien addition lines of Brassica napus with one of the seven chromosomes of Isatis indigotica and the recombinant mitochondria was developed and characterized. Monosomic alien addition lines (MAALs) are valuable for elucidating the genome structure and transferring the useful genes and traits in plant breeding. Isatis indigotica (Chinese woad, 2n = 14, II) in Isatideae tribe of Brassicaceae family has been widely cultivated as a medicinal and dye plant in China. Herein, the intertribal somatic hybrid (2n = 52, AACCII) between B. napus cv. Huashuang 3 (2n = 38, AACC) and I. indigotica produced previously was backcrossed recurrently to parental B. napus, and 32 MAAL plants were isolated. Based on their phenotype, 5S and 45S rDNA loci and chromosome-specific SSR markers, these MAALs were classified into seven groups corresponding to potential seven types of MAALs carrying one of the seven I. indigotica chromosomes. One of the MAALs could be distinguishable by expressing the brown anthers of I. indigotica, other two hosted the chromosome with 5S or 45S rDNA locus, but the remaining four were identifiable by SSR markers. The simultaneous detection of the same SSR maker and gene locus in different MAALs revealed the paralogs on the chromosomes involved. The recombinant mitochondrial genome in MAALs was likely related with their male sterility with carpellody stamens, while the MAAL with normal brown anthers probably carried the restoring gene for the male sterility. The complete set of MAALs should be useful for exploiting the I. indigotica genome and for promoting the introgression of valuable genes to B. napus.

One or three species in Megadenia (Brassicaceae): insight from molecular studies

Megadenia Maxim. is a small genus of the Brassicaceae endemic to East Asia with three disjunct areas of distribution: the eastern edge of the Qinghai-Tibetan Plateau, the Eastern Sayan Mountains in southern Siberia, and Chandalaz Ridge in the southern Sikhote-Alin Mountains. Although distinct species (M. pygmaea Maxim., M. bardunovii Popov, and M. speluncarum Vorob., Vorosch. and Gorovoj) have been described from each area, they have lately been reduced to synonymy with M. pygmaea due to high morphological similarity. Here, we present the first molecular study of Megadenia. Using the sequences of 11 noncoding regions from the cytoplasmic (chloroplast and mitochondrial) and nuclear genomes, we assessed divergence within the genus and explored the relationships between Megadenia and Biscutella L. Although M. bardunovii, M. speluncarum, and M. pygmaea were found to be indiscernible with regard to the nuclear and mitochondrial markers studied, our data on the plastid genome revealed their distinctness and a clear subdivision of the genus into three lineages matching the three described species. All of the phylogenetic analyses of the chloroplast DNA sequences provide strong support for the inclusion of Megadenia and Biscutella in the tribe Biscutelleae. A dating analysis shows that the genus Megadenia is of Miocene origin and diversification within the genus, which has led to the three extant lineages, most likely occurred during the Early-Middle Pleistocene, in agreement with the vicariance pattern. Given the present-day distribution, differences in habitat preferences and in some anatomical traits, and lack of a direct genealogical relationship, M. pygmaea, M. bardunovii, and M. speluncarum should be treated as distinct species or at least subspecies.

Molecular basis of natural variation and environmental control of trichome patterning

Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning.

Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards)

The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships.