Intergenic Spacer Sequences Research Articles

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

BackgroundOnly a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex.ResultsPhylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA.ConclusionsBased on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia.

Borrelia burgdorferi Bacteria in Domestic Animals China

Background: Borreliosis are among both the longest known and most recently recognized infectious diseases. Although Borrelia species have been isolated in many parts of the world including China, Little is known about the epidemiology of Borrelia burgdorferi pathogen in domestic animals from Xinjiang Autonomous Region of China (XUAR). Methods: In an attempt to assess the potential risk of B. burgdorferi infection in Xinjiang Uygur Autonomous Region of China, a total of 99 blood samples collected from domestic animals in the north of XUAR were screened by polymerase chain reaction based on the 5S-23S rRNA intergenic spacer and flagellin gene. Results: 14 of the 99 specimens (14%) were found to be positive by PCR. Phylogenetic analysis of 5S-23S rRNA intergenic spacer and flagellin gene sequences identified a B. burgdorferi- like bacteria, Ili district (10/72, 13.8%) and Altay district (4/27, 14.8%). Conclusions: This study has reported the occurrence of B. burgdorferi- like bacteria in Xinjiang Autonomous Region of China and suggested that B. burgdorferi bacteria encompassed a large area in China. Further studies on the characterization and culture of B. burgdorferi- like bacteria found in domestic animals should be performed to further clarify this. Additionally, the screening of human specimens for borreliosis in this region will define the incidence of infection.

Сравнительная характеристика межгенных спейсеров кластера генов рибосомной РНК комаров родаCulex(Diptera: Culicidae)

Nucleotide sequences of intergenic spacer of ribosomal RNA gene cluster (rIGS) were identified in mosquitoes Culex modestus, Culex torrentium and Culex pipiens pallens. The level of interpopulation variability of the rIGS in the subspecies C. pipiens pipiens (form pipiens--mosquitoes that inhabit the open waters, and form molestus--mosquitoes that inhabit basements) living in Russia was estimated. No extensive repetitive sequences characteristic of the rIGS of all previously described species of mosquitoes were found within the rIGS of Culex mosquitoes. At the same time, evolutionarily conserved motifs and relatively short degenerate sequences of different classes of transposable elements, as well as multiple blocks of variable microsatellite repeats were identified. Our data demonstrated that the rIGS of Culex mosquitoes can be considered as a promising molecular marker for the analysis of population and phylogenetic relationships within this group of insects.

Comparative Study of PCR-Based Approaches for the Genetic Characterization of Three Strains of Acidithiobacillus caldus Isolated from Different Sites in China

Comparative study of the genetic characteristics among three Acidithiobacillus caldus strains isolated from different typical environments in China was performed using a combination of molecular methods, namely sequencing analysis of PCR-amplified 16S rRNA genes and 16S-23S rRNA gene intergenic spacers (ITS), repetitive element PCR (rep-PCR), arbitrarily primed PCR (AP-PCR) fingerprinting and random amplified polymorphic DNA (RAPD). Both of the 16S rRNA gene and 16S-23S rRNA gene intergenic spacers sequences of the three strains exhibited small variations, with 99.9-100%, 99.7-100% identity respectively. In contrast, according to the analysis of bacterial diversity based on rep-PCR and AP-PCR fingerprinting, they produced highly discriminatory banding patterns, and the similarity values between them varied from 61.97% to 71.64%. RAPD analysis showed that banding profiles of their genomic DNA exhibited obvious differences from each other with 53.44-75% similarity. These results suggested that in contrast to 16S rRNA genes and 16S-23S rRNA gene intergenic spacers sequencing analysis, rep-PCR, AP-PCR fingerprinting and RAPD analysis possessed higher discriminatory power in identifying these closely related strains. And they could be used as rapid and highly discriminatory typing techniques in studying bacterial diversity, especially in differentiating bacteria within Acidithiobacillus caldus.

Rapid and sensitive detection of Acinetobacter baumannii using loop-mediated isothermal amplification

Here we report the design and evaluation of a loop-mediated isothermal amplification (LAMP) assay for detecting Acinetobacter baumannii DNA based on the 16S–23S rRNA intergenic spacer (ITS) sequence. The results showed that target DNA was amplified and visualized within 30min and with a detection limit 100-fold greater than PCR.

Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

BackgroundTandemly arranged nuclear ribosomal DNA (rDNA), encoding 18S, 5.8S and 26S ribosomal RNA (rRNA), exhibit concerted evolution, a pattern thought to result from the homogenisation of rDNA arrays. However rDNA homogeneity at the single nucleotide polymorphism (SNP) level has not been detailed in organisms with more than a few hundred copies of the rDNA unit. Here we study rDNA complexity in species with arrays consisting of thousands of units.MethodsWe examined homogeneity of genic (18S) and non-coding internally transcribed spacer (ITS1) regions of rDNA using Roche 454 and/or Illumina platforms in four angiosperm species, Nicotiana sylvestris, N. tomentosiformis, N. otophora and N. kawakamii. We compared the data with Southern blot hybridisation revealing the structure of intergenic spacer (IGS) sequences and with the number and distribution of rDNA loci.Results and ConclusionsIn all four species the intragenomic homogeneity of the 18S gene was high; a single ribotype makes up over 90% of the genes. However greater variation was observed in the ITS1 region, particularly in species with two or more rDNA loci, where >55% of rDNA units were a single ribotype, with the second most abundant variant accounted for >18% of units. IGS heterogeneity was high in all species. The increased number of ribotypes in ITS1 compared with 18S sequences may reflect rounds of incomplete homogenisation with strong selection for functional genic regions and relaxed selection on ITS1 variants. The relationship between the number of ITS1 ribotypes and the number of rDNA loci leads us to propose that rDNA evolution and complexity is influenced by locus number and/or amplification of orphaned rDNA units at new chromosomal locations.

Biogeography of Phormidium autumnale (Oscillatoriales, Cyanobacteria) in western and central Spitsbergen

AbstractFilamentous types from the order Oscillatoriales, particularly the speciesPhor-midium autumnale, have widely diverse morphotypes, which dominate in Arctic aquatic microbial mats and wet soils. We cultivated 25 strains ofPh.autumnalefrom Svalbard and compared them with available strains from surrounding regions. The comparison of strains, based on 16S rDNA and 16S-23S rDNA intergenic spacer sequences, revealed the similar- ity of strains from Ellesmere Island, the Canadian Arctic and Abisko, Sweden with strains from Svalbard. The rate of colonization ofPh. atumnalefrom aquatic habitats is relatively high and we suggest geese as a main transmission vector from surrounding lands. Strains ofPh. autumnalewere positioned in the phylogenetic tree according to their occurrence in similar habitats. An apparent clustering factor is the duration of availability of water in lakes and long-lasting streams in contrast to rapid and repeated desiccation in soil and on wetted rock in the spray zone of waterfalls. Strains that grow in very cold waters just above the melting point of snow or ice form a distinct genetic group. The strains investigated in this study show morphological similarity in the shape of the trichomes of the studied specimens. Overall, the cell diameter, except for terminal cells, of our strains varied between 3 and 10 μm. Comparison of 16S rDNA sequences of the genusPh. autumnalewith the previ- ously published definition of the speciesMicrocoleus vaginatusrevealed the identity of these two species.

Genome size in Filago L. (Asteraceae, Gnaphalieae) and related genera: phylogenetic, evolutionary and ecological implications

Recent studies have proposed a monophyletic circumscription of Filago and a new subgeneric treatment for this genus. The aim of this study was to analyse the nuclear genome size in a phylogenetic framework in order to evaluate the systematic significance of this trait to provide insights into the dynamics of genome size evolution and to assess relationships among DNA content, specific life and ecological features within the study group. A holoploid genome size of 76 samples corresponding to 27 taxa was determined using flow cytometry, which represents the first estimates of genome size in Bombycilaena, Filago, Ifloga and Logfia. Chromosome counts were performed for six species. Parsimony and Bayesian analysis of ITS, ETS and rpl32-trnL intergenic spacer sequence data were used to construct molecular phylogenetic trees. The evolution of genome size was investigated troughout the Brownian motion model with the three scaling parameters λ, κ and δ. The mean 2C-value in the Filago group is relatively low (1.3644 ± 0.0079 pg) and homogeneous among species. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages obtained. The generally accepted assumption that annual, ephemeral and autogamous species show low genome sizes was confirmed. Also the relatively high DNA contents found for a couple of species could be correlated with their highly specific ecological requirements. Phylogeny seems to represent the most important factor explaining the pattern of DNA amount variation in the Filago group. The DNA amount does not seem to be strongly influenced by selection.

Candida guilliermondii and Other Species of Candida Misidentified as Candida famata: Assessment by Vitek 2, DNA Sequencing Analysis, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry in Two Global Antifungal Surveillance Programs

Candida famata (teleomorph Debaryomyces hansenii) has been described as a medically relevant yeast, and this species has been included in many commercial identification systems that are currently used in clinical laboratories. Among 53 strains collected during the SENTRY and ARTEMIS surveillance programs and previously identified as C. famata (includes all submitted strains with this identification) by a variety of commercial methods (Vitek, MicroScan, API, and AuxaColor), DNA sequencing methods demonstrated that 19 strains were C. guilliermondii, 14 were C. parapsilosis, 5 were C. lusitaniae, 4 were C. albicans, and 3 were C. tropicalis, and five isolates belonged to other Candida species (two C. fermentati and one each C. intermedia, C. pelliculosa, and Pichia fabianni). Additionally, three misidentified C. famata strains were correctly identified as Kodomaea ohmeri, Debaryomyces nepalensis, and Debaryomyces fabryi using intergenic transcribed spacer (ITS) and/or intergenic spacer (IGS) sequencing. The Vitek 2 system identified three isolates with high confidence to be C. famata and another 15 with low confidence between C. famata and C. guilliermondii or C. parapsilosis, displaying only 56.6% agreement with DNA sequencing results. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) results displayed 81.1% agreement with DNA sequencing. One strain each of C. metapsilosis, C. fermentati, and C. intermedia demonstrated a low score for identification (<2.0) in the MALDI Biotyper. K. ohmeri, D. nepalensis, and D. fabryi identified by DNA sequencing in this study were not in the current database for the MALDI Biotyper. These results suggest that the occurrence of C. famata in fungal infections is much lower than previously appreciated and that commercial systems do not produce accurate identifications except for the newly introduced MALDI-TOF instruments.

English

Great burdock (Arctium lappa&nbsp;L.) of the Compositae has economic importance in East Asian countries. In Taiwan, major cultivated areas are located in Gueilai Township, Pingtung County and Jiali Township, Tainan County. The present work was undertaken with two objectives of determining intraspecific genetic variations and studying the population dynamics of&nbsp;A. lappa&nbsp;L. In total, 23 individuals were collected from Gueilai (n = 15) and Jiali (n = 8). Chloroplast trnL-trnF intergenic spacer (IGS) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences were subcloned and sequenced. Length variations among IGS sequences ranged from 805 to 808 bp and among ITS sequences ranged from 360 to 362 bp. Intraspecific genetic distances within IGS sequences ranged from 0 to 0.01 and within ITS sequences ranged from 0 to 0.023, which were lower than interspecific distances. All IGS and ITS sequences being separately scattered on each of the neighbor-joining trees with insignificant genetic differentiation indices (p&nbsp;&gt; 0.05) suggested that both samples shared a recent common ancestor. Minimum spanning trees, Tajima&rsquo;s and Fu&rsquo;s parameters, and mismatch distributions implied that&nbsp;A. lappa&nbsp;L. had experienced a historical population expansion. &nbsp; Key words:&nbsp;Compositae, Gueilai, Jiali, genetic distance, population expansion.

Identification of Clinical Isolates of α-Hemolytic Streptococci by 16S rRNA Gene Sequencing, Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using MALDI Biotyper, and Conventional Phenotypic Methods: a Comparison

Fifty-six α-hemolytic streptococcal isolates were identified using MALDI Biotyper MS (Bruker Daltonics), API 20 Strep (bioMérieux), and BD Phoenix (Becton, Dickinson). The gold standard for identification was 16S rRNA gene sequence analysis with 16S-23S rRNA intergenic spacer sequencing. The following percentages of isolates were correctly identified to the species level: MALDI Biotyper, 46%; BD Phoenix, 35%; and API 20 Strep, 26%.

Inferring Multiple Refugia and Phylogeographical Patterns in Pinus massoniana Based on Nucleotide Sequence Variation and DNA Fingerprinting

Background Pinus massoniana, an ecologically and economically important conifer, is widespread across central and southern mainland China and Taiwan. In this study, we tested the central–marginal paradigm that predicts that the marginal populations tend to be less polymorphic than the central ones in their genetic composition, and examined a founders' effect in the island population.Methodology/Principal FindingsWe examined the phylogeography and population structuring of the P. massoniana based on nucleotide sequences of cpDNA atpB-rbcL intergenic spacer, intron regions of the AdhC2 locus, and microsatellite fingerprints. SAMOVA analysis of nucleotide sequences indicated that most genetic variants resided among geographical regions. High levels of genetic diversity in the marginal populations in the south region, a pattern seemingly contradicting the central–marginal paradigm, and the fixation of private haplotypes in most populations indicate that multiple refugia may have existed over the glacial maxima. STRUCTURE analyses on microsatellites revealed that genetic structure of mainland populations was mediated with recent genetic exchanges mostly via pollen flow, and that the genetic composition in east region was intermixed between south and west regions, a pattern likely shaped by gene introgression and maintenance of ancestral polymorphisms. As expected, the small island population in Taiwan was genetically differentiated from mainland populations.Conclusions/SignificanceThe marginal populations in south region possessed divergent gene pools, suggesting that the past glaciations might have low impacts on these populations at low latitudes. Estimates of ancestral population sizes interestingly reflect a recent expansion in mainland from a rather smaller population, a pattern that seemingly agrees with the pollen record.

Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus

The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88% of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5'-TGC GGC TGA GGA GGA CT-3') and BbasCG1024R (5'-TGC GGC TGA GTG TAG AAC-3') were designed for detecting and monitoring this isolate in the field.

ASSESSMENT OF GENETIC DIVERSITY IN SOME WILD PLANTS OF ASTERACEAE FAMILY BY RIBOSOMAL DNA SEQUENCE

Ribosomal DNA genes are organized in clusters of tandem repeated units, each of which consists of coding regions (18S, 5.8S and 28S) and two internal transcribed spacers (ITS), in addition to intergenic spacer (IGS) region. Accordingly this article is focused on clarifying the sequence divergence of complete rDNA of ITS and IGS regions among four wild and endemic species of Asteraceae family in Egypt. Results indicated that there were a total of 754 and 667 positions across the final dataset for ITS and IGS sequences, respectively. IGS regions were superior compared to ITS region in several parameters like nucleotide diversity rate (π = 0.60), the estimated values of transition/transversion rate ratios (k1 = 38.28, purines), (K2 = 12.58, pyrimidines) and the overall transition/transversion bias (R = 12.10), respectively. This reflects that transitions are more dominant than transversion in Asteraceae germplasm across IGS markers. Thus, it was concluded that the IGS region could be more suitable for measuring genetic relationship in different subspecies of Asteraceae, with more informative sites than ITS sequences. Generally ribosomal DNA particularly intergenic spacer of the rDNA cluster evolves quickly and is highly polymorphic, providing a useful tool for assessing genetic diversity, taxonomic and phylogenetic studies in Asteraceae germplasm.

Geographic variation of chloroplast DNA in Platycarya strobilacea (Juglandaceae)

Abstract The monotypic genus Platycarya (Juglandaceae) is one of the most widespread temperate tree species in East Asia. In this research, we implemented a phylogeographical study using chloroplast DNA (cpDNA) (psbA‐trnH and atpB‐rbcL intergenic spacer) sequences on Platycarya strobilacea, in order to identify the locations of the species’ main refugia and migration routes. A total of 180 individuals of P. stobilacea from 27 populations from China and Jeju Island (Korea) were collected. The results revealed that P. strobilacea had 35 haplotypes for the two intergenic spacers and high genetic diversity (hT= 0.926). This surprisingly high diversity of haplotypes indicates its long evolutionary history, which is in agreement with previous phylogenetic analyses and fossil records. Significant cpDNA population subdivision was detected (GST= 0.720; NST= 0.862), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (NST &gt; GST, P &lt; 0.05). The construction of phylogenetic relationships of the 35 chlorotypes detected four major cpDNA clades. Divergence dating analyses using BEAST suggest that the divergence of the major cpDNA clades occurred before the Miocene. Demographic analysis indicated that the Eastern clade underwent localized demographic expansions. The molecular phylogenetic data, together with the geographic distribution of the haplotypes, suggest the existence of multiple glacial refugia in most of its current range in China through Quaternary climatic oscillations.

Discrimination of Phellodendron amurense and P. chinense based on DNA analysis and the simultaneous analysis of alkaloids

Phellodendri Cortex is the bark of the stems of Phellodendron amurense Ruprecht or P. chinense Schneider (Rutaceae), which is orginated from periderm. The internal transcribed spacer sequences of 20 originated plants and identified samples were analyzed. The result showed that the 99% of the base sequences of P. amurense were identical to that of P. chinense, but the differentiation of P. amurense and P. chinense was difficult. In addition, the ribulose-1, 5-bisphospate carboxylase large subunit (rbcL) intergenic spacer sequences of specific parts produced the same result. However, when the analysis was carried out by using the RAPD (randomly amplification polymorphism DNA) analysis method, which utilizes 48 randomly primers, it allowed us to confirm the polymorphism of P. amurense and P. chinense in 12 primers. A high-performance liquid chromatographic (HPLC) method was developed and validated for the simultaneous quantitation of berberine, palmatine and jatrorrhizine in a traditional herbal drug, Phellodendri Cortex. The HPLC method was applied successfully to the quantification of three constituents in the extract of twenty Phellodendri Cortex. The results indicated that the established HPLC and RAPD methods are suitable for the quantitative analysis and the quality control multi-simultaneous discrimination in Phellodendri Cortex.

Epidemiological characteristics and genetic structure of blaNDM-1 in non-baumannii Acinetobacter spp. in China

The goal of this study was to investigate the epidemiological characteristics and the surrounding genetic structure of bla(NDM-1) in non-baumannii Acinetobacter spp. in China. Non-baumannii Acinetobacter spp. were collected from 28 provinces in China and were screened for the presence of bla(NDM-1) using PCR. The following four methods were used to classify the Acinetobacter isolates: the Vitek 2 system, 16S-23S rRNA gene intergenic spacer sequencing, amplified rDNA restriction analysis and partial rpoB sequence analysis. An S1-PFGE assay and Southern blot hybridization were performed to determine the plasmid location of bla(NDM-1). The transferability of bla(NDM-1)-harbouring plasmids was confirmed by conjugation experiments and electrotransformation. The surrounding genetic structure of the bla(NDM-1) gene was analysed using a restriction endonuclease-based cloning approach and primer walking. Among 726 non-baumannii Acinetobacter spp., nine isolates collected from six different provinces and assigned to seven different Acinetobacter spp. contained the bla(NDM-1) gene. None of these isolates was directly infectious to the patients or demonstrated an epidemiological importation from abroad. These bla(NDM-1) genes were located on plasmids that could be transferred to Escherichia coli J53 by conjugation and Acinetobacter baylyi ADP1 by electrotransformation. Seven of the nine strains shared a common genetic structure in which bla(NDM-1) was flanked by two copies of ISAba125. The clinical challenge posed by bla(NDM-1) is currently minimal in China; however, more attention should be devoted to monitoring the dissemination of this gene due to its potential transferability via the ISAba125-associated transposon.

Diversity and evolution of major Panax species revealed by scanning the entire chloroplast intergenic spacer sequences

Ginseng is an important medicinal plant, but almost no genomic information is known for it. For the primary step to understand the Panax genome, we inspected the chloroplast genome sequence diversity and used that to infer the evolution of Panax species using them. We inspected a total of 101 intergenic spacers (IGS) covering 44,563 bp (96.8 % of the total IGS) from four Panax species. Diversity was inspected by three steps: gel electrophoresis, high resolution melting (HRM) analysis, and further confirmation by sequencing. Even though low levels of InDel polymorphism were detected by gel electrophoresis, high levels of reproducible polymorphisms were identified by HRM analysis. Sequencing of the HRM-polymorphic spaces and pair-wise multiple sequence alignments revealed up to 247 sequence variations between species. We have identified 62 IGS showing polymorphism between species. Among them, the trnE-trnT, trnT-psbD, ndhF-rpl32, and rpl14-rpl16 spaces are more informative for studying the diversity of Panax relatives. Phylogenetic analysis and molecular evolution studies revealed that P. notoginseng is most diverged from the other Panax species, with a nucleotide substitution rate of 0.0039. P. quinquefolius shows a close relationship with P. ginseng and P. japonicus, with a nucleotide substitution rate of 0.0009. Meanwhile, no sequence variation was detected between P. ginseng and P. japonicus. Calculation of molecular clocks revealed that P. notoginseng diverged more than 1.30 million years ago from the other Panax species and then, P. quinquefolius diverged from P. ginseng by migration in the American continent more than 0.29 million years ago.

Revised generic delimitations for Oxypolis and Ptilimnium (Apiaceae) based on leaf morphology, comparative fruit anatomy, and phylogenetic analysis of nuclear rDNA ITS and cpDNA trnQ–trnK intergenic spacer sequence data

AbstractA phylogenetic study of Oxypolis and Ptilimnium, two small genera of tribe Oenantheae (Apiaceae: subfamily Api–oideae), was carried out. Generic circumscriptions and infrageneric and infraspecific relationships were investigated through parsimony and Bayesian inference analyses of nuclear rDNA ITS and cpDNA trnQ–5’rps16 and 3’rps16–5’trnK intergenic spacer sequences. Fruit anatomical characters were also examined and used in conjunction with leaf morphology to corroborate the results of the phylogenetic analyses. Each genus as currently delimited has both compound–leaved and rachis–leaved species. Results of the phylogenetic analyses show that neither Oxypolis nor Ptilimnium is monophyletic; each genus is split into two strongly supported clades that correspond to differences in leaf morphology within the groups. Fruit anatomical characters support these splits. The fruits of compound–leaved and rachis–leaved Oxypolis species differ in the number of commissural vittae per mericarp, the branching of the vittae, and the lignification of mericarp around the seed. The fruits of compound–leaved and rachis–leaved Ptilimnium species differ in the compression of the mericarps and the development of the marginal ribs. The fruits of rachis–leaved Oxypolis and rachis–leaved Ptilimnium species also differ in the compression of the mericarps and the development of the marginal ribs. Based on analyses of molecular data and corroboration with morphological and fruit anatomical data, new circumscriptions for the genera Oxypolis and Ptilimnium are formalized. Each of the two polyphyletic genera (Oxypolis and Ptilimnium) is split, two genera (Tiedemannia and Harperella) are resurrected, and three new combinations are made.

Molecular and morphological evidence supports the resurrection of a neglected species of Daucus (Apiaceae) from North Africa

A neglected species of Daucus (Apiaceae), D. mauritii, endemic to northern Morocco, is revived. A full description, illustrations and photographs are provided, and a lectotype is designated. This species has previously been synonymized under D. muricatus. However, although D. mauritii shares morphological features with D. muricatus and D. aureus, it shows a unique combination of characters that warrants recognition as a distinct species. Analysis of (internal transcribed spacer, ITS), trnQ-rps16 intergenic spacer and rps16 intron sequences indicates that D. mauritii is closely related to D. aureus. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 320–337.