Evolution of the 5.8S nrDNA gene and internal transcribed spacers in Carapichea ipecacuanha (Rubiaceae) within a phylogeographic context

Allopatric Lineage Divergence of the East Asian Endemic Herb Conandron ramondioides Inferred from Low-Copy Nuclear and Plastid Markers

The evolutionary histories of ornamental plants have been receiving only limited attention. We examined the origin and divergence processes of an East Asian endemic ornamental plant, Conandron ramondioides. C. ramondioides is an understory herb occurring in primary forests, which has been grouped into two varieties. We reconstructed the evolutionary and population demography history of C. ramondioides to infer its divergence process. Nuclear and chloroplast DNA sequences were obtained from 21 Conandron populations on both sides of the East China Sea (ECS) to explore its genetic diversity, structure, and population differentiation. Interestingly, the reconstructed phylogeny indicated that the populations should be classified into three clades corresponding to geographical regions: the Japan (Honshu+Shikoku) clade, the Taiwan-Iriomote clade, and the Southeast China clade. Lineage divergence between the Japan clade and the Taiwan-Iriomote and Southeast China clades occured 1.14 MYA (95% HPD: 0.82-3.86), followed by divergence between the Taiwan-Iriomote and Southeast China clades approximately 0.75 MYA (95% HPD: 0.45-1.3). Furthermore, corolla traits (floral lobe length to tube length ratios) correlated with geographical distributions. Moreover, restricted gene flow was detected among clades. Lastly, the lack of potential dispersal routes across an exposed ECS seafloor during the last glacial maximum suggests that migration among the Conandron clades was unlikely. In summary, the extant Conandron exhibits a disjunct distribution pattern as a result of vicariance rather than long-distance dispersal. We propose that allopatric divergence has occurred in C. ramondioides since the Pleistocene. Our findings highlight the critical influence of species' biological characteristics on shaping lineage diversification of East Asian relic herb species during climate oscillations since the Quaternary.

Extensive nrDNA ITS polymorphism in Lycium: Non-concerted evolution and the identification of pseudogenes

The internal transcribed spacer (ITS) is one of the most extensively sequenced molecular markers in plant systematics due to its generally concerted evolution. While non-concerted evolution has been found in some plant taxa, such information is missing in Lycium. Molecular studies of six species and two variants of the genus Lycium revealed high levels of intra- and inter-individual polymorphism in the ITS, indicating non-concerted evolution. All genomic DNA ITS paralogues were identified as putative pseudogenes or functional paralogues through a series of comparisons of sequence features, including length and substitution variation, GC content, secondary structure stability, and the presence of conserved motifs in the 5.8S gene, and the rate of evolution. Approximately, 60% of ITS pseudogenes could be easily detected. Based on phylogenetic analysis, all pseudogenes were highly distinct from their corresponding functional copies, tended to evolve neutrally, and clustered randomly together in the evolutionary tree. The results probably suggest that this ITS non-concerted evolution is related to the recent divergence between tandem repeats within the Lycium genome and hybridization between species. Our study complements those of pseudogenes in plant taxa and provides a theoretical basis for the phylogeny and genetic origin of the genus Lycium while having important implications for the use of ITS molecular markers for phylogenetic reconstruction.

Phylogenomic incongruence in Ceratocystis: a clue to speciation?

Background

The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. Species delineation in Ceratocystis primarily relied on genealogical concordance phylogenetic species recognition (GCPSR) using multiple standard molecular markers.

Results

Questions have arisen regarding the utility of these markers e.g., ITS, BT and TEF1-α due to evidence of intragenomic variation in the ITS, as well as genealogical incongruence, especially for isolates residing in a group referred to as the Latin-American clade (LAC) of the species. This study applied a phylogenomics approach to investigate the extent of phylogenetic incongruence in Ceratocystis. Phylogenomic analyses of a total of 1121 shared BUSCO genes revealed widespread incongruence within Ceratocystis, particularly within the LAC, which was typified by three equally represented topologies. Comparative analyses of the individual gene trees revealed evolutionary patterns indicative of hybridization. The maximum likelihood phylogenetic tree generated from the concatenated dataset comprised of 1069 shared BUSCO genes provided improved phylogenetic resolution suggesting the need for multiple gene markers in the phylogeny of Ceratocystis.

Conclusion

The incongruence observed among single gene phylogenies in this study call into question the utility of single or a few molecular markers for species delineation. Although this study provides evidence of interspecific hybridization, the role of hybridization as the source of discordance will require further research because the results could also be explained by high levels of shared ancestral polymorphism in this recently diverged lineage. This study also highlights the utility of BUSCO genes as a set of multiple orthologous genes for phylogenomic studies.

Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences

Background

Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information.

Methods

We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry.

Results

We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades.

Conclusions

Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.

Molecular evolution of the internal transcribed spacers in red oaks (Quercus sect. Lobatae)

Previous studies of the Internal Transcribed Spacers of the nuclear ribosomal DNA (ITS) in sections Quercus (white oaks), Protobalanus (intermediate or golden cup oaks), Cerris (Cerris oaks), and Ilex (Ilex oaks) suggest that ITS regions undergo full concerted evolution in oaks; however, ITS evolution patterns in red oaks (section Lobatae) are unknown due to scant representation in published work. To determine whether full concerted evolution occurs in red oaks, the purpose of this study was to examine ITS sequences from 40 red oak species. The results show incomplete concerted evolution and the presence of three ITS ribotypes of lengths 505, 609, 601 bp, hereafter referred to as ITS-S (small), I ITS-M (medium), and ITS-L (large), respectively. Thirty species had only one ribotype (ITS-M), nine species had two ribotypes (different combinations of ITS-L, ITS-M, and ITS-S), and only one species had all three ribotypes. Furthermore, examination of these three ribotypes showed that only ITS-M is putatively functional and ITS-L and ITS-S are pseudogenes. Bayesian analysis strongly supported (100%) two pseudogenes clades but provided weak support for the monophyly of a putative functional clade (ITS-M); moreover, within the "functional" clade, species relationships were uncertain and, in most cases, sequences from the same species failed to group together. The results of the current study suggest that ITS may not be appropriate for phylogeny reconstruction of red oaks due to low levels of interspecific variation and incomplete concerted evolution.

Genetic polymorphism of Japanese cultivated Rheum species in the internal transcribed spacer region of nuclear ribosomal DNA

In order to develop new domestic production of Rhei Rhizoma (RR) from Rheum specimens cultivated in the Sugadaira Medicinal Plant Cultivation Test Field (SMPCF), the ITS sequences of 12 SMPCF specimens and Chinese Rheum specimens of four species, as well as RR samples produced in North Korea, China and Japan, were determined by subcloning and their sequences were compared. As the ITS sequences of 10 SMPCF specimens showed significant intra-individual polymorphism, identification of pseudogenes was conducted by detecting the three motifs of the 5.8S sequence and the stability of the 5.8S secondary structure. Approximately 46% of sequences obtained from the SMPCF specimens were putative pseudogenes. The maximum likelihood tree based on ITS sequences showed three main groups-the outer group and inner clusters I and II; clones from 10 SMPCF specimens including putative pseudogenes belonged to the outer group. Cluster I was composed of two clades, one including clones from R. officinale specimens and R. palmatum-derived samples with matK genotype Rp9, and another including clones from R. coreanum-derived samples. Cluster II consisted of three clades, one including clones from R. palmatum specimens with genotype Rp5, another including clones mainly from R. tanguticum specimens with genotype Rt4, and the third including clones from R. palmatum or R. tanguticum specimens with various matK genotypes. Clones from SMPCF specimen RC5 showed a close relationship with those from R. tanguticum specimens with matK genotype Rt4, whereas those from specimen RC9 related to R. coreanum-derived samples. As a result, specimens RC5 and RC9 were considered as candidates for the development of domestic RR.

Common Origin of Brazilian and Colombian Populations of the Neotropical Coffee Leaf Miner, Leucoptera coffeella (Lepidoptera: Lyonetiidae)

The coffee leaf miner, Leucoptera coffeella (Guérin-Mèneville & Perrottet, 1842), probably infested coffee plants in Neotropical America during the 19th century. The species subsequently became a key pest of coffee plants in Brazil, but not in Colombia, the two main coffee producers in the region. The contrasting importance of the coffee leaf miner in Brazil and Colombia may be the result of the evolutionary and demographic history of this species. Therefore, our goal was to test two alternative hypotheses regarding the possible genetic origins of this species: 1) leaf miners in both countries share the same origin and 2) the leaf miner arrived in both countries independently from distinct sources and subsequently diversified without genetic exchange between countries. Thus, DNA sequence data of 21 populations were collected (Brazil, 16; Colombia, 5), and partial sequences of their cytochrome oxidase subunit I (COI), cytochrome b (Cytb), and the nuclear internal transcribed spacer (ITS) region were obtained to test these hypotheses. Both nuclear and mitochondrial molecular markers showed low nucleotide diversity. Analyses of molecular variance indicated higher variability within population in both concatenated mitochondrial genes and ITS region (70.57 and 84.01%, respectively). Finally, geno/haplotype networks showed each central geno/haplotypes that displayed high frequency and were distributed widely in both countries. Low-frequency geno/haplotypes were at tip positions connected to the central geno/haplotypes through single mutation steps, suggesting that the Neotropical coffee leaf miner in both Brazil and Colombia consists of a single species and exhibits a common and recent genetic origin.

Birth-and-Death Evolution and Reticulation of ITS Segments of Metschnikowia andauensis and Metschnikowia fructicola rDNA Repeats

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) separates the genes coding for the SSU 18S and the LSU 26S genes in the rDNA units which are organized into long tandem arrays in the overwhelming majority of fungi. As members of a multigenic family, these units are subject of concerted evolution, which homogenizes their sequences. Exceptions have been observed in certain groups of plants and in a few fungal species. In our previous study we described exceptionally high degree of sequence diversity in the D1/D2 domains of two pulcherrimin-producing Metschnikowia (Saccharomycotina) species which appeared to evolve by reticulation. The major goals of this study were the examination of the diversity of the ITS segments and their evolution. We show that the ITS sequences of these species are not homogenized either, differ from each other by up to 38 substitutions and indels which have dramatic effects on the predicted secondary structures of the transcripts. The high intragenomic diversity makes the D1/D2 domains and the ITS spacers unsuitable for barcoding of these species and therefore the taxonomic position of strains previously assigned to them needs revision. By analyzing the genome sequence of the M. fructicola type strain, we also show that the rDNA of this species is fragmented, contains pseudogenes and thus evolves by the birth-and-death mechanism rather than by homogenisation, which is unusual in yeasts. The results of the network analysis of the sequences further indicate that the ITS regions are also involved in reticulation. M. andauensis and M. fructicola can form interspecies hybrids and their hybrids segregate, providing thus possibilities for reticulation of the rDNA repeats.

Secondary structure of nrDNA Internal Transcribed Spacers as a useful tool to align highly divergent species in phylogenetic studies

Recently, it has been suggested that internal transcribed spacer (ITS) sequences are under selective constraints to preserve their secondary structure. Here, we investigate the patterns of the ITS nucleotide and secondary structure conservation across the Passiflora L. genus to evaluate the potential use of secondary structure data as a helpful tool for the alignment in taxonomically complex genera. Considering the frequent use of ITS, this study also presents a perspective on future analyses in other plant groups. The ITS1 and ITS2 sequences presented significant differences for mean values of the lowest energy state (LES) and for number of hairpins in different Passiflora subgenera. Statistical analyses for the subgenera separately support significant differences between the LES values and the total number of secondary structures for ITS. In order to evaluate whether the LES values of ITS secondary structures were related to selective constraints, we compared these results among 120 ITS sequences from Passiflora species and 120 randomly generated sequences. These analyses indicated that Passiflora ITS sequences present characteristics of a region under selective constraint to maintain the secondary structure showing to be a promising tool to improve the alignments and identify sites with non-neutral substitutions or those correlated evolutionary steps.

ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza (Fabaceae)

The internal transcribed spacer (ITS) as one part of nuclear ribosomal DNA is one of the most extensively sequenced molecular markers in plant systematics. The ITS repeats generally exhibit high-level within-individual homogeneity, while relatively small-scale polymorphism of ITS copies within individuals has often been reported in literature. Here, we identified large-scale polymorphism of ITS copies within individuals in the legume genus Lespedeza (Fabaceae). Divergent paralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS copies were sometimes detected in the same individual. Thirty-seven ITS pseudogenes could be easily detected according to nucleotide changes in conserved 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lost ability of 5.8S rDNA sequence to fold into a conserved secondary structure. The distribution patterns of the putative functional clones were highly different between the traditionally recognized two subgenera, suggesting different rates of concerted evolution in two subgenera which could be attributable to their different extents/frequencies of hybridization, confirmed by our analysis of the single-copy nuclear gene PGK. These findings have significant implications in using ITS marker for reconstructing phylogeny and studying hybridization.

Allopolyploid Origin of Chenopodium album s. str. (Chenopodiaceae): A Molecular and Cytogenetic Insight

Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolyploidization events. We sampled 122 individuals of the C. album aggregate, covering most of its distribution range in Eurasia. Our samples included putative progenitors of C. album s. str. of both ploidy levels, i.e. diploids (C. ficifolium, C. suecicum) and tetraploids (C. striatiforme, C. strictum). To fulfil these objectives, we analysed sequence variation in the nrDNA ITS region and the rpl32-trnL intergenic spacer of cpDNA and performed genomic in-situ hybridization (GISH). Our study confirms the allohexaploid origin of C. album s. str. Analysis of cpDNA revealed tetraploids as the maternal species. In most accessions of hexaploid C. album s. str., ITS sequences were completely or nearly completely homogenized towards the tetraploid maternal ribotype; a tetraploid species therefore served as one genome donor. GISH revealed a strong hybridization signal on the same eighteen chromosomes of C. album s. str. with both diploid species C. ficifolium and C. suecicum. The second genome donor was therefore a diploid species. Moreover, some individuals with completely unhomogenized ITS sequences were found. Thus, hexaploid individuals of C. album s. str. with ITS sequences homogenized to different degrees may represent hybrids of different ages. This proves the existence of at least two different allopolyploid lineages, indicating a polyphyletic origin of C. album s. str.

Application of the Ribosomal DNA ITS2 Region of Physalis (Solanaceae): DNA Barcoding and Phylogenetic Study

Recently, commercial interest in Physalis species has grown worldwide due to their high nutritional value, edible fruit, and potential medicinal properties. However, many Physalis species have similar shapes and are easily confused, and consequently the phylogenetic relationships between Physalis species are poorly understood. This hinders their safe utilization and genetic resource conservation. In this study, the nuclear ribosomal ITS2 region was used to identify species and phylogenetically examine Physalis. Eighty-six ITS2 regions from 45 Physalis species were analyzed. The ITS2 sequences were aligned using Clustal W and genetic distances were calculated using MEGA V6.0. The results showed that ITS2 regions have significant intra- and inter-specific divergences, obvious barcoding gaps, and higher species discrimination rates (82.2% for both the BLASTA1 and nearest distance methods). In addition, the secondary structure of ITS2 provided another way to differentiate species. Cluster analysis based on ITS2 regions largely concurred with the relationships among Physalis species established by many previous molecular analyses, and showed that most sections of Physalis appear to be polyphyletic. Our results demonstrated that ITS2 can be used as an efficient and powerful marker in the identification and phylogenetic study of Physalis species. The technique provides a scientific basis for the conservation of Physalis plants and for utilization of resources.

Molecular evidence of hybrid zones of Cedrela (Meliaceae) in the Yungas of Northwestern Argentina

In the Yungas of Northwestern Argentina, three endangered species of Cedrela (C. angustifolia, C. saltensis, and C. balansae) follow altitudinal gradients of distribution with contact zones between them. We sampled 210 individuals from 20 populations that spanned most of Cedrela's geographical range in the Yungas, and used Amplified Fragment Length Polymorphism (AFLP) markers and DNA sequences of the nuclear Internal Transcribed Spacer (ITS) to investigate hybrid zones. Data analyses employed an array of complementary methods, including principal coordinate analyses, Bayesian clustering analyses, maximum likelihood tree-building, and network techniques. Both nuclear molecular systems - AFLP and ITS - provided insights into the evolutionary history of Cedrela in the Yungas in a congruent manner. We uncovered strong support for the occurrence of natural hybridization between C. balansae and C. saltensis. Additionally, we identified hybrid zones in areas of sympatry (at both the Calilegua National Park and the San Andrés farm) and in transition zones from 820 to 1100meters above sea level (localities of Pintascayo and Acambuco). There was no evidence for hybridization of either C. balansae or C. saltensis with C. angustifolia. The role of hybrid populations in conservation and use of genetic resources in the Yungas were discussed.

Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study

The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium.

ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex

The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the Ranunculus auricomus complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogenetic network analyses indicate additivity of parental ITS variants in both synthetic and natural hybrids. The triploid synthetic hybrids are genetically much closer to their maternal progenitors, probably due to ploidy dosage effects, although exhibiting a paternal-like leaf morphology. The natural hybrids are genetically and morphologically closer to the putative paternal progenitor species. Secondary structures of ITS1-5.8S-ITS2 were rather conserved in all taxa. The observed similarities in ITS polymorphisms suggest that the natural apomict R. variabilis is an ancient hybrid of the diploid sexual species R. notabilis and the sexual species R. cassubicifolius. The additivity pattern shared by R. variabilis and the synthetic hybrids supports an evolutionary and biogeographical scenario that R. variabilis originated from ancient hybridization. Concerted evolution of ITS copies in R. variabilis is incomplete, probably due to a shift to asexual reproduction. Under the condition of comprehensive inter- and intraspecific sampling, ITS polymorphisms are powerful for elucidating reticulate evolutionary histories.

Concordance between phylogeographical and biogeographical patterns in the Brazilian Cerrado: diversification of the endemic tree Dalbergia miscolobium (Fabaceae)

Few studies have addressed the phylogeography of species of the Cerrado, the largest savanna biome of South America. Here we aimed to investigate the phylogeographical structure of Dalbergia miscolobium, a widespread tree from the Cerrado, and to verify its concordance with plant phylogeographical and biogeographical patterns so far described. A total of 287 individuals from 32 populations were analyzed by sequencing the trnL intron of the chloroplast DNA and the internal transcribed spacer of the nuclear ribosomal DNA. Analysis of population structure and tests of population expansion were performed and the time of divergence of haplotypes was estimated. Twelve and 27 haplotypes were identified in the cpDNA and nrDNA data, respectively. The star-like network configuration and the mismatch distributions indicated a recent spatial and demographic expansion of the species. Consistent with previous tree phylogeographical studies of Cerrado trees, the cpDNA also suggested a recent expansion towards the southern Cerrado. The diversity of D. miscolobium was widespread but high levels of genetic diversity were found in the Central Eastern and in the southern portion of Central Western Cerrado. The combined analysis of cpDNA and nrDNA supported a phylogeographic structure into seven groups. The phylogeographical pattern showed many concordances with biogeographical and phylogeographical studies in the Cerrado, mainly with the Cerrado phytogeographic provinces superimposed to our sampling area. The data reinforced the uniqueness of Northeastern and Southeastern Cerrados and the differentiation between Eastern and Western Central Cerrados. The recent diversification of the species (estimated between the Pliocene and the Pleistocene) and the ‘genealogical concordances’ suggest that a shared and persistent pattern of species diversification might have been present in the Cerrado over time. This is the first time that an extensive ‘genealogical concordance’ between phylogeographic and phytogeographic patterns is shown for the Cerrado biome.

(Cryptic) sex in the microsporidian Nosema granulosis--evidence from parasite rDNA and host mitochondrial DNA

Microsporidia are single-celled, intracellular eukaryotes that parasitise a wide range of animals. The Nosema/Vairimorpha group includes some putative asexual species, and asexuality is proposed to have originated multiple times from sexual ancestors. Here, we studied the variation in the ribosomal DNA (rDNA) of 14 isolates of the presumed apomictic and vertically transmitted Nosema granulosis to evaluate its sexual status. The analysed DNA fragment contained a part of the small-subunit ribosomal gene (SSU) and the entire intergenic spacer (IGS). The mitochondrial cox1 gene of the host Gammarus duebeni (Crustacea) was analysed to temporally calibrate the system and to test the expectation of cophylogeny of host and parasite genealogies. Genetic variability of the SSU gene was very low within and between the isolates. In contrast, intraisolate (within a single host) variability of the IGS felt in two categories, because 12 isolates possess a very high IGS genetic diversity and two isolates were almost invariable in the IGS. This difference suggests variable models of rDNA evolution involving birth-and-death and unexpectedly concerted evolution. An alternative explanation could be a likewise unattended mixed infection of host individuals by more than one parasite strain. Despite considerable genetic divergence between associated host mitochondrial haplotypes, some N. granulosis 'IGS populations' seem not to belong to different gene pools; the relevant tests failed to show significant differences between populations. A set of recombinant IGS sequences made our data incompatible with the model of a solely maternally inherited, asexual species. In line with recent reports, our study supports the hypothesis that some assumed apomictic Microsporidia did not entirely abstain from the evolutionary advantages of sex. In addition, the presented data indicate that horizontal transmission may occur occasionally. This transmission mode could be a survival strategy of N. granulosis whose host often populates ephemeral habitats.

Cyclotide discovery in Gentianales revisited--identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plants

Cyclotides are a unique class of ribosomally synthesized cysteine-rich miniproteins characterized by a head-to-tail cyclized backbone and three conserved disulfide-bonds in a knotted arrangement. Originally they were discovered in the coffee-family plant Oldenlandia affinis (Rubiaceae) and have since been identified in several species of the violet, cucurbit, pea, potato, and grass families. However, the identification of novel cyclotide-containing plant species still is a major challenge due to the lack of a rapid and accurate analytical workflow in particular for large sampling numbers. As a consequence, their phylogeny in the plant kingdom remains unclear. To gain further insight into the distribution and evolution of plant cyclotides, we analyzed ∼300 species of >40 different families, with special emphasis on plants from the order Gentianales. For this purpose, we have developed a refined screening methodology combining chemical analysis of plant extracts and bioinformatic analysis of transcript databases. Using mass spectrometry and transcriptome-mining, we identified nine novel cyclotide-containing species and their related cyclotide precursor genes in the tribe Palicoureeae. The characterization of novel peptide sequences underlines the high variability and plasticity of the cyclotide framework, and a comparison of novel precursor proteins from Carapichea ipecacuanha illustrated their typical cyclotide gene architectures. Phylogenetic analysis of their distribution within the Psychotria alliance revealed cyclotides to be restricted to Palicourea, Margaritopsis, Notopleura, Carapichea, Chassalia, and Geophila. In line with previous reports, our findings confirm cyclotides to be one of the largest peptide families within the plant kingdom and suggest that their total number may exceed tens of thousands.

Intragenomic Profiling Using Multicopy Genes: The rDNA Internal Transcribed Spacer Sequences of the Freshwater Sponge Ephydatia fluviatilis

Multicopy genes, like ribosomal RNA genes (rDNA), are widely used to describe and distinguish individuals. Despite concerted evolution that homogenizes a large number of rDNA gene copies, the presence of different gene variants within a genome has been reported. Characterization of an organism by defining every single variant of tens to thousands of rDNA repeat units present in a eukaryotic genome would be quite unreasonable. Here we provide an alternative approach for the characterization of a set of internal transcribed spacer sequences found within every rDNA repeat unit by implementing direct sequencing methodology. The prominent allelic variants and their relative amounts characterizing an individual can be described by a single sequencing electropherogram of the mixed amplicon containing the variants present within the genome. We propose a method for rational analysis of heterogeneity of multicopy genes by compiling a profile based on quantification of different sequence variants of the internal transcribed spacers of the freshwater sponge Ephydatia fluviatilis as an example. In addition to using conventional substitution analysis, we have developed a mathematical method, the proportion model method, to quantify the relative amounts of allelic variants of different length using data from direct sequencing of the heterogeneous amplicon. This method is based on determining the expected signal intensity values (corresponding to peak heights from the sequencing electropherogram) by sequencing clones from the same or highly similar amplicon and comparing hypothesized combinations against the values obtained by direct sequencing of the heterogeneous amplicon. This method allowed to differentiate between all specimens analysed.

Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis

The internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) has been widely used as a molecular marker in phylogenetic studies and has been selected as a DNA barcode for fungi. It is generally believed that nrDNA conforms to concerted evolution in most eukaryotes; however, intraindividual-intraspecific polymorphisms of this region were reported in various organisms, suggesting a non-concerted evolutionary process. In Ophiocordyceps sinensis, one of the most valuable medicinal fungi, a remarkable variation of the ITS region has been revealed. Some highly divergent sequences were thought to represent cryptic species, different species or genotypes in previous studies. To clarify the unusual ITS polymorphisms observed in O. sinensis, specific primers were designed to amplify ITS paralogs from pure cultures of both single-ascospore and tissue isolates in this study. All of the available ITS sequences, including those generated by this group and those in GenBank, were analyzed. Several AT-biased ITS paralogs were classified as pseudogenes based on their nucleotide compositions, secondary structures and minimum free energies of their 5.8S rRNAs, substitution rates, phylogenetic positions and gene expression analyses. Furthermore, ITS pseudogenes were amplified with specific primers from 10 of the 28 strains tested, including eight single-ascospore and two tissue isolates. Divergent ITS paralogs were proved to coexist in individual genomes, suggesting a non-concerted mechanism of evolution in the ITS region of O. sinensis. The hypotheses that divergent ITS paralogs represent cryptic or other species or different genotypes were thus rejected.

Concerted evolution in the ribosomal RNA cistron

BACKGROUND

Gene conversion is the mechanism proposed to be responsible for the homogenization of multigene families such as the nuclear ribosomal gene clusters. This concerted evolutionary process prevents individual genes in gene clusters from accumulating mutations. The mechanism responsible for concerted evolution is not well understood but recombination during meiosis has been hypothesized to play a significant role in this homogenization. In this study we tested the hypothesis of unequal crossing over playing a significant role in gene conversion events within the ribosomal RNA cistron during meiosis, mitosis or both life stages in the fungal tree pathogen Ceratocystis manginecans.

METHODS

Ceratocystis manginecans, a haploid ascomycete, reproduces homothallically and was found to have two distinct sequences within the internally transcribed spacer (ITS) region of the ribosomal RNA cistron. The different ITS types were scored using PCR-RFLP assays and chi-square analyses to determine the level of significance of the changes in the ratios of the ITS types.

RESULTS

The relative ratios of the two ITS sequence types changed when the fungal isolates were cultured vegetatively or allowed to produced sexual structures and spores. These active changes were shown to occur more frequently during meiosis than mitosis.

CONCLUSION

The evidence presented provides concrete support for homogenization in the rRNA gene clusters found in this fungus and that the most reasonable explanation for this process is unequal crossing over.

Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi

Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.

Nucleotide polymorphism in the 5.8S nrDNA gene and internal transcribed spacers in Phakopsora pachyrhizi viewed from structural models

The assessment of nucleotide polymorphisms in environmental samples of obligate pathogens requires DNA amplification through the polymerase chain reaction (PCR) and bacterial cloning of PCR products prior to sequencing. The drawback of this strategy is that it can give rise to false polymorphisms owing to DNA polymerase misincorporation during PCR or bacterial cloning. We investigated patterns of nucleotide polymorphism in the internal transcribed spacer (ITS) region for Phakopsora pachyrhizi, an obligate biotrophic fungus that causes the Asian soybean rust. Field-collected samples of P. pachyrhizi were obtained from all major soybean production areas worldwide, including Brazil and the United States. Bacterially-cloned, PCR products were obtained using a high fidelity DNA polymerase. A total of 370 ITS sequences that were subjected to an array of complementary sequence analyses, which included analyses of secondary structure stability, the pattern of nucleotide polymorphisms, GC content, and the presence of conserved motifs. The sequences exhibited features of functional rRNAs. Overall, polymorphisms took place within less conserved motives, such as loops and bulges; alternatively, they gave rise to non-canonical G-U pairs within conserved regions of double stranded helices. We discuss the usefulness of structural analyses to filter out putative 'suspicious' bacterially cloned ITS sequences, thus keeping artificially-induced sequence variation to a minimum.