The rDNA ITS region in the lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): intragenomic variability and putative pseudogenic sequences

ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea

Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.

Biosynthesis of metal nanoparticles using three marine plant species: anti-algal efficiencies against "Oscillatoria simplicissima"

This study aims at controlling of the cyanobacteria Oscillatoria simplicissima, those that produce neurotoxins and have negative impacts on the aquatic organisms, using biosynthesized metal nanoparticles (NPs). Silver-NPs (Ag-NPs) have been successfully biosynthesized using Nannochloropsis oculata and Tetraselmis tetrathele cultures. Also, Ag-NPs and iron oxide-NPs (Fe₃O₄-NPs) were synthesized by Halophila stipulacea aqueous extract. The structural composition of the different biosynthesized NPs was studied. The algae cultures and the extract were used as reductants of AgNO₃, and brown colors due to Ag-NP biosynthesis were observed. Silver signals were recorded in their corresponding EDX spectra. FTIR analyses showed that proteins in N. oculata and T. tetrathele cultures reduced AgNO₃, and aromatic compounds stabilized the biogenic Ag-NPs. H. stipulacea extract contains proteins and polyphenols that could be in charge for the reduction of silver and iron ions into nanoparticles and polysaccharides which stabilized the biosynthesized Ag-NPs and Fe₃O₄-NPs. The Ag-NPs biosynthesized by T. tetrathele cultures and H. stipulacea aqueous extract exerted outstanding negative impacts on O. simplicissima (optical density and total chlorophyll) and the Ag-NPs biosynthesized using N. oculata culture exerted the moderate performance. The study results suggest that the bioactive compounds present in the FTIR profiles of the Ag-NPs and or ionic silver may be the main contributors in their anti-algal effects. A trial to use the biosynthesized Fe₃O₄-NPs using H. stipulacea aqueous extract to separate Ag-NPs was successfully carried out. Since the synthesis and applications of nanomaterials is a hot subject of research, the study outcomes not only provide a green approach for the synthesis of metal-NPs but also open the way for more nanoparticle applications.

Variation in the number of nucleoli and incomplete homogenization of 18S ribosomal DNA sequences in leaf cells of the cultivated Oriental ginseng (Panax ginseng Meyer)

BACKGROUND

Wild ginseng, Panax ginseng Meyer, is an endangered species of medicinal plants. In the present study, we analyzed variations within the ribosomal DNA (rDNA) cluster to gain insight into the genetic diversity of the Oriental ginseng, P. ginseng, at artificial plant cultivation.

METHODS

The roots of wild P. ginseng plants were sampled from a nonprotected natural population of the Russian Far East. The slides were prepared from leaf tissues using the squash technique for cytogenetic analysis. The 18S rDNA sequences were cloned and sequenced. The distribution of nucleotide diversity, recombination events, and interspecific phylogenies for the total 18S rDNA sequence data set was also examined.

RESULTS

In mesophyll cells, mononucleolar nuclei were estimated to be dominant (75.7%), while the remaining nuclei contained two to four nucleoli. Among the analyzed 18S rDNA clones, 20% were identical to the 18S rDNA sequence of P. ginseng from Japan, and other clones differed in one to six substitutions. The nucleotide polymorphism was more expressed at the positions 440-640 bp, and distributed in variable regions, expansion segments, and conservative elements of core structure. The phylogenetic analysis confirmed conspecificity of ginseng plants cultivated in different regions, with two fixed mutations between P. ginseng and other species.

CONCLUSION

This study identified the evidences of the intragenomic nucleotide polymorphism in the 18S rDNA sequences of P. ginseng. These data suggest that, in cultivated plants, the observed genome instability may influence the synthesis of biologically active compounds, which are widely used in traditional medicine.

Seagrass radiation after Messinian salinity crisis reflected by strong genetic structuring and out-of-Africa scenario (Ruppiaceae)

Many aquatic plant and seagrass species are widespread and the origin of their continent-wide ranges might result from high gene flow levels. The response of species when extending northwards since the Last Glacial Maximum can be opposed to the structuring of their populations that survived glaciation cycles in southern regions. The peri-Mediterranean is a complex series of sea basins, coastlines, islands and river deltas with a unique history since the Messinian Crisis that potentially influenced allopatric processes of aquatic life. We tested whether vast ranges across Europe and the peri-Mediterranean of a global seagrass group (Ruppia species complexes) can be explained by either overall high levels of gene flow or vicariance through linking population genetics, phylogeography and shallow phylogenetics. A multigene approach identified haplogroup lineages of two species complexes, of ancient and recent hybrids with most of the diversity residing in the South. High levels of connectivity over long distances were only observed at recently colonized northern ranges and in recently-filled seas following the last glaciation. A strong substructure in the southern Mediterranean explained an isolation-by-distance model across Europe. The oldest lineages of the southern Mediterranean Ruppia dated back to the period between the end of the Messinian and Late Pliocene. An imprint of ancient allopatric origin was left at basin level, including basal African lineages. Thus both vicariance in the South and high levels of connectivity in the North explained vast species ranges. Our findings highlight the need for interpreting global distributions of these seagrass and euryhaline species in the context of their origin and evolutionary significant units for setting up appropriate conservation strategies.

Intra-genomic ribosomal RNA polymorphism and morphological variation in Elphidium macellum suggests inter-specific hybridization in foraminifera

Elphidium macellum is a benthic foraminifer commonly found in the Patagonian fjords. To test whether its highly variable morphotypes are ecophenotypes or different genotypes, we analysed 70 sequences of the SSU rRNA gene from 25 specimens. Unexpectedly, we identified 11 distinct ribotypes, with up to 5 ribotypes co-occurring within the same specimen. The ribotypes differ by varying blocks of sequence located at the end of stem-loop motifs in the three expansion segments specific to foraminifera. These changes, distinct from typical SNPs and indels, directly affect the structure of the expansion segments. Their mosaic distribution suggests that ribotypes originated by recombination of two or more clusters of ribosomal genes. We propose that this expansion segment polymorphism (ESP) could originate from hybridization of morphologically different populations of Patagonian Elphidium. We speculate that the complex geological history of Patagonia enhanced divergence of coastal foraminiferal species and contributed to increasing genetic and morphological variation.

Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana

Background

As a result of concerted evolution, coding regions of ribosomal DNA sequences are highly conserved within species and variation is generally thought to be limited to a few nucleotides. However, rDNA sequence variation has not been systematically examined in plant genomes, including that of the model plant Arabidopsis thaliana whose genome was the first to be sequenced.

Findings

Both genomic and transcribed 18 S sequences were sampled and revealed that most deviation from the consensus sequence was limited to single nucleotide substitutions except for a variant with a 270 bp deletion from position 456 to 725 in Arabidopsis numbering. The deletion maps to the functionally important and highly conserved 530 loop or helix18 in the structure of E. coli 16 S. The expression of the deletion variant is tightly controlled during developmental growth stages. Transcripts were not detectable in young seedlings but could be amplified from RNA extracts of mature leaves, stems, flowers and roots of Arabidopsis thaliana ecotype Columbia. We also show polymorphism for the deletion variant among four Arabidopsis ecotypes examined.

Conclusion

Despite a strong purifying selection that might be expected against functionally impaired rDNAs, the newly identified variant is maintained in the Arabidopsis genome. The expression of the variant and the polymorphism displayed by Arabidopsis ecotypes suggest a transition state in concerted evolution.

Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise

BACKGROUND

Hieracium s.str. is a complex species-rich group of perennial herbs composed of few sexual diploids and numerous apomictic polyploids. The existence of reticulation and the near-continuity of morphological characters across taxa seriously affect species determination, making Hieracium one of the best examples of a 'botanist's nightmare'. Consequently, its species relationships have not previously been addressed by molecular methods. Concentrating on the supposed major evolutionary units, we used nuclear ribosomal (ETS) and chloroplast (trnT-trnL) sequences in order to disentangle the phylogenetic relationships and to infer the origins of the polyploids.

RESULTS

Despite relatively low interspecific variation, the nuclear data revealed the existence of two major groups roughly corresponding to species with a Western or Eastern European origin. Extensive reticulation was mainly inferred from the character additivity of parental ETS variants. Surprisingly, many diploid species were of hybrid origin whilst several polyploid taxa showed no evidence of reticulation. Intra-individual ETS sequence polymorphism generally exceeded interspecific variation and was either independent of, or additional to, additive patterns accounted for by hybrid origin. Several ETS ribotypes occurred in different hybrid taxa, but never as the only variant in any species analyzed.

CONCLUSION

The high level of intra-individual ETS polymorphism prevented straightforward phylogenetic analysis. Characterization of this variation as additive, shared informative, homoplasious, or unique made it possible to uncover the phylogenetic signal and to reveal the hybrid origin of 29 out of 60 accessions. Contrary to expectation, diploid sexuals and polyploid apomicts did not differ in their molecular patterns. The basic division of the genus into two major clades had not previously been intimated on morphological grounds. Both major groups are thought to have survived in different glacial refugia and to have hybridized as a result of secondary contact. Several lines of evidence suggest the data is best explained by the presence of an extinct range of variation and a larger diversity of ancestral diploids in former times rather than by unsampled variation. Extinct diversity and extensive reticulation are thought to have largely obscured the species relationships. Our study illustrates how multigene sequences can be used to disentangle the evolutionary history of agamic complexes or similarly difficult datasets.

Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes

Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions. Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine. Postmutation processes also introduce a bias, particularly selection for codon-usage bias in coding regions. It is generally assumed, however, that there is a universal bias in favour of transitions over transversions, possibly as a result of the underlying chemistry of mutation. Surprisingly, this underlying trend has been evaluated only in two types of metazoan, namely Drosophila and the Mammalia. Here, we investigate a third group, and find no such bias. We characterize the point substitution spectrum in Podisma pedestris, a grasshopper species with a very large genome. The accumulation of mutations was surveyed in two pseudogene families, nuclear mitochondrial and ribosomal DNA sequences. The cytosine-guanine (CpG) dinucleotides exhibit the high transition frequencies expected of methylated sites. The transition rate at other cytosine residues is significantly lower. After accounting for this methylation effect, there is no significant difference between transition and transversion rates. These results contrast with reports from other taxa and lead us to reject the hypothesis of a universal transition/transversion bias. Instead we suggest fundamental interspecific differences in point substitution processes.

Some mutations occur more frequently than others. We need to understand these biases if we are to interpret the differences that have accumulated between species and individuals. Applications include estimating the time since evolutionary lineages diverged and detecting the signature of natural selection in DNA sequences. However, mutational biases have been obscured because, since mutations arose, natural selection has eliminated some whilst allowing others to persist to the present. We therefore study mutations that have accumulated in regions of the genome that are free from selection in a grasshopper with a gigantic genome. All other animal studies using this approach find an excess of mutations between DNA bases having similar biochemical properties (transitions rather than transversions). This bias has been widely interpreted as a consequence of the fundamental biochemical basis of mutation. However, once we exclude mutations associated with DNA methylation, we find no evidence of a transition bias, unlike the few comparable animal studies that make the same correction. We propose that this result indicates previously unanticipated differences between species in the selection on or mutation of their DNA.

Ribosomal DNA in the grasshopper Podisma pedestris: escape from concerted evolution

Eukaryote nuclear ribosomal DNA (rDNA) typically exhibits strong concerted evolution: a pattern in which several hundred rDNA sequences within any one species show little or no genetic diversity, whereas the sequences of different species diverge. We report a markedly different pattern in the genome of the grasshopper Podisma pedestris. Single individuals contain several highly divergent ribosomal DNA groups. Analysis of the magnitude of divergence indicates that these groups have coexisted in the Podisma lineage for at least 11 million years. There are two putatively functional groups, each estimated to be at least 4 million years old, and several pseudogene groups, many of which are transcribed. Southern hybridization and real-time PCR experiments show that only one of the putatively functional types occurs at high copy number. However, this group is scarcely amplified under standard PCR conditions, which means that phylogenetic inference on the basis of standard PCR would be severely distorted. The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris. We propose that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.

Non-concerted ITS evolution in Mammillaria (Cactaceae)

Molecular studies of 21 species of the large Cactaceae genus Mammillaria representing a variety of intrageneric taxonomic levels revealed a high degree of intra-individual polymorphism of the internal transcribed spacer region (ITS1, 5.8S rDNA, ITS2). Only a few of these ITS copies belong to apparently functional genes, whereas most are probably non-functional (pseudogenes). As a multiple gene family, the ITS region is subjected to concerted evolution. However, the high degree of intra-individual polymorphism of up to 36% in ITS1 and up to 35% in ITS2 suggests a non-concerted evolution of these loci in Mammillaria. Conserved angiosperm motifs of ITS1 and ITS2 were compared between genomic and cDNA ITS clones of Mammillaria. Some of these motifs (e.g., ITS1 motif 1, 'TGGT' within ITS2) in combination with the determination of GC-content, length comparisons of the spacers and ITS2 secondary structure (helices II and III) are helpful in the identification of pseudogene rDNA regions.

ITS1 sequence variabilities correlate with 18S rDNA sequence types in the genus Acanthamoeba (Protozoa: Amoebozoa)

The subgenus classification of the ubiquitously spread and potentially pathogenic acanthamoebae still poses a great challenge. Fifteen 18S rDNA sequence types (T1-T15) have been established, but the vast majority of isolates fall into sequence type T4, and so far, there is no means to reliably differentiate within T4. In this study, the first internal transcribed spacer (ITS1), a more variable region than the 18S rRNA gene, was sequenced, and the sequences of 15 different Acanthamoeba isolates were compared to reveal if ITS1 sequence variability correlates with 18S rDNA sequence typing and if the ITS1 sequencing allows a differentiation within T4. It was shown that the variability in ITS1 is tenfold higher than in the 18S rDNA, and that ITS1 clusters correlate with the 18S rDNA clusters and thus corroborate the Acanthamoeba sequence type system. Moreover, high sequence dissimilarities and distinctive microsatellite patterns could enable a more detailed differentiation within T4.