Morphological and molecular confirmation of Albugo resedae (Albuginales; Oomycota) as a distinct species from A. candida

The genus Albugo s.str. causes white blister rust on four families of the Brassicales, Brassicaceae, Capparaceae, Cleomaceae, and Resedaceae. Recent phylogenetic studies have revealed that several host specific lineages are present within Albugo on Brassicales, while it was also confirmed that Albugo candida has an exceptionally wide host range which extends from Brassicaceae to Cleomaceae and Capparaceae. The Albugo species infecting the Resedaceae was attributed in monographic studies as well as local floras to either A. resedae or, applying a broader species concept, to A. candida. In the present study, A. resedae specimens were morphologically and molecularly compared to the five Albugo species so far confirmed from Brassicales, A. candida, A. koreana, A. laibachii, A. lepidii, and A. voglmayrii. Both morphological differences of oospore ornamentation and phylogenetic analysis of cox2 mtDNA sequences provided evidence that A. resedae is distinct from A. candida and from the additional four species so far described from Brassicaceae. It thus seems possible that so far unknown factors restrict Albugo candida to Brassicaceae and its sister families, Cleomaceae and Capparaceae.     

Embryology of Koeberlinia (Koeberliniaceae): Evidence for core-Brassicalean affinities

Koeberlinia, comprising a single xerophytic species K. spinosa, had previously been placed in various families, mainly Capparaceae. Current molecular evidence now places it in its own family Koeberliniaceae, thought to be related to the Bataceae/Salvadoraceae among the 17 other families of the Brassicales. We investigated 55 embryological characters of the genus, most of which are not understood yet, and thereby assessed its systematic relationships. Koeberlinia has many embryological features in common with the Capparaceae and seven other core-Brassicalean families (i.e., Brassicaceae, Cleomaceae, Emblingiaceae, Gyrostemonaceae, Pentadiplandraceae, Resedaceae, and Tovariaceae), specifically by possessing a campylotropous ovule with a nonmultiplicative (two-cell-layered) outer integument, reniform seeds with a curved embryo, and a fibrous exotegmen in the mature seed coat. However, Koeberlinia is clearly distinguished from them by a tenuinucellate rather than crassinucellate ovule as previously reported, markedly enlarged apical nucellar epidermal cells, and an "exotestal" seed coat. Embryologically, Koeberlinia resembles neither the Bataceae nor the Salvadoraceae, although only limited embryological data are available for these two families. Embryological evidence thus favors its joining the core Brassicales, but additional molecular analyses and embryological studies on the missing data of the Bataceae and Salvadoraceae are needed for final confirmation of its phylogenetic position.     

Epidermal Patterning in Seedling Roots of Eudicotyledons

Three types of epidermal patterning occur in roots of angiosperms:in Type 1, all the epidermal cells can potentially produce roothairs (hair cells); in Type 2, asymmetric cell divisions produceshort cells that develop into hair cells and larger cells thatdo not (non-hair cells); and in Type 3, hair cells occur infiles separated by one to three files of non-hair cells. Inthe present study we examined the epidermal patternings of seedlingroots of 77 eudicotyledonous species from 43 families. We foundthat Type 1 patterning was the most common and no species hadType 2 patterning. Previously, Type 3 epidermal patterning hadbeen described only in the family Brassicaceae. In additionto the Brassicaceae (including the Capparaceae), we found Type3 patterning in the Brassicales families Limnanthaceae and Resedaceae,whereas the other Brassicales families we examined, Caricaceaeand Tropaeolaceae, had Type 1 patterning. We also found Type3 patterning in six families of the Caryophyllales sensu lato:Amaranthaceae, Basellaceae, Caryophyllaceae, Plumbaginaceae,Polygonaceae and Portulacaceae. However, the family Cactaceae,which is also in this order, had Type 1 patterning. Only oneother species, Nemophila maculata(Boraginaceae), had Type 3patterning; the other two species that we examined in this familyhad Type 1 patterning. Type 3 patterning thus occurs more widelyin the eudicotyledons than was previously thought. Copyright2001 Annals of Botany Company Brassicales, Caryophyllales, eudicotyledons, epidermal patterning, phylogeny, root hairs, roots, seedlings     

Parallel evolution of glucosinolate biosynthesis inferred from congruent nuclear and plastid gene phylogenies

The phytochemical system of mustard-oil glucosides (glucosinolates) accompanied by the hydrolytic enzyme myrosinase (beta-thioglucosidase), the latter usually compartmented in special myrosin cells, characterizes plants in 16 families of angiosperms. Traditional classifications place these taxa in many separate orders and thus imply multiple convergences in the origin of this chemical defense system. DNA sequencing of the chloroplast rbcL gene for representatives of all 16 families and several putative relatives, with phylogenetic analyses by parsimony and maximum likelihood methods, demonstrated instead a single major clade of mustard-oil plants and one phylogenetic outlier. In a further independent test, DNA sequencing of the nuclear 18S ribosomal RNA gene for all these exemplars has yielded the same result, a major mustard-oil clade of 15 families (Akaniaceae, Bataceae, Brassicaceae, Bretschneideraceae, Capparaceae, Caricaceae, Gyrostemonaceae, Koeberliniaceae, Limnanthaceae, Moringaceae, Pentadiplandraceae, Resedaceae, Salvadoraceae, Tovariaceae, and Tropaeolaceae) and one outlier, the genus Drypetes, traditionally placed in Euphorbiaceae. Concatenating the two gene sequences (for a total of 3254 nucleotides) in a data set for 33 taxa, we obtain robust support for this finding of parallel origins of glucosinolate biosynthesis. From likely cyanogenic ancestors, the "mustard oil bomb" was invented twice.     

Glucosinolate biochemical diversity and innovation in the Brassicales

Glucosinolates were analysed from herbarium specimens and living tissues from representative of all families of the Brassicales, following the phylogenetic schemes of Rodman et al. (1998) and Hall et al. (2002, 2004), including specimens of Akania, Setchellanthus, Emblingia, Stixis, Forchhammeria and members of the Capparaceae for which glucosinolate content had not previously been reported. The results are reviewed along with additional published data on glucosinolate content of members of the Brassicales. In addition to providing an overview of the evolution of glucosinolate biochemical diversity within the core Brassicales, there were three main findings. Firstly, the glucosinolate content of some 'orphan' taxa of the Brassicales, such as Setchellanthus and Emblingia were consistent with recent phylogentic analyses based upon DNA sequence comparisons, while further analyses of Tirania and Stixis is required. Secondly, methyl glucosinolate is found within the Capparaceae and Cleomaceae, but also, unexpectedly, within Forchhammeria, with implications for the biochemical and evolutionary origin of methyl glucosinolate and the phylogenetic relationships of Forchhammeria. Thirdly, whereas Old World Capparaceae contain methyl glucosinolate, New World Capparaceae, including New World Capparis, either contain methyl glucosinolates or glucosinolates of complex and unresolved structures, indicative of continued innovation in glucosinolate biosynthesis. These taxa may be productive sources of glucosinolate biosynthetic genes and alleles that are not found in the model plant Arabidopsis thaliana.     

Chemosystematics of Brassicales

The order Brassicales, sensu APG III, belongs to Eurosids, and comprises 17 families and 398 genera. The present work discusses the chemical features of Brassicales through the micromolecular chemical data of its taxa and selected taxonomic markers to assess pertinent affinities between its families by correlating their chemosystematic parameters. Although the chemical data of all families were obtained, the data of Brassicaceae, Capparaceae, and Cleomaceae were the most studied. The chemistry of the Brassicales species is diverse, but it reveals the chemical affinity of its families due to occurrence of flavonoids (35%) and glucosinolates (25%), which were characterized as good chemical markers. The flavonoids consist primarily of flavones and flavonols, presenting a low flavone/flavonol ratio. These micromolecules commonly contain unprotected hydroxyls, which are mainly protected by glucosilation, revealing the basal features of its taxa. In Brassicales, the predominantly allyl glucosinolates are usually found in Brassicaceae, Capparaceae, and Cleomaceae families. In the present study, the results of the chemosystematic analysis confirmed the affinity among the Brassicaceae, Capparaceae, and Cleomaceae families, and supported the concept of their monophyly in the Brassicales order. However, more chemical data of the other families is required to improve the chemosystematic conclusions.     

Myrosin cells and dilated cisternae of the endoplasmic reticulum in the order Capparales

Ultrastructural results for different types of protein–rich cells in five families generally accepted as Capparalean (Brassicaceae, Capparaceae, Resedaceae, Tovariaceae and Moringaceae) and two others (Gyrostemonaceae and Bataceae) considered by some workers to be Capparalean, support their alignment in the order Capparales. The term myrosin cell is used for those protein–rich cells which are typically idio–blastic and characterized by a homogenous, granular proteinaceous material in the vacuole and a cytoplasm which is filled with an extensive rough endoplasmic reticulum. This idioblastic myrosin cell type is characteristic for the Brassicaceae, Capparaceae, Tovariaceae, Moringaceae and Gyrostemonaceae. The guard cells of stomata may appear as myrosin cells, in which case they are termed guard–cell myrosin cells; they are found in the Resedaceae, Tovariaceae and Bataceae. Other proteinaceous cells are those with protein–rich dilated cisternae (DC) of the endoplasmic reticulum (ER). One type is the organelle–like DC, utricular or irregular dilations of the ER, filled with protein and ribosome–studded. Utricular DC are characteristic for the Brassicaceae and Capparaceae. Another type of DC is represented by protein–containing vacuoles derived from the ER, protein–rich ER–dependent vacuoles; these are found in the Brassicaceae, Capparaceae, Resedaceae, Tovariaceae and Gyrostemonaceae. The myrosin cells and cells with protein–rich dilated cisternae are here regarded as taxonomic criteria for the order Capparales.     

A new perspective on the evolution of white blister rusts: <Emphasis Type="Italic">Albugo</Emphasis> s.str. (Albuginales; Oomycota) is not restricted to Brassicales but also present on Fabales

For almost all groups of pathogens, unusual and rare host species have been reported. Often, such associations are based on single or few collections only, which are frequently hard to access. Many of them later prove to be due to misidentification of the host, the pathogen, or both. Therefore, such reports are often disregarded, or treated anecdotally in taxonomic and phylogenetic studies, regardless of their potential importance to unravelling the evolution of the entire group. Concerning oomycete biotrophs there are several reports of unusual and rare hosts for hardly known pathogens. In the order Fabales, for example, a single species of Albugo, A. mauginii, was described as parasitic to Onobrychis crista-galli about 80 years ago, but not recorded again. All other confirmed members of Albugo s.str. are parasitic to representatives of the families Brassicaceae, Capparaceae, Cleomaceae, and Resedaceae in the order Brassicales. In the present study, molecular phylogenetic analysis of cox2 mtDNA sequences and morphological investigations on an original specimen confirmed the occurrence of a member of Albugo on Fabaceae hosts, with the characteristic thin wall of the secondary sporangia, which is almost uniform in thickness. In phylogenetic analyses the species results as embedded within Albugo s.str. Therefore, it is concluded that the natural host range of Albugo s.str. extends from Brassicales to Fabales via host jumping. Our results underscore that unrevised reports of pathogens from unusual hosts should be reconsidered carefully to obtain a more complete picture of pathogen diversity and evolution.     

Whole genome duplication of intra- and inter-chromosomes in the tomato genome

Whole genome duplication(WGD)events have been proven to occur in the evolutionary history of most angiosperms.Tomato is considered a model species of the Solanaceae family.In this study,we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods:synonymous substitution rates(Ks)and phylogenetic trees.In total,593 collinearity blocks were discovered out of 12 pseudo-chromosomes constructed. It was evident that chromosome 2 had experienced an intra-chromosomal duplication event.Major inter-chromosomal duplication occurred among all the pseudo-chromosome.We calculated the Ks value of these collinearity blocks.Two peaks of Ks distribution were found,corresponding to two WGD events occurring approximately 36-82 million years ago(MYA)and 148-205 MYA.Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosidasterid clade,but before the major diversification in Solanaceae.The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis(monocot-dicot).     

BRASSICALES – AN ORDER OF PLANTS CHARACTERISED BY SHARED CHEMISTRY

Among the many advances in our understanding of angiosperm relationships in recent decades due to the advent of DNA sequence data is the confirmation that all plants (apart from Drypetes) that produce mustard oil precursors are related to each other and should be treated as one order, Brassicales. Due to the lack of obvious shared morphological characters, this is one of the more unexpected of these advances. Here we give the background to this development and introduce the families in Brassicales, including Tropaeolaceae, the subject of this issue.     

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.     

Floral anatomy and systematics of Bretschneidera (Bretschneideraceae)

External morphology and anatomy of the flower and pollen of Bretschneidera sinensis Hemsl. are described to clarify the position of the family Bretschneideraceae relative to the Sapindales and the glucosinolate-producing families. Anatomical and micromorphological characters are investigated and sections are used to understand the structure of the flower. Observation of buds and sections reveal that the flower is obliquely monosymmetric, with the symmetry line running from one petal to a sepal. The upper petal shields the stamens and pistil and becomes positioned apically by the partial resupination of the pedicel. The octomerous androecium is characterized by variable empty positions which are related to the variable insertion of the three carpels. The loss of stamens is linked with a displacement of the remaining stamens. Floral anatomy demonstrates the presence of a nectary extending on the hypanthium from the base of the filaments to the base of the gynoecium. Details of floral anatomy are compared with members of Sapindaceae, Hippocastanaceae, Moringaceae, Akaniaceae, Tropaeolaceae and Capparaceae. Comparison with other characters supports a close relationship with Akaniaceae and Tropaeolaceae in an order Tropaeolales, in concordance with macromolecular results, either at the base of the glucosinolate clade, or in remote connection with the Sapindales. A number of floral anatomical characters with a strong phylogenetic signal are highlighted. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 29–45.     

基于转录组数据揭示4种兜兰的全基因组复制历史

多倍化或全基因组复制(WGD)是物种多样性发生的重要驱动力。目前, 在蕨类、菊科以及豆科等类群丰富的植物中已多次报道全基因组复制事件, 而兰科(Orchidaceae)全基因组复制事件报道极少, 与其丰富的物种多样性存在矛盾, 推测与前期样本量小但类群跨度大的研究策略有关。选取染色体数目变异丰富且多样性较高的兜兰属(Paphiopedilum)为兰科植物代表类群, 基于共享数据库中4种兜兰的转录组数据, 采用同义替换率(K_s)、系统发生基因组学以及相对定年的方法分析兜兰属植物是否发生过全基因组复制事件。结果表明, 在4种兜兰中均检测到3次全基因组复制事件, 分别发生在110.17-119.77 Mya (WGD1)、60.95-74.19 Mya (WGD2)和38.19-45.85 Mya (WGD3)。其中, WGD3为新检测到的全基因组复制事件, 推测其发生在杓兰亚科(Cypripedioideae)与姐妹类群分化后, 兜兰属与姐妹类群分化之前。此外, 3次全基因组复制事件发生后优先保留的基因拷贝在功能上多与当时的环境胁迫响应相关, 推测全基因组复制提高了兜兰属植物祖先对当时极端环境变化的适应性。     

Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution

The long-term evolutionary impacts of whole-genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologs) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnolog sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent “explosion” of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnolog divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial “wave” of rediploidization in the late Cretaceous (85–106 Ma). This was followed by a period of relative genomic stasis lasting 17–39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnolog divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.     

Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

Many large and economically important plant groups (e.g. Brassicaceae, Poaceae, Asteraceae, Fabaceae and Solanaceae) have had ancient whole genome duplications (WGDs) occurring near or at the time of their origins, suggesting that WGD contributed to the origin of novel key traits and drove species diversification. However, these large clades show phylogenetic asymmetries with a species-rich crown group and a species-poor sister clade, suggesting significant 'lag-times' between WGDs and radiations. The species-poor sister groups share many key traits, but are often restricted to the hypothesized center of origin for the larger clade. Thus, the ultimate success of the crown group does not only involve the WGD and novel key traits, but largely subsequent evolutionary phenomena including later migration events, changing environmental conditions and/or differential extinction rates.     

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Background  

Based on the observation of an increased number of paralogous genes in teleost fishes compared with other vertebrates and on the conserved synteny between duplicated copies, it has been shown that a whole genome duplication (WGD) occurred during the evolution of Actinopterygian fish. Comparative phylogenetic dating of this duplication event suggests that it occurred early on, specifically in teleosts. It has been proposed that this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish, notably by allowing the sub- or neo-functionalization of many duplicated genes.     

Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis

Mesopolyploid whole-genome duplication (WGD) was revealed in the ancestry of Australian Brassicaceae species with diploid-like chromosome numbers (n = 4 to 6). Multicolor comparative chromosome painting was used to reconstruct complete cytogenetic maps of the cryptic ancient polyploids. Cytogenetic analysis showed that the karyotype of the Australian Camelineae species descended from the eight ancestral chromosomes (n = 8) through allopolyploid WGD followed by the extensive reduction of chromosome number. Nuclear and maternal gene phylogenies corroborated the hybrid origin of the mesotetraploid ancestor and suggest that the hybridization event occurred ~6 to 9 million years ago. The four, five, and six fusion chromosome pairs of the analyzed close relatives of Arabidopsis thaliana represent complex mosaics of duplicated ancestral genomic blocks reshuffled by numerous chromosome rearrangements. Unequal reciprocal translocations with or without preceeding pericentric inversions and purported end-to-end chromosome fusions accompanied by inactivation and/or loss of centromeres are hypothesized to be the main pathways for the observed chromosome number reduction. Our results underline the significance of multiple rounds of WGD in the angiosperm genome evolution and demonstrate that chromosome number per se is not a reliable indicator of ploidy level.     

Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae

Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome­level genome for Cornus controversa. This was generated using high-fidelity plus Hi–C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.