Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings

BACKGROUND

Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis.

RESULTS

The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments.

CONCLUSION

This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.

Chromosomal evolution in Cryptangieae Benth. (Cyperaceae): Evidence of holocentrism and pseudomonads

Cryptangieae has recently been revised based on morphology and molecular phylogeny, but cytogenetic data is still scarce. We conducted this study with the aim of investigating the occurrence of holocentric chromosomes and pseudomonads, as well as understanding the mode of chromosomal evolution in the tribe. We performed analyses of meiotic behavior, chromosome counts, and reconstruction of the ancestral state for the haploid number. We present novel cytogenetic data for eight potentially holocentric species: Cryptangium verticillatum, Krenakia junciforme, K. minarum, Lagenocarpus bracteosus, L. griseus, L. inversus, L. rigidus, and L. tenuifolius. Meiotic abnormalities were observed, with parallel spindles being particularly noteworthy. Intra-specific variations in chromosome number were not found, which may indicate an efficient genetic control for the elimination of abnormal nuclei. The inferred ancestral haploid number was n = 16, with dysploidy being the main evolutionary mechanism. At least five chromosomal fissions occurred in Krenakia (n = 21), followed by a further ascending dysploidy event in Lagenocarpus (n = 17). As proposed for Cyperaceae, it is possible that cladogenesis events in Cryptangieae were marked by numerical and structural chromosomal changes.

Chromosome-Scale Genome Assembly for Clubrush (Bolboschoenus planiculmis) Indicates a Karyotype with High Chromosome Number and Heterogeneous Centromere Distribution

Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration in wetland ecosystems. Previous studies have reported that the chromosomes of B. planiculmis are holocentric; i.e. they have kinetic activity along their entire length and carry multiple centromeres. This feature was suggested to lead to a rapid genome evolution through chromosomal fissions and fusions and participate to the diversification and ecological success of the Bolboschoenus genus. However, the specific mechanism remains uncertain, partly due to the scarcity of genetic information on Bolboschoenus. We present here the first chromosome-level genome assembly for B. planiculmis. Through the integration of high-quality long-read and short-read data, together with chromatin conformation using Hi-C technology, the ultimate genome assembly was 238.01 Mb with a contig N50 value of 3.61 Mb. Repetitive elements constituted 37.04% of the genome, and 18,760 protein-coding genes were predicted. The low proportion of long terminal repeat retrotransposons (∼9.62%) was similar to that reported for other Cyperaceae species. The Ks (synonymous substitutions per synonymous site) distribution suggested no recent large-scale genome duplication in this genome. The haploid assembly contained a large number of 54 pseudochromosomes with a small mean size of 4.10 Mb, covering most of the karyotype. The results of centromere detection support that not all the chromosomes in B. planiculmis have multiple centromeres, indicating more efforts are needed to fully reveal the specific style of holocentricity in cyperids and its evolutionary significance.

Inheritance and stacking effect of mutant ALS genes in Schoenoplectiella juncoides (Roxb.) Lye (Cyperaceae)

Schoenoplectiella juncoides, a noxious sedge weed in Japanese rice paddy, has two ALS genes, and ALS-inhibitor-resistant plants have a mutation in one of the ALS genes. The authors aimed (a) to quantitate the effect of the number of mutant alleles of ALS genes on whole-plant resistance of S. juncoides and (b) to clarify a mode of inheritance of the resistance by investigating resistance levels of the progenies of a hybrid between two S. juncoides plants with Trp574Leu substitution in different ALS. A dose-response analysis on the parental lines and the F1 population suggested that the two ALS genes contribute equally to whole-plant resistant levels. A dose-response study on the F2 population indicated that it could be classified into five groups based on the sensitivities to metsulfuron-methyl. The five groups (in ascending order of resistance levels) were considered to have zero, one, two, three, and four mutant alleles. The stacking effect of mutant alleles on resistance enhancement was more significant when the number of mutant alleles was low than when it was high; in other words, each additional mutant allele stacking increases plant resistance, but the effect saturates as the number of mutant alleles increases. A chi-square test supported that the segregation ratio of the five groups corresponds to 1:4:6:4:1 of Mendelian independence for the two ALS loci.

Molecular characterization of oleosin genes in Cyperus esculentus, a Cyperaceae plant producing oil in underground tubers

KEY MESSAGE

CeOLE genes exhibit a tuber-predominant expression pattern and their mRNA/protein abundances are positively correlated with oil accumulation during tuber development. Overexpression could significantly increase the oil content of tobacco leaves. Oleosins (OLEs) are abundant structural proteins of lipid droplets (LDs) that function in LD formation and stabilization in seeds of oil crops. However, little information is available on their roles in vegetative tissues. In this study, we present the first genome-wide characterization of the oleosin family in tigernut (Cyperus esculentus L., Cyperaceae), a rare example accumulating high amounts of oil in underground tubers. Six members identified represent three previously defined clades (i.e. U, SL and SH) or six out of seven orthogroups (i.e. U, SL1, SL2, and SH1-3) proposed in this study. Comparative genomics analysis reveals that lineage-specific expansion of Clades SL and SH was contributed by whole-genome duplication and dispersed duplication, respectively. Moreover, presence of SL2 and SH3 in Juncus effuses implies their appearance sometime before Cyperaceae-Juncaceae divergence, whereas SH2 appears to be Cyperaceae specific. Expression analysis showed that CeOLE genes exhibit a tuber-predominant expression pattern and transcript levels are considerably more abundant than homologs in the close relative Cyperus rotundus. Moreover, CeOLE mRNA and protein abundances were shown to positively correlate with oil accumulation during tuber development. Additionally, two dominant isoforms (i.e. CeOLE2 and -5) were shown to locate in LDs as well as the endoplasmic reticulum of tobacco (Nicotiana benthamiana) leaves, and are more likely to function in homo and heteromultimers. Furthermore, overexpression of CeOLE2 and -5 in tobacco leaves could significantly increase the oil content, supporting their roles in oil accumulation. These findings provide insights into lineage-specific family evolution and putative roles of CeOLE genes in oil accumulation of vegetative tissues, which facilitate further genetic improvement for tigernut.

Investigating the diversification of holocentromeric satellite DNA Tyba in Rhynchospora (Cyperaceae)

BACKGROUND AND AIMS

Satellite DNAs (satDNAs) are repetitive sequences composed by tandemly arranged, often highly homogenized units called monomers. Although satDNAs are usually fast evolving, some satDNA families can be conserved across species separated by several millions of years, probably because of their functional roles in the genomes. Tyba was the first centromere-specific satDNA described for a holocentric organism, until now being characterized for only eight species of the genus Rhynchospora Vahl. (Cyperaceae). Here, we characterized Tyba across a broad sampling of the genus, analysing and comparing its evolutionary patterns with other satDNAs.

METHODS

We characterized the structure and sequence evolution of satDNAs across a robust dadated phylogeny based on Hybrid Target-Capture Sequencing (hyb-seq) of 70 species. We mined the repetitive fraction for Tyba-like satellites to compare its features with other satDNAs and to construct a Tyba-based phylogeny for the genus.

KEY RESULTS

Our results show that Tyba is present in the majority of examined species of the genus, spanning four of the five major clades and maintaining intrafamily pairwise identity of 70.9% over 31 Myr. In comparison, other satellite families presented higher intrafamily pairwise identity but are phylogenetically restricted. Furthermore, Tyba sequences could be divided into 12 variants grouped into three different clade-specific subfamilies, showing evidence of traditional models of satDNA evolution, such as the concerted evolution and library models. Besides, a Tyba-based phylogeny showed high congruence with the hyb-seq topology. Our results show structural indications of a possible relationship of Tyba with nucleosomes, given its high curvature peaks over conserved regions and overall high bendability values compared with other non-centromeric satellites.

CONCLUSIONS

Overall, Tyba shows a remarkable sequence conservation and phylogenetic significance across the genus Rhynchospora, which suggests that functional roles might lead to long-term stability and conservation for satDNAs in the genome.

A non-homogeneous model of chromosome-number evolution to reveal shifts in the transition patterns across the phylogeny

Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.

Complex patterns of ploidy in a holocentric plant clade (Schoenus, Cyperaceae) in the Cape biodiversity hotspot

BACKGROUND AND AIMS

It is unclear how widespread polyploidy is throughout the largest holocentric plant family - the Cyperaceae. Because of the prevalence of chromosomal fusions and fissions, which affect chromosome number but not genome size, it can be impossible to distinguish if individual plants are polyploids in holocentric lineages based on chromosome count data alone. Furthermore, it is unclear how differences in genome size and ploidy levels relate to environmental correlates within holocentric lineages, such as the Cyperaceae.

METHODS

We focus our analyses on tribe Schoeneae, and more specifically the southern African clade of Schoenus. We examine broad-scale patterns of genome size evolution in tribe Schoeneae and focus more intensely on determining the prevalence of polyploidy across the southern African Schoenus by inferring ploidy level with the program ChromEvol, as well as interpreting chromosome number and genome size data. We further investigate whether there are relationships between genome size/ploidy level and environmental variables across the nutrient-poor and summer-arid Cape biodiversity hotspot.

KEY RESULTS

Our results show a large increase in genome size, but not chromosome number, within Schoenus compared to other species in tribe Schoeneae. Across Schoenus, there is a positive relationship between chromosome number and genome size, and our results suggest that polyploidy is a relatively common process throughout the southern African Schoenus. At the regional scale of the Cape, we show that polyploids are more often associated with drier locations that have more variation in precipitation between dry and wet months, but these results are sensitive to the classification of ploidy level.

CONCLUSIONS

Polyploidy is relatively common in the southern African Schoenus, where a positive relationship is observed between chromosome number and genome size. Thus, there may be a high incidence of polyploidy in holocentric plants, whose cell division properties differ from monocentrics.

Carex borealifujianica (Cyperaceae), a new species of the core Carex clade from Fujian, southeastern China

A new species, Carex borealifujianica Y.F. Lu & X.F. Jin (Cyperaceae, sect. Occlusae of core Carex clade) is described and illustrated from northern Fujian, China. In addition to morphological comparisons with its relatives, comparative micromorphology of utricles and achenes of seven species in Carex sect. Occlusae was examined. Micromorphology of utricles and achenes revealed the similarity of Carex borealifujianica and C. ligulata. Morphologically, this new species is similar to Carex ligulata in having lateral spikes remote and densely flowered, as well as utricles densely hispidulous, but differs in having 2 or 3 narrowly clavate staminate spikes, leaves 2.5–5 mm wide with sheaths sparsely pilose, and achenes emarginate at the apex. The phylogenetic analysis from two nuclear DNA regions (ETS and ITS) and two chloroplast DNA regions (matK and trnL-F) of 68 taxa resolved C. borealifujianica as a distinct species.

Functional ecology of congeneric variation in the leaf economics spectrum

Variation in resource availability can lead to phenotypic plasticity in the traits comprising the world-wide leaf economics spectrum (LES), potentially impairing plant function and complicating the use of tabulated values for LES traits in ecological studies. We compared 14 Carex (Cyperaceae) species in a factorial experiment (unshaded/shaded × sufficient/insufficient P) to analyze how changes in the network of allometric scaling relationships among LES traits influenced growth under favorable and resource-limited conditions. Changes in leaf mass per area (LMA) shifted the scaling relationships among LES traits expressed per unit area vs mass in ways that helped to sustain growth under resource limitation. Increases in area-normalized photosynthetic capacity and foliar nitrogen (N) were correlated with increased growth, offsetting losses associated with mass-normalized dark respiration and foliar N. These shifts increased the contributions to growth associated with photosynthetic N-use efficiency and the N : P ratio. Plasticity in LMA is at the hub of the functional role of the LES as an integrated and resilient complex system that balances the relationships among area- and mass-based aspects of gas exchange and foliar nutrient traits to sustain at least some degree of plant growth under differing availabilities of above- and below-ground resources.

Selection and validation of reference genes for target gene analysis with quantitative real-time PCR in the leaves and roots of Carex rigescens under abiotic stress

Carex rigescens is an ornamental turfgrass in northern China which has a relatively low maintenance cost and robust tolerance to many adverse environmental conditions, so it could be considered a new material for researching into plant stress resistance. However, suitable reference genes are vacant for obtaining reliable results in quantitative real-time PCR (qRT-PCR) analysis of C. rigescens in adversity research. In this study, we tested the expression stability of nine potential reference genes in leaves and roots under five different abiotic stress conditions, including cold, salt, heat, osmotic and cadmium (Cd). We then selected the best reference genes according to the analysis results calculated by three algorithmic programs (geNorm, NormFinder and BestKeeper) and used the RankAggreg package to merge the outputted data. The results showed that combinations of at least two reference genes should be used for reliable normalization except in heat-treated root samples, which require three reference genes. eIF-4α, GADPH, SAND and PEPKR1 and their combination were found to be the most stably expressed reference genes, while SAM, TUA-α and UPL7 were the three least stable reference genes among most of experimental samples. In addition, five stress-induced genes (Cu-Zn SOD, P5CS, LEA, GST, and APX) were chosen to verify the stability of the selected reference genes in various tissues and under various stress conditions. The results of this study will provide an important fundamental basis both for gene expression verification for transcriptomic and proteomic analyses and for gene expression analysis for future gene function research in C. rigescens.

Contrasting fine-scale genetic structure of two sympatric clonal plants in an alpine swampy meadow featured by tussocks

Tussocks are unique vegetation structures in wetlands. Many tussock species mainly reproduce by clonal growth, resulting in genetically identical offspring distributed in various spatial patterns. These fine-scale patterns could influence mating patterns and thus the long-term evolution of wetland plants. Here, we contribute the first genetic and clonal structures of two key species in alpine wetlands on the Qinghai–Tibet Plateau, Kobresia tibetica and Blysmus sinocompressus, using > 5000 SNPs identified by 2b-RAD sequencing. The tussock-building species, K. tibetica, has a phalanx (clumping) growth form, but different genets could co-occur within the tussocks, indicating that it is not proper to treat a tussock as one genetic individual. Phalanx growth does not necessarily lead to increased inbreeding in K. tibetica. B. sinocompressus has a guerilla (spreading) growth form, with the largest detected clone size being 18.32 m, but genets at the local scale tend to be inbred offspring. Our results highlight that the combination of clone expansion and seedling recruitment facilitates the contemporary advantage of B. sinocompressus, but its evolutionary potential is limited by the input genetic load of the original genets. The tussocks of K. tibetica are more diverse and a valuable genetic legacy of former well-developed wet meadows, and they are worthy of conservation attention.

Molecular phylogenetic study of Scleria subgenus Hypoporum (Sclerieae, Cyperoideae, Cyperaceae) reveals several species new to science

Scleria subgen. Hypoporum (Cyperaceae), with 68 species, is the second largest subgenus in Scleria. Species of this pantropically distributed subgenus generally occur in seasonally or permanently wet grasslands or on shallow soils over sandstone or lateritic outcrops, less often they can be found in (open) woodlands. Previous studies established the monophyly of the subgenus, but the relationships between the species remained uncertain. In this study, DNA sequence data of 61 taxa of Scleria subgen. Hypoporum, where possible represented by multiple accessions from across their distributional range, were obtained for four molecular markers: the coding chloroplast marker ndhF, the chloroplast intron rps16 and the nuclear ribosomal regions ETS and ITS. Phylogenetic trees were constructed using Bayesian inference and maximum likelihood approaches. A species tree was constructed to summarise the results. The results indicate the existence of three sections: the monotypic, pantropically occurring, Scleria sect. Lithospermae, a new section from central and south America containing two species, and Scleria sect. Hypoporum, also pantropically distributed, containing the remainder of the species of the subgenus. Relationships in the latter section are not fully resolved. However, three or four different clades can be distinguished supported by some morphological characters. Our results indicate at least six new species in Scleria sect. Hypoporum. The new section and species are described in a taxonomical treatment. Their morphology is compared with (morphologically) closely related species.

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

In the history of life, some phenotypes have been acquired several times independently, through convergent evolution. Recently, lots of genome-scale studies have been devoted to identify nucleotides or amino acids that changed in a convergent manner when the convergent phenotypes evolved. These efforts have had mixed results, probably because of differences in the detection methods, and because of conceptual differences about the definition of a convergent substitution. Some methods contend that substitutions are convergent only if they occur on all branches where the phenotype changed toward the exact same state at a given nucleotide or amino acid position. Others are much looser in their requirements and define a convergent substitution as one that leads the site at which they occur to prefer a phylogeny in which species with the convergent phenotype group together. Here, we suggest to look for convergent shifts in amino acid preferences instead of convergent substitutions to the exact same amino acid. We define as convergent shifts substitutions that occur on all branches where the phenotype changed and such that they correspond to a change in the type of amino acid preferred at this position. We implement the corresponding model into a method named PCOC. We show on simulations that PCOC better recovers convergent shifts than existing methods in terms of sensitivity and specificity. We test it on a plant protein alignment where convergent evolution has been studied in detail and find that our method recovers several previously identified convergent substitutions and proposes credible new candidates.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

Genetic analysis of Japanese and American specimens of Scirpus hattorianus suggests its introduction from North America

Scirpus hattorianus is a possible alien species in Japan, and a clarification of its unclear taxonomy is required to reveal its origin. It is not known whether the plants initially described from Japan represent the same species distributed in North America. To clarify the origin of the species, we attempted to sequence old specimens collected about 80 years ago using newly designed primer pairs specific for short sequences, including the variable sites. Chloroplast sequences of ndhF were compared among Japanese and North American S. hattorianus, and the closely related species, S. atrovirens, S. flaccidifolius, and S. georgianus. We succeeded in sequencing all samples, and two haplotypes were detected in S. hattorianus: one was unique to the species and the other, detected from specimens potentially collected from the same population as the types, was shared by both North American S. hattorianus and two closely related species, S. atrovirens and S. flaccidifolius. Our results suggest that Japanese S. hattorianus is an alien species that was introduced from North America at least twice.

Are holocentrics doomed to change? Limited chromosome number variation in Rhynchospora Vahl (Cyperaceae)

Karyotype evolution in species with non-localised centromeres (holocentric chromosomes) is usually very dynamic and associated with recurrent fission and fusion (also termed agmatoploidy/symploidy) events. In Rhynchospora (Cyperaceae), one of the most species-rich sedge genera, all analysed species have holocentric chromosomes and their numbers range from 2n = 4 to 2n = 84. Agmatoploidy/symploidy and polyploidy were suggested as the main processes in the reshuffling of Rhynchospora karyotypes, although testing different scenarios of chromosome number evolution in a phylogenetic framework has not been attempted until now. Here, we used maximum likelihood and model-based analyses, in combination with genome size estimation and ribosomal DNA distribution, to understand chromosome evolution in Rhynchospora. Overall, chromosome number variation showed a significant phylogenetic signal and the majority of the lineages maintained a karyotype of 2n = 10 (~48% of the species), the most likely candidate for the ancestral number of the genus. Higher and lower chromosome numbers were restricted to specific clades, whilst polyploidy and/or fusion/fission events were present in specific branches. Variation in genome size and ribosomal DNA site number showed no correlation with ploidy level or chromosome number. Although different mechanisms of karyotype evolution (polyploidy, fusion and fission) seem to be acting in distinct lineages, the degree of chromosome variation and the main mechanisms involved are comparable to those found in some monocentric genera and lower than expected for a holocentric genus.

Cut from the same cloth: The convergent evolution of dwarf morphotypes of the Carex flava group (Cyperaceae) in Circum-Mediterranean mountains

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5'trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution.

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.

Cd accumulation and subcellular distribution in two ecotypes of Kyllinga brevifolia Rottb as affected by Cd treatments

The Cadmium (Cd) accumulation capacity and subcellular distribution in the mining ecotype (ME) and non-mining ecotype (NME) of Kyllinga brevifolia Rottb were investigated in pot experiments. The results showed that average Cd contents in shoots of the two ecotypes of K. brevifolia were higher than those in roots, whereas Cd concentrations in roots were greater than those in shoots. Also, shoot Cd contents in NME of K. brevifolia were 1.65-45.45 times greater than those in ME when the plants were grown at 5, 25, 50, and 100 mg Cd kg(-1) soil. Moreover, Cd contents in the roots in NME were 1.75-45.45 times higher than those in ME. Subcellular distribution of Cd demonstrated that the majority of Cd in the two ecotypes of K. brevifolia was distributed in the cell walls and soluble fraction, and a small percentage of Cd existed in organelle fraction. In addition, proportions of Cd distributed in shoots and roots cell walls of NME were greater than those in ME. It could be assumed that compared with ME, NME of K. brevifolia has better Cd accumulation capacity, and the subcellular distribution of Cd might be one of the mechanisms to explain such phenomena.

Evolutionary divergence of β-expansin structure and function in grasses parallels emergence of distinctive primary cell wall traits

Expansins are wall-loosening proteins that promote the extension of primary cell walls without the hydrolysis of major structural components. Previously, proteins from the EXPA (α-expansin) family were found to loosen eudicot cell walls but to be less effective on grass cell walls, whereas the reverse pattern was found for EXPB (β-expansin) proteins obtained from grass pollen. To understand the evolutionary and structural bases for the selectivity of EXPB action, we assessed the extension (creep) response of cell walls from diverse monocot families to EXPA and EXPB treatments. Cell walls from Cyperaceae and Juncaceae (families closely related to grasses) displayed a typical grass response ('β-response'). Walls from more distant monocots, including some species that share with grasses high levels of arabinoxylan, responded preferentially to α-expansins ('α-response'), behaving in this regard like eudicots. An expansin with selective activity for grass cell walls was detected in Cyperaceae pollen, coinciding with the expression of genes from the divergent EXPB-I branch that includes grass pollen β-expansins. The evolutionary origin of this branch was located within Poales on the basis of phylogenetic analyses and its association with the 'sigma' whole-genome duplication. Accelerated evolution in this branch has remodeled the protein surface in contact with the substrate, potentially for binding highly substituted arabinoxylan. We propose that the evolution of the divergent EXPB-I group made a fundamental change in the target and mechanism of wall loosening in the grass lineage possible, involving a new structural role for xylans and the expansins that target them.

Radiation and repeated transoceanic dispersal of Schoeneae (Cyperaceae) through the southern hemisphere

PREMISE OF THE STUDY

The broad austral distribution of Schoeneae is almost certainly a product of long-distance dispersal. Owing to the inadequacies of existing phylogenetic data and a lack of rigorous biogeographic analysis, relationships within the tribe remain poorly resolved and its pattern of radiation and dispersal uncertain. We employed an expanded sampling of taxa and markers and a rigorous analytic approach to address these limitations. We evaluated the roles of geography and ecology in stimulating the initial radiation of the group and its subsequent dispersal across the southern hemisphere.

METHODS

A dated tree was reconstructed using reversible-jump Markov chain Monte Carlo (MCMC) with a polytomy prior and molecular dating, applied to data from two nuclear and three cpDNA regions. Ancestral areas and habitats were inferred using dispersal-extinction-cladogenesis models.

KEY RESULTS

Schoeneae originated in Australia in the Paleocene. The existence of a "hard" polytomy at the base of the clade reflects the rapid divergence of six principal lineages ca. 50 Ma, within Australia. From this ancestral area, Schoeneae have traversed the austral oceans with remarkable frequency, a total of 29 distinct dispersal events being reported here. Dispersal rates between landmasses are not explicable in terms of the geographical distances separating them. Transoceanic dispersal generally involved habitat stasis.

CONCLUSIONS

Although the role of dispersal in explaining global distribution patterns is now widely accepted, the apparent ease with which such dispersal may occur has perhaps been under-appreciated. In Schoeneae, transoceanic dispersal has been remarkably frequent, with ecological opportunity, rather than geography, being most important in dictating dispersal patterns.

Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae)

PREMISE OF THE STUDY

Understanding heterogeneity in species richness across the tree of life is a challenge in evolutionary biology. The sedge family, Cyperaceae, is classified into tribes that exhibit a roughly 200-fold range in species richness. The Cyperaceae present an excellent case study in the determinants of species richness within higher-level taxa.

METHODS

We used secondary calibration based on prior studies and fossils from a rush (Juncaceae) and five sedges to calibrate two previously published Cyperaceae phylogenies, then compared our results to previous molecular clock analyses. We used an information-theoretic approach to identify shifts in lineage diversification rates and phylogenetic generalized least squares to fit alternative models of clade species richness.

KEY RESULTS

Our results suggest a late Cretaceous origin for Cyperaceae (76-89 mya). The inferred 0.06 speciation events Ma(-1) is comparable to overall diversification rates in the order Poales but faster than angiosperm background rates. A threefold increase in diversification rate at the base of the species-rich SDC+FAEC clade is correlated with climatic changes during the Paleocene-Eocene boundary (ca. 55 mya). The greater driver of among-clade variance in species richness, however, is clade age (simple R(2) = 0.334, P = 0.0006).

CONCLUSIONS

Although shifts in diversification rates play a role in the generation of heterogeneous patterns of species richness, our study demonstrates that variance in clade age alone explains ca. 33% of among-clade variation in species diversity, which stands in contrast to the general pattern for angiosperms.

Characterization of sulfonylurea-resistant Schoenoplectus juncoides having a target-site Asp(376)Glu mutation in the acetolactate synthase

Schoenoplectus juncoides, a noxious weed for paddy rice, is known to become resistant to sulfonylurea (SU) herbicides by a target-site mutation in either of the two acetolactate synthase (ALS) genes (ALS1 and ALS2). SU-resistant S. juncoides plants having an Asp376Glu mutation in ALS2 were found from a paddy rice field in Japan, but their resistance profile has not been quantitatively investigated. In this study, dose-response of the SU-resistant accession was compared with that of a SU-susceptible accession at in vivo whole-plant level as well as at in vitro enzymatic level. In whole-plant tests, resistance factors (RFs) based on 50% growth reduction (GR50) for imazosulfuron (ISF), bensulfuron-methyl (BSM), metsulfuron-methyl (MSM), bispyribac-sodium (BPS), and imazaquin (IMQ) were 176, 40, 14, 5.2 and 1.5, respectively. Thus, the accession having an Asp376Glu mutation in ALS2 was highly resistant to the three SU herbicides and moderately resistant to BPS, but was not substantially resistant to IMQ. This is slightly different from the earlier results reported from other weeds with an Asp376Glu mutation, in which the mutation confers resistance to broadly all the chemical classes of ALS-inhibiting herbicides. In enzymatic tests, ALS2 of S. juncoides was expressed in E. coli; the resultant ALS2 was subjected to an in vitro assay. RFs of the mutated ALS2 based on 50% enzymatic inhibition (I50) for ISF, BSM, MSM, BPS, and IMQ were 3699, 2438, 322, 80, and 4.8, respectively. The RFs of ALS2 were highly correlated with those of the whole-plant; this suggests that the Asp376Glu mutation in ALS2 is a molecular basis for the whole-plant resistance. The presence of two ALS genes in S. juncoides can at least partially explain why the whole-plant RFs were less than those of the expressed ALS2 enzymes.

Floral ontogeny and gene protein localization rules out euanthial interpretation of reproductive units in Lepironia (Cyperaceae, Mapanioideae, Chrysitricheae)

BACKGROUND AND AIMS

In the sedge subfamily Mapanioideae there are considerable discrepancies between the standard trimerous monocot floral architecture expected and the complex floral and inflorescence morphologies seen. Decades of debate about whether the basic reproductive units are single flowers or pseudanthia have not resolved the question. This paper evaluates current knowledge about Mapaniid reproductive structures and presents an ontogenetic study of the Mapaniid genus Lepironia with the first floral protein expression maps for the family, localizing the products of the APETALA1/FRUITFULL-like (AP1/FUL) MADS-box genes with the aim of shedding light on this conundrum.

METHODS

A range of reproductive developmental stages, from spikelet primordia through to infructescence material, were processed for anatomical and immunohistochemical analyses.

KEY RESULTS

The basic reproductive unit is subtended by a bract and possesses two prophyll-like structures, the first organs to be initiated on the primordium, which grow rapidly, enclosing two whorls of initiating leaf-like structures with intervening stamens and a central gynoecium, formed from an annular primordium. The subtending bract and prophyll-like structures possess very different morphologies from that of the internal leaf-like structures and do not show AP1/FUL-like protein localization, which is otherwise strongly localized in the internal leaf-like structures, stamens and gynoecia.

CONCLUSIONS

Results support the synanthial hypothesis as the evolutionary origin of the reproductive unit. Thus, the basic reproductive unit in Lepironia is an extremely condensed pseudanthium, of staminate flowers surrounding a central terminal pistillate female flower. Early in development the reproductive unit becomes enclosed by a split-prophyll, with the whole structure subtended by a bract.

Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges

We aim to present phylogenetic major groups within the subfamily Cyperoideae (Cyperaceae) on the basis of three molecular data sets; nuclear ribosomal internal transcribed spacer and 5.8S ribosomal RNA region, the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene, and trnL intron and trnL-F intergenic spacer. Three molecular data and two combined data sets were used to obtain robust and detailed phylogenetic trees by using maximum parsimony and Bayesian inference, respectively. We analyzed 81 genera and 426 species of Cyperaceae, including Korean species. We suggest one early diverged group (EDGs), and two major clades (FAEC and SDC) within the subfamily Cyperoideae. And the clade EDGs comprises six tribes (Schoeneae, Bisboeckelereae, Sclerieae, Cryptangieae, Trilepideae, and Rhynchosporeae) at the basal nodes of Cyperoideae. The FAEC clade (posterior probability [PP]/bootstrap value [BS] = 1.00/85) comprises four tribes (Fuireneae, Abildgaardieae, Eleocharideae, Cypereae), and the SDC clade (PP/BS = 1.00/86) comprises three tribes (Scirpeae, Dulichieae, Cariceae). These three clades used for phylogenetic groups in our study will be useful for establishing the major lineage of the sedge family. The phylogeny of Korean sedges was also investigated within the whole phylogeny of Cyperaceae. The 20 genera of Korean sedges were placed in 10 tribes forming 14 clades.

Characterization and cross application of novel microsatellite markers for a rare sedge, Lepidosperma gibsonii (Cyperaceae)

PREMISE OF THE STUDY

Ten polymorphic microsatellite loci for the rare sword sedge Lepidosperma gibsonii (Cyperaceae) were characterized for the future study of population structure, hybridization, and clonality.

METHODS AND RESULTS

Twenty samples from each of three populations were screened with the markers to assess genetic variation. Observed population heterozygosities ranged from 0.35 to 1.00, and number of alleles observed per locus ranged from eight to 23. No departures from Hardy-Weinberg equilibrium were detected for any locus in any population. Single samples from 14 species were screened to examine the transferability of the microsatellites to other species of Lepidosperma. At least eight out of 10 loci amplified in all species tested.

CONCLUSIONS

These loci will be useful for studying genetic variation, hybridization, dispersal, and breeding systems in Lepidosperma, a ubiquitous element of the flora of southern Australia.

Distribution of 5S and 45S rDNA sites in plants with holokinetic chromosomes and the "chromosome field" hypothesis

Secondary constrictions or 45S rDNA sites are commonly reported to be located mainly in the terminal regions of the chromosomes. This distribution has been assumed to be related to the existence of a "chromosome field" lying between the centromere and the telomere, an area in which certain cytogenetic events may predominantly occur. If this hypothesis is true this distribution should not be observed in holokinetic chromosomes, as they do not have a localized centromere. In order to evaluate this hypothesis, a comparative study was made of the distributions of 5S and 45S rDNA sites using fluorescence in situ hybridization in representatives of the genera Eleocharis, Diplacrum, Fimbristylis, Kyllinga and Rhynchospora, all of which belong to the family Cyperaceae. The numbers of sites per diploid chromosome complement varied from 2 to ∼10 for 5S rDNA, and from 2 to ∼45 for 45S rDNA. All of the 11 species analyzed had terminally located 45S rDNA sites on the chromosomes whereas the 5S rDNA sites also generally had terminal distributions, except for the Rhynchospora species, where their position was almost always interstitial. These results, together with other previously published data, suggest that the variation in the number and position of the rDNA sites in species with holokinetic chromosomes is non-random and similar to that reported for species with monocentric chromosomes. Therefore, the predominant terminal position of the 45S rDNA sites does not appear to be influenced by the centromere-telomere polarization as suggested by the "chromosome field" hypothesis. Additionally, the hybridization of 5S and 45S rDNA sites provides interesting markers to distinguish several chromosomes on the rather symmetrical karyotypes of Cyperaceae.

Isolation and characterization of microsatellite loci in Schoenoplectus juncoides (Cyperaceae)1

PREMISE OF THE STUDY

We developed microsatellite markers for Schoenoplectus juncoides, a weed found in rice paddy fields in eastern Asia.

METHODS AND RESULTS

Ten dinucleotide microsatellite loci were isolated, and genetic variability within and among local populations were characterized. The number of alleles per locus ranged from 2 to 6 with a mean of 3.6. Expected heterozygosity per locus ranged from 0.067 to 0.471, whereas observed heterozygosity showed much lower values ranging from 0.000 to 0.083. Most of the loci showed significant deviation from Hardy-Weinberg equilibrium and high inbreeding coefficient values (0.525-1.000).

CONCLUSIONS

All the 10 microsatellite loci displayed polymorphism within and among populations. These loci are useful genetic markers for microevolution and ecological studies of S. juncoides populations.

Spikelet structure and development in Cyperoideae (Cyperaceae): a monopodial general model based on ontogenetic evidence

BACKGROUND AND AIMS

In Cyperoideae, one of the two subfamilies in Cyperaceae, unresolved homology questions about spikelets remained. This was particularly the case in taxa with distichously organized spikelets and in Cariceae, a tribe with complex compound inflorescences comprising male (co)florescences and deciduous female single-flowered lateral spikelets. Using ontogenetic techniques, a wide range of taxa were investigated, including some controversial ones, in order to find morphological arguments to understand the nature of the spikelet in Cyperoideae. This paper presents a review of both new ontogenetic data and current knowledge, discussing a cyperoid, general, monopodial spikelet model.

METHODS

Scanning electron microscopy and light microscopy were used to examine spikelets of 106 species from 33 cyperoid genera.

RESULTS

Ontogenetic data presented allow a consistent cyperoid spikelet model to be defined. Scanning and light microscopic images in controversial taxa such as Schoenus nigricans, Cariceae and Cypereae are interpreted accordingly.

CONCLUSIONS

Spikelets in all species studied consist of an indeterminate rachilla, and one to many spirally to distichously arranged glumes, each subtending a flower or empty. Lateral spikelets are subtended by a bract and have a spikelet prophyll. In distichously organized spikelets, combined concaulescence of the flowers and epicaulescence (a newly defined metatopic displacement) of the glumes has caused interpretational controversy in the past. In Cariceae, the male (co)florescences are terminal spikelets. Female single-flowered spikelets are positioned proximally on the rachis. To explain both this and the secondary spikelets in some Cypereae, the existence of an ontogenetic switch determining the development of a primordium into flower, or lateral axis is postulated.

Characterisation of ALS genes in the polyploid species Schoenoplectus mucronatus and implications for resistance management

BACKGROUND

The polyploid weed Schoenoplectus mucronatus (L.) Palla has evolved target-site resistance to ALS-inhibiting herbicides in Italian rice crops. Molecular and genetic characterisation of the resistance mechanism is relevant to the evolution and management of herbicide resistance. The authors aimed (a) to study the organisation of the target-site loci in two field-selected S. mucronatus populations with different cross-resistance patterns, (b) to identify the mutations endowing resistance to ALS inhibitors and determine the role of these mutations by using transgenesis and (c) to analyse the implications for the management of the S. mucronatus populations.

RESULTS

Two complete ALS genes (ALS1 and ALS2) having an intron and a third partial intronless ALS gene (ALS3) were identified. The presence of multiple ALS genes was confirmed by Southern blot analyses, and ALS loci were characterised by examining cytosine methylation. In S. mucronatus leaves, the transcripts of ALS1, ALS2 and ALS3 were detected. Two mutations endowing resistance (Pro(197) to His and Trp(574) to Leu) were found in both resistant populations, but at different frequencies. Tobacco plants transformed with the two resistant alleles indicated that the Pro(197)-to-His substitution conferred resistance to SU and TP herbicides, while the allele with the Trp(574)-to-Leu substitution conferred cross-resistance to SU, TP, IMI and PTB herbicides.

CONCLUSION

Schoenoplectus mucronatus has multiple ALS genes characterised by methylated sites that can influence the expression profile. The two mutated alleles proved to be responsible for ALS resistance. At population level, the resistance pattern depends on the frequency of various resistant genotypes, and this influences the efficacy of various ALS-inhibiting herbicides.

Resistance mechanism to bensulfuron-methyl in biotypes of Scirpus mucronatus L. collected in Chilean rice fields

Two biotypes of Scirpus mucronatus not controlled with the herbicide bensulfuron-methyl in rice fields were characterized by using field, greenhouse, and laboratory techniques. Seeds were collected in two rice areas [Parral (R1) and Linares (R2)], where bensulfuron-methyl at 150 g ha(-1) did not control S. mucronatus. A third seed sample of S. mucronatus susceptible (S) to bensulfuron-methyl was collected in an area from Chile. The dose-response studies confirmed resistance to bensulfuron-methyl in R1 and R2 S. mucronatus biotypes; ratios (R/S) of the ED(50) values of resistant to susceptible plants were 1719 and 1627 for R1 and R2, respectively. The biotype R1 also showed strong cross-resistance (ratios ranging from 1719 to 43) to sulfonylureas (bensulfuron-methyl, cyclosulfamuron, ethoxysulfuron, imazosulfuron, and pyrazosulfuron-ethyl) and imidazolinone (imazamox) and a weak cross-resistance (ratio of 1.705) to pyrimidinyloxybenzoates (bispyribac-sodium), all ALS inhibiting herbicides used in rice. Absorption, translocation, and metabolism results did not explain the differences in susceptibility among biotypes. The in vitro assays confirmed cross-resistance to all ALS inhibitors tested and the level of cross resistance was bensulfuron-methyl > imazosulfuron ≫ cyclosulfamuron ≫ pyrazosulfuron-ethyl ≫ ethoxysulfuron > imazamox ≫ bispiribac-sodium. Molecular studies demonstrated that the Pro197His amino acid substitution on the ALS enzyme could explain the loss of affinity for the ALS-inhibiting herbicides.

Genetic diversity of five Kobresia species along the eastern Qinghai-Tibet plateau in China

Plants of the genus Kobresia are alpine grass species of high ecological and economic importance. Vegetative growth is the dominant means of reproduction for the Kobresia. Studies suggest that substantial vegetative growth can reduce genetic diversity and renders populations less able to buffer changing and extreme conditions. Kobresia are dominant species in the Qinghai-Tibet plateau in China where they face harsh conditions and frequent disturbance. The genetic diversity of five Kobresia species (K. humilis, K. royleana, K. kansuensis , K. tibetica and K. setchwanensis) from the Qinghai-Tibet plateau was assessed. The results reveal high genetic diversity at the population level for all of the species and there does not appear to be a relationship between altitude and genetic diversity. AMOVA analysis shows that most genetic variability resides among individuals within populations, whereas only a minor portion is found among populations. Of the five species, K. royleana and K. kansuensis have the highest levels of gene flow and the lowest genetic differentiation. While K. setchwanensis has the lowest gene flow and the greatest genetic differentiation. The level of gene flow between populations and the mating system play a critical role in the genetic structure of these Kobresia populations. Despite the predominance of vegetative growth enough sexual reproduction occurs to maintain the relatively high genetic diversity in Kobresia populations.

A Bayesian model of AFLP marker evolution and phylogenetic inference

Amplified Fragment Length Polymorphism (AFLP) markers are formed by selective amplification of DNA fragments from digested total genomic DNA. The technique is popular because it is a relatively inexpensive way to produce large numbers of reproducible genetic markers. In this paper, we describe a Bayesian approach to modeling AFLP marker evolution by nucleotide substitution and an MCMC approach to estimate phylogeny from AFLP marker data. We demonstrate the method on species in Carex section Ovales, a group of sedges common in North America. We compare the results of our analysis with a clustering method based on Nei and Li's restriction-site distance and a two-state Bayesian analysis using MrBayes.

Evolutionary Ecology: When Relatives Cannot Live Together

The importance of competition in determining species coexistence has been much debated. A phylogenetic analysis of sedges indicates that competitive exclusion may inhibit co-occurrence among closely related species, but not among more distant relatives.

Phylogenetic Relatedness Limits Co‐occurrence at Fine Spatial Scales: Evidence from the Schoenoid Sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa

Species co-occurrence at fine spatial scales is expected to be nonrandom with respect to phylogeny because of the joint effects of evolutionary (trait convergence and conservatism) and ecological (competitive exclusion and habitat filtering) processes. We use data from 11 existing vegetation surveys to test whether co-occurrence in schoenoid sedge assemblages in the Cape Floristic Region shows significant phylogenetic structuring and to examine whether this changes with the phylogenetic scale of the analysis. We provide evidence for phylogenetic overdispersion in an alliance of closely related species (the reticulate-sheathed Tetraria clade) using both quantile regression analysis and a comparison between the mean observed and expected phylogenetic distances between co-occurring species. Similar patterns are not evident when the analyses are performed at a broader phylogenetic scale. Examination of six functional traits suggests a general pattern of trait conservatism within the reticulate-sheathed Tetraria clade, suggesting a potential role for interspecific competition in structuring co-occurrence within this group. We suggest that phylogenetic overdispersion of communities may be common throughout many of the Cape lineages, since interspecific interactions are likely intensified in lineages with large numbers of species restricted to a small geographic area, and we discuss the potential implications for patterns of diversity in the Cape.

Mitotic Microtubule Development and Histone H3 Phosphorylation in the Holocentric Chromosomes of Rhynchospora Tenuis (Cyperaceae)

In the present work we report the phosphorylation pattern of histone H3 and the development of microtubular structures using immunostaining techniques, in mitosis of Rhynchospora tenuis (2n = 4), a Cyperaceae with holocentric chromosomes. The main features of the holocentric chromosomes of R. tenuis coincide with those of other species namely: the absence of primary constriction in prometaphase and metaphase, and the parallel separation of sister chromatids at anaphase. Additionaly, we observed a highly conserved chromosome positioning at anaphase and early telophase sister nuclei. Four microtubule arrangements were distinguished during the root tip cell cycle. Interphase cells showed a cortical microtubule arrangement that progressively forms the characteristic pre-prophase band. At prometaphase the microtubules were homogeneously distributed around the nuclear envelope. Metaphase cells displayed the spindle arrangement with kinetochore microtubules attached throughout the entire chromosome extension. At anaphase kinetochoric microtubules become progressively shorter, whereas bundles of interzonal microtubules became increasingly broader and denser. At late telophase the microtubules were observed equatorially extended beyond the sister nuclei and reaching the cell wall. Immunolabelling with an antibody against phosphorylated histone H3 revealed the four chromosomes labelled throughout their entire extension at metaphase and anaphase. Apparently, the holocentric chromosomes of R. tenuis function as an extended centromeric region both in terms of cohesion and H3 phosphorylation.

A phylogeny of the schoenoid sedges (Cyperaceae: Schoeneae) based on plastid DNA sequences, with special reference to the genera found in Africa

Despite its large size (about 700 species), the australy-centred sedge tribe Schoeneae has received little explicit phylogenetic study, especially using molecular data. As a result, generic relationships are poorly understood, and even the monophyly of the tribe is open to question. In this study, plastid DNA sequences (rbcL, trnL-trnF, and rps16) drawn from a broad array of Schoeneae are analysed using Bayesian and parsimony-based approaches to infer a framework phylogeny for the tribe. Both analytical methods broadly support the monophyly of Schoeneae, Bayesian methods doing so with good support. Within the schoenoid clade, there is strong support for a series of monophyletic generic groupings whose interrelationships are unclear. These lineages form a large polytomy at the base of Schoeneae that may be indicative of past radiation, probably following the fragmentation of Gondwana. Most of these lineages contain both African and non-African members, suggesting a history of intercontinental dispersal. The results of this study clearly identify the relationships of the African-endemic schoenoid genera and demonstrate that the African-Australasian genus Tetraria, like Costularia, is polyphyletic. This pattern is morphologically consistent and suggests that these genera require realignment.

Floral ontogeny in Scirpus, Eriophorum and Dulichium (Cyperaceae), with special reference to the perianth

BACKGROUND AND AIMS

Based on molecular phylogenetic analysis, it has been suggested recently that the Cyperaceae comprises only two subfamilies: the Mapanioideae and the Cyperoideae. In most flowers of the Cyperoideae, the whorl of inner stamens is reduced, resulting in tetracyclic flowers. In the more primitive (scirpoid) genera within the Cyperoideae, the perianth consists of two polysymmetric whorls, whereas the perianth parts in the more derived genera have been subject to modifications and/or reduction. Comparative studies of the many silky hairs of Eriophorum and of the eight bristles of Dulichium have given rise to much discussion about their homology.

METHODS

The spikelet and floral ontogeny in freshly collected inflorescences was investigated using scanning electron microscopy.

KEY RESULTS

Complete floral ontogenies are presented for Scirpus sylvaticus L., Eriophorum latifolium Hoppe and Dulichium arundinaceum (L.) Britton, with special reference to the perianth. The results in S. sylvaticus confirm the trimerous monocot-like organization of the flower. It is used as a model for floral development in Cyperoideae. In the early developmental stages, the androecium of E. latifolium is surrounded by a massive perigonial primordium, from which the many hair-like bristles originate. Consequently, the stamens develop among the hair primordia, more or less simultaneously. The hairs are arranged in whorls, which develop centripetally. The development of the perianth in D. arundinaceum starts with the formation of three initial perianth primordia opposite the stamens. Subsequently, two more abaxial bristle primordia, alternating with the stamens, originate simultaneously with the appearance of three adaxial bristle primordia in the zone where an adaxial inner perianth primordium is expected.

CONCLUSIONS

The floral development in E. latifolium and D. arundinaceum can be considered as variations upon the scirpoid floral ontogenetic theme.

Phylogenetic analysis of the nuclear alcohol dehydrogenase (Adh) gene family in Carex section Acrocystis (Cyperaceae) and combined analyses of Adh and nuclear ribosomal ITS and ETS sequences for inferring species relationships

We analyzed sequence variation for the alcohol dehydrogenase (Adh) gene family in Carex section Acrocystis (Cyperaceae) to reconstruct Adh gene trees for Acrocystis species and to characterize the structure of the Adh gene family in Carex. Two Adh loci were included with ITS and ETS sequences in a combined Bayesian inference analysis of Carex section Acrocystis to gain a better understanding of species relationships in the section. In addition, we comment on how the results presented here contribute to our knowledge of the birth-death process of the Adh gene family in angiosperms. It appears that the structure of the Adh gene family in Carex is complex with possibly six loci present in the gene family. Additionally, variation among Acrocystis species within loci is quite low, and there is little phylogenetic resolution in the individual datasets. Bayesian inference analysis of the combined ITS, ETS, Adh1, and Adh2 datasets resulted in a moderately well-supported phylogenetic hypothesis of relationships in the section which is discussed in relation to previous hypotheses of relationships.

Genetic Diversity in Cymophyllus fraserianus (Cyperaceae), a Rare Monotypic Genus

Cymophyllus fraserianus (Fraser's sedge) is a rare perennial evergreen herb found in late-successional forest communities in the Appalachian Mountains of the U.S. Genetic diversity was assessed at 19 allozyme loci for 12 populations sampled from the southern and central portions of the range of this primitive monotypic genus. Species variation was comparable to that found for other narrowly distributed species, although mean population genetic diversity was somewhat higher. Sixteen of the 19 loci (84%) were polymorphic, with a mean of 46% polymorphic within populations. On average, 2.7 alleles were detected per polymorphic locus. Genetic diversity within populations (Hep) averaged 0.113, whereas species' genetic diversity (Hes) was 0.131. Although a twofold range of within-population genetic diversity (Hep = 0.075-0.158) was found, less than 13% of the genetic variation was distributed among populations (G(ST) = 0.129). An indirect estimate of historical levels of gene flow (Nm = 1.69) was consistent with the high mean genetic identity (mean I = 0.96) found between populations. Despite the relictual nature of C. fraserianus, its rarity and fragmented distribution, genetic diversity within the genus is typical of herbs with similar life-history characteristics. No association was found between geographic and genetic distances between populations (r = -0.01; p > 0.9), suggesting that present day populations are relatively isolated.

Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL–trnF intergenic spacer sequences

Within the tribe Schoeneae (Cyperaceae), the relationships between Carpha and its relatives have not been certain, and the limits and definition of Carpha have been controversial. Further, the relationships of species within Carpha have been unclear. In this study, cladistic analyses based on chloroplast trnL intron and trnL-trnF intergenic spacer sequence data were undertaken to estimate phylogenetic relationships in and around Carpha. This study found that Trianoptiles is sister to Carpha; Ptilothrix is sister to Cyathochaeta rather than to Carpha as suggested by some former authors; and Gymnoschoenus is distant from Carpha and its close relatives. The merging of Schoenoides back into Oreobolus is supported. The findings also revealed the non-monophyletic status of Costularia and of Schoenus, and indicated the phylogenetic relationships of species within Carpha.

AFLP markers and cytotaxonomic analysis reveal hybridisation in the genus Schoenus (Cyperaceae)

Molecular, cytological, and morphological data support the existence of a hybrid population between Schoenus nigricans and Schoenus ferrugineus. This population was found in northeastern Italy, where S. nigricans is central with respect to its natural range and S. ferrugineus is marginal, being most common in the Alps and in central and northern Europe. Molecular marker data show that the putative hybrid population is genetically intermediate between nearby populations of the parent species. Cytological evidence confirmed the hybrid nature of this population, as does the almost complete sterility of plants within the population. Although no seeds were produced by the hybrid population, some possibly fertile pollen grains were produced; this suggests that the possibility of introgression between the two species through the hybrids cannot completely be excluded.