A consensus secondary structure of ITS2 for the diatom Order Cymatosirales (Mediophyceae, Bacillariophyta) and reappraisal of the order based on DNA, morphology, and reproduction

Structural evolution of SLA promoter in mosquito-borne flaviviruses: A sequence-structure based phylogenetic framework

All the flaviviruses have a Y-shaped stem-loop secondary structure known as the SLA element, and the structural features of this element are crucial to initiating the infection cycle. The present study particularly investigated how flaviviruses retained the common core SLA element secondary structure during the species evolution by selecting mosquito-borne flaviviruses (MBFVs) as a case study. The detailed search of nucleotide substitutions in species-wise consensus SLA secondary structure models suggested that the compensatory and hemi-compensatory base changes in the helices are crucial to preserving the common core secondary structure. In contrast to the coding region-based phylogeny, the SLA sequence-structure-based phylogenetic tree revealed an intriguing evolutionary relationship among MBFVs. Overall, this paper demonstrated for the first time the efficacy of RNA secondary structures as a phylogenetic marker to study the RNA virus evolution.

Response of protist community dynamics and co-occurrence patterns to the construction of artificial reefs: A case study in Daya Bay, China

Artificial reefs (ARs) are widely used for biodiversity conservation and coastal habitat restoration. Although protists play an important ecological role in marine ecosystems, the response of the protist community to ARs is still poorly understood. In the current study, an Illumina sequencing analysis of 18S rDNA was performed, and the diversity, community structure, and co-occurrence networks of protists in the ARs and open sea area (OW) in Daya Bay were described. The results indicated that significant seasonal differences occur in the seawater protists between the surface and bottom of the ARs and OW. However, the protists in the ARs and OW had different seasonal variations. The ARs always affected the alpha diversity of marine protists in different seasons, while the surface and bottom OW sites had different seasonal effects. The ARs sites had different effects on the community composition of the surface and bottom seawater in different seasons relative to the OW sites. The linear discriminant analysis (LDA) effect size (LEfSe) method showed that 85 biomarkers mainly belonging to 11 taxa, including Bacillariophyta, Chlorophyta, and Dinophyceae, were affected by the ARs (P < 0.05, LDA > 2.0). The ARs played an important role in the seasonal changes in the protist community composition and had different effects on the dominant species of protists in the surface and bottom seawater. A redundancy analysis (RDA) significance test showed that the structure of the protist community in Daya Bay was mainly affected by environmental factors, such as seawater temperature, salinity and dissolved oxygen. Compared with the OW group, the surface and bottom layers of the ARs had more complex protist interactions or more niches. The ARs increased the degree of spatial heterogeneity, which may lead to significant niche differentiation, indicating that ARs as habitat factors affect the complexity and stability of the symbiotic network of protists. The results could provide basic data on the response of the protist community to the ARs in Daya Bay and a reference for assessments of the impact of ARs on the ecological environment.

Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint

The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of ITS2 secondary structure, including structure form, structural motifs, cleavage sites, and base-pair interactions. We then review the phylogenetic implications and applications of this structure information, including structure-guiding sequence alignment, base-pair mutation model, and species distinguishing. We give the rationale for why incorporating structure information into tree construction could improve reliability and accuracy, and some perspectives of bioinformatics coding that allow for a meaningful evolutionary character to be extracted. In sum, this review of the integration of function, structure and evolution of ITS2 will expand the traditional sequence-based ITS2 phylogeny and thus contributes to the tree of life. The generality of ITS2 characteristics may also inspire phylogenetic use of other similar structural regions.

Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach

As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k-mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.

Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)

BACKGROUND AND AIMS

Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models.

METHODS

We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing.

KEY RESULTS

Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models.

CONCLUSIONS

Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.

Toward a multigene phylogeny of the Cymatosiraceae (Bacillariophyta, Mediophyceae) II: morphological and molecular insights into the taxonomy of the forgotten species Campylosira africana and of Extubocellulus, with a description of two new taxa

New molecular and morphological insights are presented on Campylosira africana and two new species, Extubocellulus cupola sp. nov. and Plagiogrammopsis castigatus sp. nov. Species descriptions were based on LM/SEM micrographs and a data set with concatenated sequences of SSU, rbcL and psbC loci constructed from 56 cymatosiroid strains isolated from global geographic locations. Extubocellulus cupola is distinguished by a mesh-like marginal ridge and dome-shaped areolation, and P. castigatus, by a prominent marginal extension at the valve center. Campylosira africana, a species from South Africa described by Professor Malcolm Giffen, has never been documented through LM or SEM, which led some authors to place it in synonymy under Campylosira cymbelliformis. We confirm that C. africana is a distinct species and provide microphotographic documentation and DNA sequences. We present morphological evidence for the well-known cymatosiroid species Extubocellulus spinifer possessing complete pili, and we emend the generic description of Extubocellulus.