GC balance in the internal transcribed spacers ITS 1 and ITS 2 of nuclear ribosomal RNA genes

Interspecific molecular variation of Tunisian complex Lolium perenne L. and Festuca arundinacea Schreb. based on the internal transcribed spacer locus (ITS)

To establish phylogenetic relationships and estimate the intra and interspecific divergence, the amplification and the sequencing of the internal transcribed spacers of ribosomal DNA (ITS = ITS1 + 5.8S + ITS2) were analyzed in Tunisian complex Lolium-Festuca DNA. These spacer regions have evolved mainly by point mutations. Results revealed a high level of polymorphism within studied species. Significant similarities were observed between these two species and showed the existence of an important phylogenetic relationship. Besides, this molecular approach has revealed two new clusterings, with a homologous ITS gene namely: Bromus hordeaceus and Hordeum murinum subsp. This could be explained by the conservation of an ancestral ITS gene in some fescue plants. Thus, Tunisian tall fescue and perennial ryegrass may derive from Bromus hordeaceus and Hordeum murinum subsp. Considerable morphology and bioclimatic distribution similarities were discovered in ITS sequences within the same species. This study can be of great help to identify suitable accessions that could be used in local fescue and ryegrass improvement program.

Evolution of ribosomal internal transcribed spacers in Deuterostomia

Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown. A possible role of GC-based gene conversion in Deuterostomia ITS evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra. The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well.

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

Evolution of helix formation in the ribosomal Internal Transcribed Spacer 2 (ITS2) and its significance for RNA secondary structures

Helices are the most common elements of RNA secondary structure. Despite intensive investigations of various types of RNAs, the evolutionary history of the formation of new helices (novel helical structures) remains largely elusive. Here, by studying the nuclear ribosomal Internal Transcribed Spacer 2 (ITS2), a fast-evolving part of the eukaryotic nuclear ribosomal operon, we identify two possible types of helix formation: one type is "dichotomous helix formation"--transition from one large helix to two smaller helices by invagination of the apical part of a helix, which significantly changes the shape of the original secondary structure but does not increase its complexity (i.e., the total length of the RNA). An alternative type is "lateral helix formation"--origin of an extra helical region by the extension of a bulge loop or a spacer in a multi-helix loop of the original helix, which does not disrupt the pre-existing structure but increases RNA size. Moreover, we present examples from the RNA sequence literature indicating that both types of helix formation may have implications for RNA evolution beyond ITS2.

Molecular organization of the 25S-18S rDNA IGS of Fagus sylvatica and Quercus suber: a comparative analysis

The 35S ribosomal DNA (rDNA) units, repeated in tandem at one or more chromosomal loci, are separated by an intergenic spacer (IGS) containing functional elements involved in the regulation of transcription of downstream rRNA genes. In the present work, we have compared the IGS molecular organizations in two divergent species of Fagaceae, Fagus sylvatica and Quercus suber, aiming to comprehend the evolution of the IGS sequences within the family. Self- and cross-hybridization FISH was done on representative species of the Fagaceae. The IGS length variability and the methylation level of 18 and 25S rRNA genes were assessed in representatives of three genera of this family: Fagus, Quercus and Castanea. The intergenic spacers in Beech and Cork Oak showed similar overall organizations comprising putative functional elements needed for rRNA gene activity and containing a non-transcribed spacer (NTS), a promoter region, and a 5′-external transcribed spacer. In the NTS: the sub-repeats structure in Beech is more organized than in Cork Oak, sharing some short motifs which results in the lowest sequence similarity of the entire IGS; the AT-rich region differed in both spacers by a GC-rich block inserted in Cork Oak. The 5′-ETS is the region with the higher similarity, having nonetheless different lengths. FISH with the NTS-5′-ETS revealed fainter signals in cross-hybridization in agreement with the divergence between genera. The diversity of IGS lengths revealed variants from ∼2 kb in Fagus, and Quercus up to 5.3 kb in Castanea, and a lack of correlation between the number of variants and the number of rDNA loci in several species. Methylation of 25S Bam HI site was confirmed in all species and detected for the first time in the 18S of Q. suber and Q. faginea. These results provide important clues for the evolutionary trends of the rDNA 25S-18S IGS in the Fagaceae family.

Evaluation of the authenticity of a highly novel environmental sequence from boreal forest soil using ribosomal RNA secondary structure modeling

The number of sequences from both formally described taxa and uncultured environmental DNA deposited in the International Nucleotide Sequence Databases has increased substantially over the last two decades. Although the majority of these sequences represent authentic gene copies, there is evidence of DNA artifacts in these databases as well. These include lab artifacts, such as PCR chimeras, and biological artifacts such as pseudogenes or other paralogous sequences. Sequences that fall in basal positions in phylogenetic trees and appear distant from known sequences are particularly suspect. Phylogenetic analyses suggest that a novel sequence type (NS1) found in two boreal forest soil clone libraries belongs to the fungal kingdom but does not fall unambiguously within any known phylum. We have evaluated this sequence type using an array of secondary-structure analyses. To our knowledge, such analyses have never been used on environmental ribosomal sequences. Ribosomal secondary structure was modeled for four rRNA loci (ITS1, 5.8S, ITS2, 5' LSU). These models were analyzed for the presence of conserved domains, conserved nucleotide motifs, and compensatory base changes. Minimal free energy (MFE) foldings and GC contents of sequences representing the major fungal clades, as well as NS1, were also compared. NS1 displays secondary rRNA structures consistent with other fungi and many, but not all, conserved nucleotide motifs found across eukaryotes. However, our analyses show that many other authentic sequences from basal fungi lack more of these conserved motifs than does NS1. Together our findings suggest that NS1 represents an authentic gene copy. The methods described here can be used on any rRNA-coding sequence, not just environmental fungal sequences. As new-generation sequencing methods that yield shorter sequences become more widely implemented, methods that evaluate sequence authenticity should also be more widely implemented. For fungi, the adjacent 5.8S and ITS2 loci should be prioritized. This region is not only suited to distinguishing between closely related species, but it is also more informative in terms of expected secondary structure.

A PCR based SNPs marker for specific characterization of English walnut (Juglans regia L.) cultivars

English walnut (Juglans regia L.) is the most economically important species from all the 21 species belonging to the genus Juglans and is an important and healthy food as well as base material for timber industry. The aim of this study was to develop a simple technique for specific characterization of English walnut using DNA method. The first and second internal transcribed spacers (ITS1 and ITS2) as well as the intervening 5.8S coding region of the rRNA gene for 18 cultivars of J. regia L. isolated from different geographic origins were characterized. The size of the spacers sequences ranged from 257 to 263 bases for ITS1 and from 217 to 219 bases for ITS2. Variation of GC contents has also been observed and scored as 55-56.7 and 57.1-58.9% for ITS1 and ITS2, respectively. This data exhibited the presence of polymorphism among cultivars. Alignment of the ITS1-5.8S-ITS2 sequences from 18 walnut cultivars showed that there were 244 single nucleotide polymorphisms (SNPs) and 1 short insertion-deletion (indel) at 5' end ITS1. Amplification refractory mutation system strategy was successfully applied to the SNP markers of the ITS1 and ITS2 sequences for the fingerprinting analysis of 17 on 18 walnut cultivars. The prediction of ITS1 and ITS2 RNA secondary structure from each cultivar was improved by detecting key functional elements shared by all sequences in the alignments. Phylogenetic analysis of the ITS1-5.8S-ITS2 region clearly separated the isolated sequences into two clusters. The results showed that ITS1 and ITS2 region could be used to discriminate these walnut cultivars.

Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium

The two internal transcribed spacers (ITS) of the nuclear ribosomal (r) DNA tandem repeat were examined in ophiostomatoid fungi belonging to the genera Grosmannia and Leptographium and closely-related taxa. Although the DNA sequence of the ITS region evolves rapidly, core features of the RNA secondary structure of the ITS1 and ITS2 segments are conserved. The results demonstrate that structural conservation of GC-rich helical regions is facilitated primarily through compensatory base changes (CBCs), hemi-CBCs, and compensating insertions/deletions (indels), although slippage of the RNA strand is potentially an additional mechanism for maintaining basepairing interactions. The major conclusion of the structural analysis of both ITS segments is that two factors appear to be involved in limiting the type of changes observed: a high GC bias for both ITS1 and ITS2 and structural constraints at the RNA level.

Populations, hybrids and the systematic concepts of species and subspecies in Chagas disease triatomine vectors inferred from nuclear ribosomal and mitochondrial DNA

In Chagas disease, triatomine vectors are the main target for control measures because of the absence of effective drugs. The broad usefulness of nuclear rDNA and mtDNA sequences explains why triatomine studies using these markers have increased so pronouncedly in recent years. This indicates the appropriateness of an updated review about these molecular markers, concentrating on aspects useful for research on Chagas disease vectors. A comparative analysis is presented on the efficiency, weight of their different characteristics, limitations and problems of each of the different DNA markers in the light of the results obtained in studies on populations, hybrids, subspecies and species of the subfamily Triatominae. The use of a standardized composite haplotype code nomenclature for both nuclear rDNA and mtDNA markers is strongly encouraged to avoid difficulties in comparative studies. Triatomine aspects related to concerted evolution, microsatellites, minisatellites and insertions/deletions in nuclear rDNA and silent/non-silent mutations, pseudogenes and weaknesses of partial sequences in mtDNA are analysed. Introgression and hybrids, nuclear and mitochondrial DNA strengths, and compared evolutionary rates of nuclear rDNA and mtDNA in triatomines are discussed. Many conclusions are obtained thanks to the availability, for the first time in triatomines, of a complete sequence of a protein-coding mtDNA gene as ND1 from very numerous triatomine species covering from different populations of a species up to members belonging to different tribes. The evolutionary rates of each nuclear rDNA marker and mtDNA marker are analysed by comparison at subspecies level (intrapopulational, interpopulational, between morphs, and between subspecies) and species level (close and distant species of the same genus, species of different genera, and species of different tribes). Weaknesses of mtDNA for systematic-taxonomic purposes detected recently and newly in insects and triatomines, respectively, are discussed in detail. Emphasis is given to taxonomic units and biological entities presenting well-known problematics, both from the systematic-taxonomic and/or epidemiological-control points of view, as well as to molecular situations which can give rise to erroneous conclusions. All these aspects constitute the background on which the key question about the systematic concepts of species and subspecies in triatomines is focused. The global purpose is to facilitate future work on triatomines by highlighting present gaps, how better choice the appropriate markers, and marker aspects which should be taken into account. Key characteristics as alpha, CI and transformation rate matrices ought to be obtained and noted to get appropriate results and allow correct interpretations. The main aim is to offer a baseline for future fundamental research on triatomines and applied research on transmission, epidemiology and control measures related to Chagas disease vectors.

Transparent Testa Glabra 1 (TTG1) and TTG1-like genes in Matthiola incana R. Br. and related Brassicaceae and mutation in the WD-40 motif

TTG1 (Transparent Testa Glabra 1), a WD-40 repeat protein, is involved in regulation of flavonoid/anthocyanin biosynthesis, seed coat (mucilage) development/pigmentation and trichome formation in leaves. Here, we characterized the TTG1 gene of Matthiola incana wild type (e locus), showing 85.3% similarity to TTG1 of A. thaliana on the nucleotide level and 96.2% on the protein level. A white-flowered and glabrous mutant, line 17, of M. incana exhibits one nucleotide change, leading to an amino acid substitution directly in the WD motif (W158R). Correspondingly, the DFR (dihydroflavonol 4-reductase) gene, in which the expression is known to be dependent on TTG1, is not expressed in Matthiola mutant lines 17 (and 19). Comparison of the GC content of the Matthiola TTG1 (54.1%) and Arabidopsis TTG1 (46.1%) genes revealed a strong difference, mostly obtained by neutral substitutions (C to T transitions). To examine whether this is an ecologically influenced trend, a fragment of TTG1 was characterized from another Matthiola species (M. tricuspidata) and from Malcolmia flexuosa subsp. naxensis from the eastern Mediterranean, near a beach with sandy and salty soils. Both Matthiola species have a higher GC content in the TTG1 gene than Arabidopsis and the closer-related Malcolmia, indicating that the GC content is rather an evolutionary than an ecological signal. A similar WD-40 repeat protein gene (containing no intron in the 3' untranslated region) with high similarity to the Arabidopsis TTG1-like (AtAN11) gene was found in Matthiola.

Molecular authentication of three Italian melon accessions by ARMS-PCR and ITS1 (internal transcribed spacer 1) secondary structure prediction

Genetic assessment was carried out on three Italian melon accessions by sequence and structural analysis of the internal transcribed spacer 1 (ITS1) from three populations belonging to two Cucumis melo L. varieties (madras and tendral). Alignment of the 18S-5.8S-26S sequences from three melon accessions showed that there were three single-nucleotide polymorphisms (SNPs) and one short insertion-deletion (indel) at the 5'end ITS1. An amplification refractory mutation system (ARMS)-PCR-based analysis was successfully applied to the SNP markers of the ITS1 sequences for the fingerprinting analysis of three melon populations. Secondary structure models for each ITS1 were derived. The prediction of ITS1 RNA secondary structure from each accession was improved by detecting key functional elements shared by all sequences in the alignments. Our results demonstrated that the ITS1secondary structure models can be used to improve the preliminary genetic assessment of the three melon accessions, suggesting a new tool in plant fingerprinting analysis.

Evolution of ITS ribosomal RNA secondary structures in fungal and algal symbionts of selected species of Cladonia sect. Cladonia (Cladoniaceae, Ascomycotina)

Evolutionary studies in lichen associations follow that of the fungal symbiont (mycobiont), which is the symbiont after which the lichen is named and forms the majority of the thallus. However, evolution of the algal partner (photobiont) is important to maintain compatibility between symbionts and to optimize productivity of the lichen association. The internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA (rDNA) were examined for primary DNA sequence patterns and for patterns in the secondary structure of the rRNA transcripts in both symbionts of the genus Cladonia. Fungal and algal symbionts show opposite trends in rates of evolution and fragment lengths. Both symbionts showed stronger conservation of the ITS2 structure than the ITS1 structure. Homology was evident in the secondary structures between the two highly divergent chlorophyte and ascomycete taxonomic groups. Most fungal species and all species complexes were polyphyletic. The ITS rDNA of the natural lichen algae from Manitoba and four known algal species is highly similar. The natural lichen algae segregate into highly supported clades by environmental features, suggesting that algae that are already adapted to the environment may associate with germinating fungal propagules in the genus Cladonia. Fungal plasticity may allow the mycobiont to adapt to the environment of the photobiont producing variation in lichen morphology. This might explain the incongruence of phylogenetic patterns between the algal and fungal partners tested and the polyphyly of the fungal species.

Ribosomal DNA second internal transcribed spacer sequence studies of Culicid vectors from an endemic area of Dirofilaria immitis in Spain

Studies were performed in an endemic area of Dirofilaria immitis in Spain to genetically characterize the potential mosquito vector species present by means of DNA sequencing and elucidate which of these species may be involved in the transmission. The rDNA ITS-2 sequences of two Culex pipiens haplotypes, H1 and H2, Aedes (Aedimorphus) vexans, Fredwardsius vittatus, Ochlerotatus (Ochlerotatus) caspius, Anopheles (Anopheles) atroparvus, and Anopheles (Anopheles) plumbeus were obtained. F. vittatus and An. plumbeus were detected for the first time. Results on abundance, presence, and activity suggest that the month of August is the period of higher transmission risk, with C. pipiens, Ae. vexans, and An. atroparvus present simultaneously. Population studies indicate that C. pipiens may be considered the most important potential vector, while Ae. vexans, An. atroparvus, and O. caspius being involved in transmission only sporadically. The absence of larval dirofilarial infection agrees with the very low prevalences known in endemic areas.

Reviewing lymnaeid vectors of fascioliasis by ribosomal DNA sequence analyses

Snails of the family Lymnaeidae are of great parasitological importance due to the numerous helminth species they transmit, mainly trematodiases (such as fascioliasis) of considerable medical and veterinary impact. The present knowledge of the genetics and host-parasite relationships of this gastropod group is far from adequate. Fascioliasis is caused by two species, Fasciola hepatica and F. gigantica, which, as in the case of other trematodes, show a marked snail host specificity. Many lymnaeid species involved in fascioliasis transmission still show a confused systematic-taxonomic status. The need for tools to distinguish and characterize species and populations of lymnaeids is evident and the present review concerns new molecular tools developed in recent years using nuclear ribosomal DNA sequences. The small subunit or 18S gene and the internal transcribed spacers ITS-2 and ITS-1 are analysed and evaluated as markers for taxon differentiation and relationships within the Lymnaeidae from genus and species levels to subspecies and population levels. rDNA sequence differences and genetic distances, and their value for reconstructing phylogenetic trees using different methods are considered. Nuclear rDNA sequences are appropriate tools on which to base a review of the systematics and taxonomy of the family Lymnaeidae, without excluding other valuable snail characteristics already available. A reconstruction of the lymnaeid system towards a more natural classification will undoubtedly be helpful in understanding parasite transmission and epidemiological features as well the dispersion of an emerging-reemerging disease such as fascioliasis. Nomenclature for nuclear rDNA genotyping in lymnaeids includes the main rDNA sequence regions able to furnish important information on interspecific differentiation and grouping as well as intraspecific variability of lymnaeid species. The composite haplotype code includes the rDNA markers arranged in order according to their well-known usefulness, in its turn related to their respective, more or less rapid evolutionary ratios, to distinguish between different taxonomic levels, from supraspecific taxa to the species level and up to the population level.

Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Siluriformes: Clariidae) inferred from ribosomal gene and spacer sequences

The catfish family Clariidae comprises species in which the body shape ranges from fusiform to anguilliform. Recent studies have shown that this body elongation is the result of convergent evolution. This paper aims to study the evolution towards anguilliformity in a phylogenetic framework. Sequences of 29 taxa were analyzed using the neighbor-joining, maximum-likelihood, maximum-parsimony, and Bayesian inference algorithms and the parsimony algorithm in POY. The study yields phylogenetic hypotheses showing well-supported clades. Anguilliformity appears to have arisen at least four times, each time having a sister group relation with a fusiform Clarias-like ancestor. Divergence time estimation indicates that the African Clariidae started radiating between 123 and 56 My ago.

Intragenomic heterogeneity of internal transcribed spacer rDNA in neotropical malaria vector Anopheles aquasalis (Diptera: Culicidae)

Intragenomic heterogeneity of the internal transcribed spacer (ITS) array was investigated in Anopheles aquasalis Curry mosquitoes from two geographic locations in each of Brazil and Venezuela, and one in Suriname. Polymerase chain reaction-amplified copies of the ITS were cloned and sequenced. The length of the entire array ranged from 782 to 990 bp, with most variation due to microsatellite insertions in ITS1. We detected 40 different ITSL sequences and 15 different ITS2 sequences of the 71 to 72 clones examined. The sequence divergence within localities ranged from 0.002 to 0.043 for ITS1 and from 0 to 0.006 for ITS2. Point mutations were common to both spacer regions, but dinucleotide microsatellite repeats were restricted to ITS1. Sequences from neither ITS1 nor ITS2 had a diagnostic distribution or were informative in distinguishing these populations, providing additional support for the status of An. aquasalis as a single species.

Phylogenetic relationships, divergence time estimation, and global biogeographic patterns of calopterygoid damselflies (odonata, zygoptera) inferred from ribosomal DNA sequences

The calopterygoid superfamily (Calopterygidae + Hetaerinidae) is composed of more than twenty genera in two families: the Calopterygidae (at least 17) and the Hetaerinidae (at least 4). Here, 62 calopterygoid (ingroup) taxa representing 18 genera and 15 outgroup taxa are subjected to phylogenetic analysis using the ribosomal 18S and 5.8S genes and internal transcribed spacers (ITS1, ITS2). The five other families of calopterid affinity (Polythoridae, Dicteriadidae, Amphipterygidae, Euphaeidae, and Chlorocyphidae) are included in the outgroup. For phylogenetic inference, we applied maximum parsimony, maximum likelihood, and the Bayesian inference methods. A molecular phylogeny combined with a geographic analysis produced a well-supported phylogenetic hypothesis that partly confirms the traditional taxonomy and describes distributional patterns. A monophyletic origin of the calopterygoids emerges, revealing the Hetaerinid clade as sister group to the Calopterygidae sensu strictu. Within Calopterygidae, seven clades of subfamily rank are recognized. Phylogenetic dating was performed with semiparametric rate smoothing by penalized likelihood, using seven reference fossils for calibration. Divergence time based on the ribosomal genes and spacers and fossil constraints indicate that Calopteryginae (10 genera, approximately 50% of all Calopterygid taxa studied here), Vestalinae (1 genus), and Hetaerinidae (1 genus out of 4 studied here) started radiating around 65 Mya (K/T boundary). The South American Iridictyon (without distinctive morphology except for wing venation) and Southeast Asian Noguchiphaea (with distinctive morphology) are older (about 86 My) and may be survivors of old clades with a Gondwanian range that went extinct at the K/T boundary. The same reasoning (and an even older age, ca. 150 My) applies to the amphipterygids Rimanella and Pentaphlebia (South America-Africa). The extant Calopterygidae show particular species and genus richness between west China and Japan, with genera originating between the early Oligocene and Pleistocene. Much of that richness probably extended much wider in preglacial times. The Holarctic Calopteryx, of Miocene age, was deeply affected by the climatic cooling of the Pliocene and by the Pleistocene glaciations. Its North American and Japanese representatives are of Miocene and Pliocene age, respectively, but its impoverished Euro-Siberian taxa are late Pliocene-Pleistocene, showing reinvasion, speciation, and introgression events. The five other calopterid families combine with the Calopterygidae and Hetaerinidae to form the monophyletic cohort Caloptera, with Polythoridae, Dicteriadidae, and Amphipterygidae sister group to Calopterygoidea. The crown node age of the latter three families has an age of about 157 My, but the Dicteriadidae and Polythoridae themselves are of Eocene age, and the same is true for the Euphaeidae and Chlorocyphidae. The cohort Caloptera itself, with about 197 My of age, goes back to the early Jurassic.

Ribosomal ITS sequences and plant phylogenetic inference

One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.

Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209-276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270-294 bp) and GC content ranged between 47 and 50% (ITS1, 43-49%; 5.8S rRNA gene, 56-57%; ITS2, 44-49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.

Molecular characterization and phylogenetic utility of the rDNA external transcribed spacer region in Stylosanthes (Fabaceae)

Supplementary Material The nucleotide sequence of the ribosomal external transcribed spacer (ETS) region of Stylosanthes mexicana was determined and used to evaluate its potential for examination of intra- and inter-specific relationships in Stylosanthes, as compared to the use of the internal transcribed spacer (ITS) region. The entire ETS region comprises 1,145 bp and is composed of a region of non-repetitive sequences consisting of three subregions with organizational and nucleotide-sequence conservation, and a triplicated segment of about 100 bp. A primer designed in the second conserved subregion allowed us to amplify and sequence directly the 3' part (423-431 bp) of the ETS from 22 genotypes of 12 representative Stylosanthes species that were previously used in phylogenetic analysis of the genus. The study revealed that the right-hand part of Stylosanthes ETS contains approximately twice as much variable and informative characters than the ITS. Moreover, pairwise sequence-divergence values are twice as high, on average, when compared to the ITS. The ITS and ETS datasets are consistent in phylogenetic reconstruction of Stylosanthes, and combined parsimony analysis resulted in a strict consensus tree that is better resolved and generally better supported than trees obtained from separate analysis of the spacer regions.

Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera)

Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers

The most economically important group of species in the genus Amaranthus is the A. hybridus species complex, including three cultivated grain amaranths, A. cruentus, A. caudatus, and A. hypochondriacus, and their putative wild progenitors, A. hybridus, A. quitensis, and A. powellii. Taxonomic confusion exists among these closely related taxa. Internal transcribed spacer (ITS) of nuclear ribosomal DNA, amplified fragment length polymorphism (AFLP), and double-primer fluorescent intersimple sequence repeat (ISSR) were employed to reexamine the taxonomic status and phylogenetic relationships of grain amaranths and their wild relatives. Low ITS divergence in these taxa resulted in poorly resolved phylogeny. However, extensive polymorphisms exist at AFLP and ISSR loci both within and among species. In phylogenetic trees based on either AFLP or ISSR or the combined data sets, nearly all intraspecific accessions can be placed in their corresponding species clades, indicating that these taxa are well-separated species. The AFLP trees share many features in common with the ISSR trees, both showing a close relationship between A. caudatus and A. quitensis, placing A. hybridus in the same clade as all grain amaranths, and indicating that A. powellii is the most divergent taxon in the A. hybridus species complex. This study has demonstrated that both AFLP and double-primer fluorescent ISSR have a great potential for generating a large number of informative characters for phylogenetic analysis of closely related species, especially when ITS diversity is insufficient.

European Lymnaeidae (Mollusca: Gastropoda), intermediate hosts of trematodiases, based on nuclear ribosomal DNA ITS-2 sequences

Freshwater snails of the family Lymnaeidae are of a great parasitological importance because of the very numerous helminth species they transmit, mainly trematodiases of large medical and veterinary impact. The present knowledge on the genetics of lymnaeids and on their parasite-host inter-relationships is far from being sufficient. The family is immersed in a systematic-taxonomic confusion. The necessity for a tool which enables species distinction and population characterization is evident. This paper aims to review the European Lymnaeidae basing on the second internal transcribed spacer ITS-2 of the nuclear ribosomal DNA. The ITS-2 sequences of 66 populations of 13 European and 1 North American lymnaeid species, including the five generic (or subgeneric) taxa Lymnaea sensu stricto, Stagnicola, Omphiscola, Radix and Galba, have been obtained. The ITS-2 proves to be a useful marker for resolving supraspecific, specific and population relationships in Lymnaeidae. Three different groupings according to their ITS-2 length could be distinguished: Radix and Galba may be considered the oldest taxa (370-406 bp lengths), and Lymnaea s. str., European Stagnicola and Omphiscola (468-491 bp lengths) the most recent, American Stagnicola and Hinkleyia being intermediate (434-450 bp lengths). This hypothesis agrees with the phylogeny of lymnaeids based on palaeontological data, chromosome numbers and radular dentition. ITS-2 sequences present a conserved central region flanked by two variable lateral regions corresponding to the 5' and 3' ends. The number of repeats of two microsatellites found in this conserved central region allows to differentiate Radix from all other lymnaeids. Phylogenetic trees showed four clades: (A) Lymnaea s. str., European Stagnicola and Omphiscola; (B) Radix species; (C) Galba truncatula; and (D) North American stagnicolines. ITS-2 results suggest that retaining Stagnicola as a subgenus of Lymnaea may be the most appropriate and that genus status for Omphiscola is justified. Radix shows a complexity suggesting different evolutionary lines, whereas G. truncatula appears to be very homogeneous. North American and European stagnicolines do not belong to the same supraspecific taxon; the genus Hinkleyia may be used for the American stagnicolines. Genetic distances and sequence differences allowed us to distinguish the upper limit to be expected within a single species and to how different sister species may be. S. palustris, S. fuscus and S. corvus proved to be valid species, but S. turricula may not be considered a species independent from S. palustris. Marked nucleotide divergences and genetic distances detected between different S. fuscus populations may be interpreted as a process of geographic differentiation developping in the present. Among Radix, six valid species could be distinguished: R. auricularia, R. ampla, R. peregra (=R. ovata;=R. balthica), R. labiata, R. lagotis and Radix sp. The information which the ITS-2 marker furnishes is of applied interest concerning the molluscan host specificity of the different trematode species. The phylogenetic trees inferred from the ITS-2 sequences are able to differentiate between lymnaeids transmitting and those non-transmitting fasciolids, as well as between those transmitting F. hepatica and those transmitting F. gigantica. The Fasciola specificity is linked to the two oldest genera which moreover cluster together in the phylogenetic trees, suggesting an origin of the Fasciola ancestors related to the origin of this branch. European Trichobilharzia species causing human dermatitis are transmitted only by lymnaeids of the Radix and Lymnaea s. str.-Stagnicola groups. Results suggest the convenience of reinvestigating compatibility differences after accurate lymnaeid species classification by ITS-2 sequencing. Similarly, ITS-2 sequencing would allow a step forward in the appropriate rearrangement of the actual systematic confusion among echinostomatids.

Phylogenetic relationships inferred from ribosomal its sequences and biogeographic patterns in representatives of the genus Calopteryx (Insecta: Odonata) of the West Mediterranean and adjacent West European zone

Western Europe is a reinvasion zone for the riverine dragonfly genus Calopteryx (Insecta: Odonata). Reinvasion may have been from central West Asia or from the West Mediterranean refugium. Phylogenetic relationships of West Mediterranean and West European taxa of the genus Calopteryx from different localities were inferred from sequences of the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal RNA genes. Twenty-six taxa belonging to the species groups C. splendens, C. meridionalis, C. haemorrhoidalis, C. virgo, C. xanthostoma, and C. exul were analyzed, with two North American species, C. amata and C. aequabilis, as outgroup. Sequence data and phylogenetic analyses were used to infer biogeographical patterns. The ribosomal spacers (ITS1 and ITS2) and the intervening 5.8S rDNA gene were amplified by PCR and sequenced. The ITS2 sequences of the West Mediterranean and West European calopterygids show no length variation but the ITS1 region was slightly variable in length. The sequence variation for ITS1 and ITS2 regions between different West Mediterranean and West European calopterygids was 14.5 and 6.1%, respectively. Phylogenetic relationships inferred from ITS sequences only partly confirm morphological data. A monophyletic origin of all West Mediterranean and West European species emerged. They are separated into two main clades; the splendens-like forms and the virgo/meridionalis/haemorrhoidalis group. Intraspecific variability, indicating different stages of speciation, was detected only in West Mediterranean representatives (e.g., C. xanthostoma) but not in invasive representatives in West Europe. The North African endemic C. exul is more closely related to the Italian C. s. caprai than to C. splendens sensu strictu. Based on the present information, Cretan populations are the only splendens-like taxa in addition to C. s. caprai that deserve subspecies status.

Comparative analysis of intra-individual and inter-species DNA sequence variation in salmonid ribosomal DNA cistrons

This study examines sequence divergence in three spacer regions of the ribosomal DNA (rDNA) cistron, to test the hypothesis of unequal mutation rates. Portions of two transcribed spacers (ITS-1 and 5' ETS) and the non-transcribed spacer (NTS) or intergenic spacer (IGS) formed the basis of comparative analyses. Sequence divergence was measured both within an individual lake trout (Salvelinus namaycush) and among several related salmonid species (lake trout; brook trout, Salvelinus fontinalis; Arctic char, Salvelinus alpinus; Atlantic salmon, Salmo salar; and brown trout, Salmo trutta). Despite major differences in the length of the rDNA cistron within individual lake trout, minimal sequence difference was detected among cistrons. Interspecies comparisons found that molecular variation in the rDNA spacers did not conform to the predicted pattern of evolution (ITS spacers<ETS spacers<IGS). Specifically, the IGS contains a region that appears to be as highly, or more conserved than the ITS-1.

Molecular evolution of the internal transcribed spacers (ITS1 and ITS2) and phylogenetic relationships among species of the family Cucurbitaceae

Phylogenetic relationships of different members of the family Cucurbitaceae were estimated from sequences of the internal transcribed spacer (ITS1 and ITS2) regions of the nuclear ribosomal RNA genes. Twenty-six species of different genera belonging to different tribes and several subtribes were analyzed. The whole ITS regions were amplified by PCR technique and cloned, and three to five different clones of each species were sequenced; for some species PCR products were sequenced directly. ITS1 and ITS2 regions are slightly variable in length, with each length appearing genus-specific. A substitution rate of 3.62 x 10(-9) substitutions per site per year was calculated assuming 40 MYA separation time. Phylogenetic relationships inferred from ITS sequences of some species is in agreement with morphological data, but deviations to the taxonomic classification were also observed. A polyphyletic origin of the New World species must be considered. In the genus Cucurbita different "types" of ITS sequences within one species exist, possibly due to the high frequency of introgression during domestication or due to polyploidization events; in contrast, low intraspecific variability was detectable in the genus Cucumis, indicating different stages of speciation.

Phylogenetic relationships of the Culicomorpha inferred from 18S and 5.8S ribosomal DNA sequences. (Diptera:Nematocera)

We investigated the evolutionary origins of the mosquito family Culicidae by examination of 18S and 5.8S ribosomal gene sequence divergence. Phylogenetic analyses demonstrated that within the infraorder Culicomorpha, taxa in the families Corethrellidae, Chaoboridae and Culicidae formed a monophyletic group; there was support for a sister relationship between this lineage and a representative of the Chironomidae. A chaoborid midge was the closest relative of the mosquitoes. Taxa from four genera of mosquitoes formed a monophyletic group; lack of a spacer in the 5.8S gene was unique to members of the Culicidae. A member of the genus Anopheles formed the most basal lineage among the mosquitoes analysed. Phylogenetic relationships were unresolved for representatives in the families Dixidae, Simuliidae and Ceratopogonidae.

Characterization of mycobionts of photomorph pairs in the peltigerineae (lichenized ascomycetes) based on internal transcribed spacer sequences of the nuclear ribosomal DNA

The "one fungus-two photomorphs" hypothesis suggests that certain lichenized fungi can establish a symbiotic relationship with either a eukaryotic or a prokaryotic photobiont. Such pairs of photomorphs are well know from cephalodiate Peltigerineae. Using an ascomycete-specific primer we amplified the internal transcribed spacer region of the nrDNA repeat of the mycobiont from total "lichen DNA" extracts of Peltigera malacea, photomorphs of P. aphthosa, P. britannica, and P. leucophlebia, Nephroma expallidum, and photomorphs of N. arcticum. Comparisons of 5.8S sequences suggest that the sequences obtained belong to the mycobiont and thus, that the ascomycete-specific primer is adequate for amplifying fungal DNA from total lichen-DNA extracts. The strict identity of nucleotide sequences of the internal transcribed spacer region of the nrDNA repeat between joined-photomorphs supports the one fungus-two photomorphs hypothesis. Photomorph may thus primarily reflect phenotypic plasticity of photomorphic fungi in response to changing environmental conditions. The cyanomorph recently reported for P. leucophlebia is shown to be based on a misidentified specimen of P. aphthosa. Comparisons of the ITS sequences further supports recognizing P. aphthosa, P. britannica, and P. leucophlebia at the species rather than the infraspecific level.

Evolution of the ITS sequences of ribosomal DNA in Enteromorpha (Chlorophyceae)

Ribosomal DNA (rDNA) region, including the 3' end of the 18S rRNA gene, the entire 5.8S rRNA gene, the 5' end of the 28S rRNA gene, and the internal transcribed spacers ITS 1 and ITS 2, of Enteromorpha green algae from the Baltic Sea, were sequenced. The evolution of the Enteromorpha sequences differed from those of other green algae in several important ways. The ITS regions were short and had a high nucleotide bias. The frequency of nucleotides G and C was up to 70% in the ITS sequences, whereas the frequencies were close to 50% in the 5.8S rDNA. Furthermore, the sequence divergence was much higher in ITS 1 than in ITS 2. Two haplotypes, differing only by two nucleotides, were detected in the E. intestinalis/compressa complex. The difference coincides with a morphological differentiation (branching of thalli) and may represent distinct gene pools.

Intraspecific variation in Cryptocaryon irritans

Intraspecific variation in the ciliate Cryptocaryon irritans was examined using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA) combined with developmental and morphological characters. Amplified rDNA sequences consisting of 151 bases of the flanking 18 S and 5.8 S regions, and the entire ITS-1 region (169 or 170 bases), were determined and compared for 16 isolates of C. irritans from Australia, Israel and the USA. There was one variable base between isolates in the 18 S region and 11 variable bases in the ITS-1 region. Despite their similar morphology, significant sequence variation (4.1% divergence) and developmental differences indicate that Australian C. irritans isolates from estuarine (Moreton Bay) and coral reef (Heron Island) environments are distinct. The Heron Island isolate was genetically closer to morphologically dissimilar isolates from Israel (1.8% divergence) and the USA (2.3% divergence) than it was to the Moreton Bay isolates. Three isolates maintained in our laboratory since February 1994 differed in sequence from earlier laboratory isolates (2.9% to 3.5% divergence), even though all were similar morphologically and originated from the same source. During this time the sequence of the isolates from wild fish in Moreton Bay remained unchanged. These genetic differences indicate the existence of a founder effect in laboratory populations of C. irritans. The genetic variation found here, combined with known morphological and developmental differences, is used to characterise four strains of C. irritans.

Mapping of the nucleolus organizer region on chromosome 4 in Arabidopsis thaliana

In Arabidopsis thaliana the ribosomal RNA genes (rRNA genes or rDNA) are clustered in tandemly repeated blocks in two nucleolus organizer regions (NORs). Cytogenetic analysis has shown that the NORs are localized on chromosome 2 (NOR 2) and 4 (NOR 4). Recently the map position of NOR 2 was determined using a RFLP which was larger than 100 kb. In the course of a fingerprint analysis of different Arabidopsis ecotypes we have detected four rDNA polymorphisms between the ecotypes Landsberg (La) and Niederzenz (Nd). Mapping of these polymorphisms using established segregating F2 populations reveals that all polymorphisms detected are dominant. Three of them map to the locus on the second chromosome that has been shown to harbour the NOR 2. The fourth polymorphism can be unambiguously assigned to the upper arm of the fourth chromosome. This is the first polymorphism found which originates in the second rDNA cluster of Arabidopsis thaliana. It enables localization of NOR 4 and thus completes the mapping of rDNA genes in the NORs of Arabidopsis.

Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L

Methylation with respect to its degree and distribution throughout the 18S, 5.8S and 25S rRNA gene clusters (rDNA) and within single rDNA repeats in seedlings of the higher plant Cucurbita pepo L. (zucchini) was investigated. In this plant, which is characterized by several thousand repeats, at least 70% are completely or nearly completely methylated in CpGs and to a lower degree in CpNpGs. Detailed methylation analysis revealed that a fraction of about 3-4% of all repeats is hypomethylated near the transcription initiation site (TIS) which may indicate the fraction of active repeats in C. pepo. However, a different fraction (3-4% of all repeats) which is not methylated in all sites tested (including those at the TIS) is present in C. pepo and may thus represent active but differentially methylated rDNA. The results are discussed in context of recent models on methylation and gene activity.

A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes

A highly conserved sequence was found in rRNA gene internal transcribed spacer 1 (ITS1) among flowering plant species. The sequence, GGCRY-(4 to 7 n)-GYGYCAAGGAA (where Y = C or T; R = G or A) is located in the central region of ITS1, and is present in published sequences from a wide range of flowering plants. The rest of ITS1 is highly variable in sequence. Therefore, the conserved motif within ITS1 may have a key function in the processing of rRNA gene transcripts. Furthermore, identification of such a conserved motif will help facilitate alignment of sequences for phylogenetic analysis.

Partial nucleotide sequence of a single ribosomal RNA coding region and secondary structure of the large subunit 25 s rRNA of Candida albicans

A rDNA cistron of Candida albicans strain WO-1 was cloned and the ITS1, ITS2, 5.8 s rDNA and 25 s rDNA coding regions sequenced in their entirety. These sequences were compared to those of three related yeast species (Saccharomyces cerevisiae, Saccharomyces carlsbergensis, and Thermomyces lanuginosus), and the 5.8 s rDNA was compared to seven additional 5.8 s rDNAs from organisms ranging in complexity from D. discoideum to H. sapiens. The C. albicans ITS regions are shorter than those of most other eukaryotes. The 25 s and 5.8 s rDNA sequences were folded into a secondary structure model based on comparative methods. In a comparison of regional similarities between the large subunit rDNAs of C. albicans, the three related yeasts and other eukaryotes, it is demonstrated that the additional sequences not present in the E. coli 23 s rDNA are more variable than the regions present in both prokaryotes and eukaryotes.

Molecular markers in plant ecology

Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations arc briefly discussed. PCR-based methods, especially arnitrary-primer-based RAPDs, are likely to be most widely used and receive most attention. The limited use of DNA markers for overall quantitative (phenetic) comparisons of 'genetic variability' and 'generic distance' is stressed and fheir power as qualitative markers for any and all relevant regions in the genome is emphasized. Specific applications relevant to plant ecology are illustrated. These are: identification of organism and genotype even where morphology is of little help, as in mycorrhiza; identification of clones in asexually-reproducing species, even when they are widespread and intermingled; determining if genetic variation in elonal populations comes from mutations within elonal lines or from independent origins of clonal lines; reconstructing the genotype phylogeny and fruit dispersal of elonal (apomicuc) and inbred selling organisms, measuring the degree of outcrossing by offspring exclusion analysis; detecting and analyzing introgression and characterizing reeombinant genotypes in hybrid zones relative to differential adaptive responses: tracing the phylogenetic origin and extent of ecologically differentiated races or species; characterizing the genetic basis, mapping and isolating the genes responsible for special adaptive responses. In a final outlook, 1 speculate about unconventional sources of genetic variation affecting the ecological characteristics of plants that will become accessible to experimental analysis with the new molecular methods. Contents Summary 403 I. Introduction 404 II. Most ecological applications concern markers in the nuclear geonome 404 III. DNA polymorphisms differ from allozyme pohmorphisms 404 IV. Types of molecular marker 405 V. The application of markers in ecology 409 VI. From marker to character 413 VII. Outlook 414 References 414.

Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of cucurbitaceae

The intergenic spacer (IGS) of a 10-kbp repeat (clone pRZ7D) of the nuclear 18S, 5.8S, and 25S ribosomal RNA genes of Cucurbita pepo (zucchini) was sequenced and compared to the IGS sequences of two other Cucurbitaceae, Curcurbita maxima (squash), and Cucumis sativus (cucumber). The nucleotide sequence and the structural organization of the IGS of C. pepo and C. maxima are rather similar (between 75 and 100% sequence similarity depending on the region compared). The IGS are mainly composed of three different repeated elements interspersed into unique sequences: GC-rich clusters, a 422-bp AT-rich element including the transcription initiation site (TIS) for RNA polymerase I, and 260-bp repeats in the 5' external transcribed spacer (D repeats). The TIS is duplicated in the 10-kbp repeat class of C. pepo, as it is also described for the 11.5-kbp rDNA repeat of C. maxima. The IGS of Cucumis sativus is also composed of different repeated elements; however, obvious sequence identity to the Cucurbita species only occurs around the TIS and the preceding AT-rich region. GC-rich clusters with different primary sequences are present in the IGS of all three plants. Remarkably, the repeated elements in the 5'ETS accumulate TpG and TpNpG motifs, whereas CpG and CpNpG motifs less frequently occur. This accumulation might be caused by the transition of methylated cytosines (in mCpG or mCpNpG motifs) into thymidine via deamination in a previously GC-rich ancestor. The following singular region exhibits 50% G + C in C. pepo, 53% G+C in C. maxima, and 63% G + C in C. sativus.(ABSTRACT TRUNCATED AT 250 WORDS)

The internal transcribed spacers of ribosomal DNA in five members of the Anopheles gambiae species complex

The primary and secondary structure of the internal transcribed spacers of ribosomal DNA (ITS1 and ITS2) and their utility for phylogenetic analysis of closely related species were examined using the Anopheles gambiae complex as a model. Restriction mapping revealed an unusual architectural feature in the ITS1 of several members of an An. gambiae cryptic species complex. Multiple spacer lengths are prevalent in An. merus and An. melas and are due to variable numbers of a repeated 250 bp sequence. Secondary structure analysis indicated that the repeat forms a helix and loop that may be involved in rDNA processing. Intra- and interspecific polymorphism within the species complex were further examined by DNA sequencing of forty-eight ITS2 clones obtained by polymerase chain reaction from individuals of the five species. Interspecies variation in the approximately 426 bp ITS2 sequence ranged between 0.4% and 1.6%; intraspecies variation ranged from 0.07% in An. arabiensis to 0.43% in An. gambiae. Intraindividual variation ranged from 0% in four individuals to a high of 0.4% in one An. quadriannulatus specimen. None of the variants were shared between species. The low level of variation supports the hypothesis that species of the complex evolved recently.

Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae)

Sequences of the internal transcribed spacers (ITS1 and ITS2) of the mosquito Aedes aegypti, and the ITS2 of six related species, A. simpsoni, A. albopictus, A. vexans, A. triseriatus, Haemagogus mesodentatus, and Psorophora ferox are reported. Intraspecific variation in A. aegypti ITS1 is 1.07% among four clones from three individuals, and in the ITS2 is 1.17% among 15 clones from four individuals. In A. simpsoni, intraspecific ITS2 variation is 0.46% among 10 clones from a single individual. Alignment of the ITS2 sequence of the seven species reveals several homologous domains. Secondary structure predictions for the ITS2 region indicate that these domains base pair to form a core region central to several stem features. The sequence outside the ITS2 homologous domains tends to be GC-rich and characteristically slippage generated; these areas preserve or add to the stem length of the predicted secondary structures. These ITS2 intraspacer variable regions resemble previously described expansion segments of the 28S gene region. Evolutionary analysis of the ITS2 of these species, using both sequence and secondary structure information, leads to the prediction of divergence in the mosquito tribe Aedini that is not clearly reflected in current taxonomic designations.