Species Of Caryophyllales Research Articles

Medullary bundles in Caryophyllales: form, function, and evolution.

The occurrence of conducting vascular tissue in the pith (CVTP) of tracheophytes is noteworthy. Medullary bundles, one of the remarkable examples of CVTP, evolved multiple times across angiosperms, notably in the Caryophyllales. Yet, information on the occurrence of medullary bundles is fragmented, hampering our understanding of their structure-function relationships, and evolutionary implications. Using three plastid molecular markers (matK, rbcL, and rps16 intron), a phylogeny is constructed for 561 species of Caryophyllales, and anatomical data are assembled for 856 species across 40 families to investigate the diversity of medullary bundles, their function, evolution, and diversification dynamics. Additionally, correlated evolution between medullary bundles and successive cambia was tested. Medullary bundles are ancestrally absent in Caryophyllales and evolved in core and noncore families. They are structurally diverse (e.g. number, arrangement, and types of bundles) and functionally active throughout the plant's lifespan, providing increased hydraulic conductivity, especially in herbaceous plants. Acquisition of medullary bundles does not explain diversification rate heterogeneity but is correlated to a higher diversification rate. Disparate developmental pathways were found leading to rampant convergent evolution of CVTP in Caryophyllales. These findings indicate the diversification of medullary bundles and vascular tissues as another central theme for functional and comparative molecular studies in Caryophyllales.

Characterization of Rheum palmatum mitochondrial genome and comparative analysis among Caryophyllales species

Objective: This work aimed to report the first complete mitochondrial genome (mitogenome) of Rheum palmatum, summarize the features of Caryophyllales mitogenomes, and to reveal the potential of utilizing the mitogenomes of R. palmatum and other Caryophyllales species for inferring phylogenetic relationships and species identification. Methods: Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of R. palmatum. A variety of bioinformatics tools were employed to characterize the R. palmatum mitogenome, compare the reported mitogenomes in Caryophyllales and conduct phylogenetic analysis. Results: The mitogenome of R. palmatum was assembled into a single master circle of 302,993 bp, encoding 35 known protein-coding genes, 18 transfer RNA genes, and three ribosome RNA genes. A total of 249 long repeats and 49 simple sequence repeats were identified in this mitogenome. The sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 Mb. Among them, 23 mitogenomes were circular molecules, one was linear, and one consisted of relaxed circles, linear molecules, and supercoiled DNA. Out of the total mitogenomes, 11 were single-chromosome structure, whereas the remaining 14 were multi-chromosomal organizations. The phylogenetic analysis is consistent with both the Engler system (1964) and the Angiosperm Phylogeny Group III system. Conclusions: We obtained the first mitogenome of R. palmatum, which consists of a master circle. Mitogenomes in Caryophyllales have variable genome sizes and structures even within the same species. Circular molecules are still the dominant pattern in Caryophyllales. Single-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales, in contrast to previous studies. It is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales.

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5Gb with a scaffold N50 of 151 756 278bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences

Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.

DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates

The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital for safe usage, avoiding adulteration, and medicinal plant trading. DNA barcoding has shown to be a valuable molecular identification tool for medicinal plants, ensuring the safety and efficacy of plant materials of therapeutic significance. Using morphological characters in genera with closely related species, species delimitation is often difficult. Here, we evaluated the capability of the nuclear barcode ITS2 and plastid DNA barcodes rbcL and matK to identify 20 medicinally important plant species of Caryophyllales. In our analysis, we applied an integrative approach for species discrimination using pairwise distance-based unsupervised operational taxonomic unit “OTU picking” methods, viz., ABGD (Automated Barcode Gap Analysis) and ASAP (Assemble Species by Automatic Partitioning). Along with the unsupervised OTU picking methods, Supervised Machine Learning methods (SML) were also implemented to recognize divergent taxa. Our results indicated that ITS2 was more successful in distinguishing between examined species, implying that it could be used to detect the contamination and adulteration of these medicinally important plants. Moreover, this study suggests that the combination of more than one method could assist in the resolution of morphologically similar or closely related taxa.

Sodium hyperaccumulators in the Caryophyllales are characterized by both abnormally large shoot sodium concentrations and [Na]shoot/[Na]root quotients greater than unity.

Some Caryophyllales species accumulate abnormally large shoot sodium (Na) concentrations in non-saline environments. It is not known whether this is a consequence of altered Na partitioning between roots and shoots. This paper tests the hypotheses (1) that Na concentrations in shoots ([Na]shoot) and in roots ([Na]root) are positively correlated among Caryophyllales, and (2) that shoot Na hyperaccumulation is correlated with [Na]shoot/[Na]root quotients. Fifty two genotypes, representing 45 Caryophyllales species and 4 species from other angiosperm orders, were grown hydroponically in a non-saline, complete nutrient solution. Concentrations of Na in shoots and in roots were determined using inductively coupled plasma mass spectrometry (ICP-MS). Sodium concentrations in shoots and roots were not correlated among Caryophyllales species with normal [Na]shoot, but were positively correlated among Caryophyllales species with abnormally large [Na]shoot. In addition, Caryophyllales species with abnormally large [Na]shoot had greater [Na]shoot/[Na]root than Caryophyllales species with normal [Na]shoot. Sodium hyperaccumulators in the Caryophyllales are characterized by abnormally large [Na]shoot, a positive correlation between [Na]shoot and [Na]root, and [Na]shoot/[Na]root quotients greater than unity.

Endemic Atlantic Forest species of Caryophyllales as inhibitors of zucchini yellow mosaic virus and cucumber mosaic virus infection in Cucurbita pepo

In Brazil, zucchini ( Cucurbita pepo L.) is a socioeconomically important vegetable species that has been increasingly affected in recent years by the association between unbalanced abiotic conditions (environment) and the damage caused primarily by zucchini yellow mosaic virus (ZYMV, genus Potyvirus ) and cucumber mosaic virus (CMV, genus Cucumovirus ). Given the non-availability of C. pepo cultivars with effective resistance genes to minimize the damage, the most widely used management technique is the preventive, albeit inefficient, application of insecticides, aimed at controlling aphids, the vectors of this virus. Thus, the search for more effective and less environmentally harmful control methods has been the target of investigations. In this respect, the purpose of the present study was to assess the action of the extracts of four native Caryophyllales species, as inhibitors of infection by CMV and ZYMV in C. pepo , in addition to evaluating the possible induced resistance in this species. Fresh leaf extracts (LEs) of Guapira opposita (Vell.) Reitz and Pisonia ambigua Heimerl (Nyctaginaceae) and Gallesia integrifolia (Spreng.) Harms and Seguieria langsdorffii Moq. (Phytolaccaceae), previously assessed in the tobacco mosaic virus / Nicotiana glutinosa L. pathosystem, were submitted to progressive dilutions sprayed on cotyledonary C. pepo leaves 30 min before inoculation with CMV and ZYMV. Leaf extracts of G. integrifolia did not induce inhibition in any of the pathosystems assessed. Guapira opposita LEs inhibited the infection of plants inoculated with ZYMV below 50% but inhibited CMV infection by 70% at a concentration of 1:40. Given that leaf extracts of P. ambigua and S. langsdorffii induced high percentage inhibition, evident in the number of asymptomatic plants and confirmed by serological tests, these species were selected to assess induced resistance in pre-treatment experiments. The LEs were efficient in inhibiting ZYMV and CMV infection in C. pepo when applied up to 48 h before inoculation. The LEs of S. langsdorffii and G . opposita , also tested for this system, were efficient when applied up to 72 h before CMV inoculation. The LEs can be prepared from dry leaves and maintained at -20 °C for at least three years, conserving their inhibitory activity. These results expand the possibilities for producers and consumers alike in the sustainable management of the main zucchini viruses, without damaging the environment.

Endemic Atlantic Forest species of Caryophyllales as inhibitors of viral infection in zucchini

ABSTRACT In Brazil, zucchini (Cucurbita pepo) is a socioeconomically important vegetable affected by damage caused primarily by zucchini yellow mosaic virus (ZYMV). Although the occurrence of cucumber mosaic virus (CMV) is less frequent, in C. pepo ‘Caserta’ plants it can cause symptoms such as mottle, mosaic, leaf and fruit distortion, as well as reduced plant development. To minimize the damage, the most widely used management technique is the preventive, albeit inefficient, application of insecticides, aimed at controlling aphids, the vectors of this virus. Thus, the search for more effective and less environmentally harmful control methods has been the target of investigations. The purpose of the present study was to assess the action of the extracts of four native Caryophyllales species, as inhibitors of infection by CMV and ZYMV in C. pepo, in addition to evaluating the possible induced resistance in this species. Fresh leaf extracts (LEs) of Guapira opposita, Pisonia ambigua (Nyctaginaceae), Gallesia integrifolia and Seguieria langsdorffii (Phytolaccaceae), previously assessed in the tobacco mosaic virus / Nicotiana glutinosa pathosystem, were submitted to progressive dilutions sprayed on cotyledonary C. pepo leaves 30 min before inoculation with CMV and ZYMV. Leaf extracts of G. integrifolia did not induce inhibition in any of the pathosystems assessed. Guapira opposita LEs inhibited the infection of plants inoculated with ZYMV below 50% but inhibited CMV infection by 70% at a concentration of 1:40. Given that leaf extracts of P. ambigua and S. langsdorffii induced high percentage inhibition, evident in the number of asymptomatic plants and confirmed by serological tests, these species were selected to assess induced resistance in pre-treatment experiments. The LEs were efficient in inhibiting ZYMV and CMV infection in C. pepo when applied up to 48 h before inoculation. The LEs of S. langsdorffii and G. opposita, also tested for this system, were efficient when applied up to 72 h before CMV inoculation. The LEs can be prepared from dry leaves and maintained at -20°C for at least three years, conserving their inhibitory activity. These results expand the possibilities for producers and consumers alike in the sustainable management of the main zucchini viruses, without damaging the environment.

Complete Chloroplast Genome of Rhipsalis baccifera, the only Cactus with Natural Distribution in the Old World: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.

Rhipsalis baccifera is the only cactus that naturally occurs in both the New World and the Old World, and has thus drawn the attention of most researchers. The complete chloroplast (cp) genome of R. baccifera is reported here for the first time. The cp genome of R. baccifera has 122, 333 base pairs (bp), with a large single-copy (LSC) region (81,459 bp), SSC (23,531 bp) and two inverted repeat (IR) regions each 8530 bp. The genome contains 110 genes, with 73 protein-coding genes, 31 tRNAs, 4 rRNAs and 2 pseudogenes. Twelve genes have introns, with loss of introns being observed in, rpoc1 clpP and rps12 genes. 49 repeat sequences and 62 simple sequence repeats (SSRs) were found in the genome. Comparative analysis with eight species of the ACPT (Anacampserotaceae, Cactaceae, Portulacaceae, and Talinaceae) clade of the suborder Portulacineae species, showed that R. baccifera genome has higher number of rearrangements, with a 19 gene inversion in its LSC region representing the most significant structural change in terms of its size. Inversion of the SSC region seems common in subfamily Cactoideae, and another 6 kb gene inversion between rbcL- trnM was observed in R. baccifera and Carnegiea gigantea. The IRs of R. baccifera are contracted. The phylogenetic analysis among 36 complete chloroplast genomes of Caryophyllales species and two outgroup species supported monophyly of the families of the ACPT clade. R. baccifera occupied a basal position of the family Cactaceae clade in the tree. A high number of rearrangements in this cp genome suggests a larger number mutation events in the history of evolution of R. baccifera. These results provide important tools for future work on R. baccifera and in the evolutionary studies of the suborder Portulacineae.

Gain-of-function mutations in beet DODA2 identify key residues for betalain pigment evolution.

The key enzymatic step in betalain biosynthesis involves conversion of l-3,4-dihydroxyphenylalanine (l-DOPA) to betalamic acid. One class of enzymes capable of this is 3,4-dihydroxyphenylalanine 4,5-dioxygenase (DODA). In betalain-producing species, multiple paralogs of this gene are maintained. This study demonstrates which paralogs function in the betalain pathway and determines the residue changes required to evolve a betalain-nonfunctional DODA into a betalain-functional DODA. Functionalities of two pairs of DODAs were tested by expression in beets, Arabidopsis and yeast, and gene silencing was performed by virus-induced gene silencing. Site-directed mutagenesis identified amino acid residues essential for betalamic acid production. Beta vulgaris and Mirabilis jalapa both possess a DODA1 lineage that functions in the betalain pathway and at least one other lineage, DODA2, that does not. Site-directed mutagenesis resulted in betalain biosynthesis by a previously nonfunctional DODA, revealing key residues required for evolution of the betalain pathway. Divergent functionality of DODA paralogs, one clade involved in betalain biosynthesis but others not, is present in various Caryophyllales species. A minimum of seven amino acid residue changes conferred betalain enzymatic activity to a betalain-nonfunctional DODA paralog, providing insight into the evolution of the betalain pigment pathway in plants.

The complete chloroplast genome sequence of the folk medicinal and vegetable plant purslane (Portulaca oleracea L.)

ABSTRACTPortulaca oleracea is an important and widely distributed medicinal and edible plant that has great economic value in the medical and food industries. We sequenced the complete chloroplast (cp) genome of P. oleracea,whichis156,533 bp in length, including a pair of inverted repeats (IRs) of 25,501 bp separated by a large single copy (LSC) region of 87,436 bp and a small single copy (SSC) region of 18,095 bp. The genome contains 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. There are 40 repeat units and 111 simple sequence repeats (SSRs) in the genome. We also carried out complete cp genome comparison with other Caryophyllales species. The size, gene content, and structural organisation of P. oleracea are relatively conserved, but the genes ycf1 and ycf2 have larger introns. The simple sequence repeats (SSR) in the introns of ycf3, ycf1, atpB, rrn23 and ndhH have significant polymorphism. Comparisons of IR boundaries among 8 Caryophyllales species showed contraction and expansion. The complete cp genome sequence will contribute to a better understanding of the evolutionary mode of the cp genome and to the development of new markers for Caryophyllales classification.

Disparity, diversity, and duplications in the Caryophyllales.

The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.

Evolutionary origins of abnormally large shoot sodium accumulation in nonsaline environments within the Caryophyllales.

Summary The prevalence of sodium (Na)‐‘hyperaccumulator’ species, which exhibit abnormally large shoot sodium concentrations ([Na]shoot) when grown in nonsaline environments, was investigated among angiosperms in general and within the Caryophyllales order in particular.Shoot Na concentrations were determined in 334 angiosperm species, representing 35 orders, grown hydroponically in a nonsaline solution.Many Caryophyllales species exhibited abnormally large [Na]shoot when grown hydroponically in a nonsaline solution. The bimodal distribution of the log‐normal [Na]shoot of species within the Caryophyllales suggested at least two distinct [Na]shoot phenotypes within this order. Mapping the trait of Na‐hyperaccumulation onto the phylogenetic relationships between Caryophyllales families, and between subfamilies within the Amaranthaceae, suggested that the trait evolved several times within this order: in an ancestor of the Aizoaceae, but not the Phytolaccaceae or Nyctaginaceae, in ancestors of several lineages formerly classified as Chenopodiaceae, but not in the Amaranthaceae sensu stricto, and in ancestors of species within the Cactaceae, Portulacaceae, Plumbaginaceae, Tamaricaceae and Polygonaceae.In conclusion, a disproportionate number of Caryophyllales species behave as Na‐hyperaccumulators, and multiple evolutionary origins of this trait can be identified within this order.

The complete chloroplast genome sequence of Fagopyrum cymosum

Fagopyrum cymosum is a traditional medicinal plant. In this study, the complete chloroplast genome of Fagopyrum cymosum is presented. The total genome size is 160,546 bp in length, containing a pair of inverted repeats (IRs) of 32,598 bp, separated by large single copy (LSC) and small single copy (SSC) of 84,237 bp and 11,014 bp, respectively. Overall GC contents of the genome were 36.9%. The chloroplast genome harbors 126 annotated genes, including 91 protein coding genes, 29 tRNA genes, and six rRNA genes. Eighteen genes contain one or two introns. Phylogenetic analyses indicated a clear evolutionary relationship among species of Caryophyllales.

Production of betalains from callus and cell suspension cultures of Pereskia aculeata Miller, an unconventional leafy vegetable

Betalains are hydrophilic pigments found in Caryophyllales species, considered important as food colorants, a source of essential amino acids and as a phytomedicine. Pigmented friable calluses were induced from leafy cotyledon and hypocotyl segments of Pereskia aculeata Mill. cultivated on MS basal medium supplemented with 4-amino-3,5,6-trichloro-2-pyridinecarboxylic acid (Picloram). The highest callus biomass accumulation with reddish-pink pigmentation was achieved in cultures initiated from hypocotyl explants on medium supplemented with 10 µM Picloram. Instead of improving callus proliferation, the use of Picloram together with either 6-Benzylaminopurine or Kinetin induced cell oxidation. In contrast, the use of half-strength MS medium (½ MS) with Picloram supplementation resulted in the proliferation calli, and the pigments were characterized as betalains. Betalain production was enhanced on modified MS medium (30 mM total nitrogen and 1:4 or 1:8 ratio of NH4 +/NO3 −). Cell suspension cultures were established in liquid media after transfer of 1 g of betalain-producing calli which had been kept on ½ MS medium with 10 µM Picloram. After 15 days of culture, cell suspensions achieved eight-fold increase in biomass accumulation. Cell suspensions were maintained through three subcultures for 12–16 days through the exponential growth phase. The in vitro system that induced the highest betalain content and biomass accumulation was achieved from cell suspension cultures on modified MS (1:4 ratio NH4 +/NO3 −). Therefore, this study established an efficient protocol for betalain and biomass accumulation from callus and cell suspensions of P. aculeata Mill. under the same culture conditions, thus providing a new source of betalain production for commercial purposes.

Betacyanin biosynthetic genes and enzymes are differentially induced by (a)biotic stress in Amaranthus hypochondriacus.

An analysis of key genes and enzymes of the betacyanin biosynthetic pathway in Amaranthus hypochondriacus (Ah) was performed. Complete cDNA sequence of Ah genes coding for cyclo-DOPA 5-O glucosyltransferase (AhcDOPA5-GT), two 4, 5-DOPA-extradiol-dioxygenase isoforms (AhDODA-1 and AhDODA-2, respectively), and a betanidin 5-O-glucosyltransferase (AhB5-GT), plus the partial sequence of an orthologue of the cytochrome P-450 R gene (CYP76AD1) were obtained. With the exception AhDODA-2, which had a closer phylogenetic relationship to DODA-like genes in anthocyanin-synthesizing plants, all genes analyzed closely resembled those reported in related Caryophyllales species. The measurement of basal gene expression levels, in addition to the DOPA oxidase tyrosinase (DOT) activity, in different tissues of three Ah genotypes having contrasting pigmentation levels (green to red-purple) was determined. Additional analyses were performed in Ah plants subjected to salt and drought stress and to two different insect herbivory regimes. Basal pigmentation accumulation in leaves, stems and roots of betacyanic plants correlated with higher expression levels of AhDODA-1 and AhB5-GT, whereas DOT activity levels coincided with pigment accumulation in stems and roots and with the acyanic nature of green plants, respectively, but not with pigmentation in leaves. Although the abiotic stress treatments tested produced changes in pigment levels in different tissues, pigment accumulation was the highest in leaves and stems of drought stressed betacyanic plants, respectively. However, tissue pigment accumulation in stressed Ah plants did not always correlate with betacyanin biosynthetic gene expression levels and/or DOT activity. This effect was tissue- and genotype-dependent, and further suggested that other unexamined factors were influencing pigment content in stressed Ah. The results obtained from the insect herbivory assays, particularly in acyanic plants, also support the proposal that these genes could have functions other than betacyanin biosynthesis.

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases and shares an ancient genome triplication with other eudicot plants. Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet. Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.

Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales

Molecular phylogenetics has revolutionized our understanding of the Caryophyllales, and yet many relationships have remained uncertain, particularly at deeper levels. We have performed parsimony and maximum likelihood analyses on separate and combined data sets comprising nine plastid genes (∼12,000 bp), two nuclear genes (∼5000 bp), and the plastid inverted repeat (∼24,000 bp), giving a combined analyzed length of 42,006 bp for 36 species of Caryophyllales and four outgroups. We have recovered strong support for deep‐level relationships across the order. Two major subclades are well supported, the noncore and core Caryophyllales; Rhabdodendron followed by Simmondsia are sisters to the core Caryophyllales, Limeum and Stegnosperma are successive sisters to the “globular inclusion” clade, Gisekia is a distinct lineage well separated from Rivina within the “raphide” clade, and Rivina and Phytolaccaceae are disparate lineages, with Rivina sister to Nyctaginaceae. The placement of Sarcobatus and relationships within the portulacaceous cohort remain problematic. Within the latter, Halophytum is sister to Basellaceae and Didiereaceae, and the clade comprising Portulaca, Talinum, and Cactaceae is well supported. Classical hypotheses argued that the early Caryophyllales had evolved in open, dry, marginal environments at a time when pollinators were scarce, and, as such, the ancestral caryophyllid flower was wind pollinated with an undifferentiated perianth. We reevaluated these hypotheses in light of our phylogeny and find little support for anemophily as the ancestral condition; however, the early caryophyllid flower is suggested to have possessed an undifferentiated perianth. A subsequent minimum of nine origins of differentiated perianth is inferred. We discuss the evidence for independent origins of differentiated perianth and highlight the research opportunities that this pattern offers to the field of evolutionary developmental genetics.

Phylogeny of Amaranthaceae and Chenopodiaceae and the Evolution of C4Photosynthesis

A phylogenetic analysis of Chenopodiaceae and Amaranthaceae was carried out using sequence variation of the chloroplast gene rbcL. Our sampling included 108 species of these two families along with 29 species of Caryophyllales serving as outgroups. Phylogeny inferences with maximum parsimony and maximum likelihood indicate that the two families form a well‐supported monophyletic clade that is sister to Achatocarpaceae. Despite extensive sampling, we found that the relationship between Chenopodiaceae and Amaranthaceae remains unclear as a result of short and weakly supported basal branches. The clearly monophyletic Polycnemoideae (traditionally considered a subfamily of Chenopodiaceae) appear as sister to Amaranthaceae sensu stricto. Within Amaranthaceae, most major lineages inferred except Gomphrenoideae and Celosieae do not correspond to recognized subfamilies and tribes. Bosea and Charpentiera branch first in the Amaranthaceae. Within Chenopodiaceae, the genera of Betoideae occur in basal and largely unresolved positions. The remaining Chenopodiaceae are divided into three major clades of unclear relationship: Chenopodioideae (Atripliceae s.str., Chenopodieae I‐III); Corispermoideae (Corispermeae); and Salicornioideae (Haplopeplideae, Salicornieae), Suaedoideae (Suaedeae, Bienertieae), and Salsoloideae (Camphorosmeae, Sclerolaeneae, Salsoleae I‐II). The rbcL tree is discussed also with regard to historical classifications and morphological support for the major clades. The molecular results are used to elucidate the evolution of C4 photosynthesis in the two families. C4 photosynthesis has evolved independently at least three times in Amaranthaceae and at least 10 times in Chenopodiaceae. A survey of C4 leaf anatomy revealed 17 different leaf types that in most cases mark an independent origin of C4 photosynthesis. The application of a molecular clock indicates an age of C4 photosynthesis of 11.5–7.9 Ma in Atriplex (Chenopodioideae) and 21.6–14.5 Ma in subfamily Salsoloideae.

Sieve-element plastids ofCaryophyllales: Additional investigations with special reference to theCaryophyllaceae andMolluginaceae

The subtype PIII plastids found in 16 additional species ofCaryophyllales investigated here corroborate the homogeneity of this order with respect to the sieve-element plastids. While two new examples (Glinus, Allmania) which exhibit the rare presence of starch grains in the PIII-plastids are found, the restriction of the three forms of PIII-plastids to distinct taxa is maintained: PIIIf inChenopodiineae; PIII c′f inCaryophyllaceae (3 species added),Stegnospermataceae andAchatocarpaceae; PIII cf in all other families (among the 11 species investigated 5 fromMolluginaceae).