Morphopathological and molecular morphometric characterization of Waitea circinata var. prodigus causing a novel sheath spot disease of maize in India

Maize brown sheath spot (MBSS), a new disease of maize, was discovered while surveying for maize leaf and sheath blight diseases in the Indian states of Assam, Jharkhand, Meghalaya, Manipur, and Odisha. Maize is the third most important cereal after rice and wheat in India. Unlike banded leaf and sheath blight (BLSB) disease caused by Rhizoctonia solani, MBSS symptoms on maize were discrete and limited to sheaths only. Symptoms of MBSS in the field were initially water soaked necrotic lesions of 1 to 2 cm in diameter on the lowermost leaf sheaths, which then progressed to the upper sheaths. Lesions coalesced and covered approximately 2 to 5% of the sheath area. Infected dried lower leaves were shed while infected upper leaves remained on the stem. The pathogen was isolated, characterized morphologically, pathologically, and molecularly, and identified as Waitea circinata var. prodigus (Wcp); a basidiomycete known to cause basal leaf blight of seashore paspalum. The internal transcribed spacer sequence 2 (ITS2) of rDNA from MBSS isolates formed a well-supported clade with known Wcp isolates. Molecular morphometric analysis of the ITS2 regions of the five known varieties of W. circinata detected distinguishing variations in GC content, compensatory base changes (CBCs), hemi-compensatory base changes (hCBCs), indels, and altered base-pairing of helices. Variation in these characteristics may indicate that varieties are distinct biological species within W. circinata sensu lato. The geographical distribution and potential impacts of MBSS on the maize crop in India necessitates further investigations on pathogen identification and disease management.

Compensatory Base Changes Reveal Sexual Incompatibility among Members of the Anopheles subpictus Sensu Lato (Diptera: Culicidae) Species Complex in Sri Lanka

The mosquito Anopheles (Cellia) subpictus sensu lato (s.l.) is a major secondary vector of malaria in Sri Lanka. The sibling species composition in this species complex in Sri Lanka remains debatable. Compensatory base changes (CBCs) in the secondary structures of internal transcribed spacer 2 (ITS2) are reliable sources to predict sexual incompatibility among closely related species. The objective of the present study was to investigate the An. subpictus s.l. populations in Sri Lanka using the CBC analysis. Mosquito DNA was amplified and sequenced for the ITS2 region. The sequences were annotated using ITS2 Database. ITS2 secondary structures were constructed and analyzed for CBCs using various bioinformatics tools. The ITS2 regions consisted of two different lengths, 575 bp and 480 bp. The two CBCs and three hemi CBCs identified in the present study suggest that there may be at least two sexually incompatible sibling species. In conclusion, it is likely that there may be only two reproductively isolated sibling species in the An. subpictus species complex in Sri Lanka. However, due to high divergence of ITS2 in these species, it is reasonable to assume that they may be undergoing a speciation event to separate as a distinct species.

A new species of Cryptomonas (Cryptophyceae) from the Western Urals (Russia)

A new species, Cryptomonas uralensis Martynenko, Gusev, Kulizin & Guseva sp. nov., is described from western slopes of the Ural Mountains (Russia) based on morphological and molecular data. Phylogenetic relationships inferred from nuclear SSU and LSU rDNA sequences show that the new species forms a clade with C. tetrapyrenoidosa Skuja emend. Hoef-Emden & Melkonian. Comparison of secondary structures of nuclear rDNA ITS2, including analysis of Compensatory Base Changes (CBC), confirms the separation between C. uralensis sp. nov. and C. tetrapyrenoidosa. Cell morphology and sizes of C. uralensis sp. nov. are very similar to C. tetrapyrenoidosa and C. pyrenoidifera, and C. uralensis sp. nov. may thus represent a species that can only be reliably identified using molecular data.

High molecular diversity in the Carabus variolosus/nodulosus complex

Starting point of this study was the problem considering the status of Carabus variolous and C. nodulosus: French and some German authors classified them as species, most German authors as subspecies and Casale as semispecies. We performed analyses of mitochondrial genes (COI-5', COI-3', ND5) as well as nuclear ones (ITS2, wingless) and analysed the DNA sequences using Seqotron, CLUSTALX (editing and alignment), MEGA, DNAML, SplitsTree (phylogeny and network), 4SALE (compensatory base changes), and BEAST (coalescence). We could study specimens from all regions except the western most part of the distribution area (Massif Central and French Jura, France). The mitochondrial DNA data resulted in a geographic pattern of high diversity within both taxa indicating a series of glacial refuges. In addition, a considerably large area was found were introgressive hybridisation took place in the past - at least two times by nodulosus of different regions into variolosus. The nuclear DNA data show a clear and constant difference between both taxa. In consequence, this complex of forms may be characterised as semispecies from an evolutionary viewpoint but taxonomically as one species because of hybridisation and the lack of compensatory bases changes.

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.

Fritschiella aquatilis (Chaetophoraceae, Chlorophyta), a new freshwater green algae species from China

A new freshwater algal species of Fritschiella aquatilis was found in a freshwater aquarium in China (Shanxi Province), floating on the surface or sinking at the bottom of the water. This new species is characterized by bright-green, globular thallus with hairy morphology, which composed numerous small single celled filamentous branches. Most characteristics are in agreement with description of Fritschiella. But the new species differs from other members in this genus by the particularly aquatic habitat and macroscopic thalli morphology (the only reported Fritschiella tuberosa Iyengar species is terrestrial). Concatenated sequences from 28S rDNA, 18S rDNA, rbcL gene phylogenetic analysis of F. aquatilis to discuss taxonomic status. All phylogenetic trees have yielded a Fritschiella clade included the sequence, and F. aquatilis formed an independent branch evidently distinguished from other species. Comparing with F. tuberosa, the internal transcribed spacer (ITS) secondary structure of the new species has some compensatory base changes (CBCs) and hemi-CBCs, especially at the Helix1 and Helix 2 end. Thus, the results of morphological and molecular characteristics support F. aquatilis to be recognized as a new species. This new alga brings the total number of recognized Fritschiella species, and the habitats circumscription of the genus Fritschiella expanded to include terrestrial and aquatic.

Spongiosarcinopsis terrestris gen. et sp. nov. (Chlorophyta, Chlorophyceae): a new genus of green algae from gray forest soil, Russia

The diversity of soil green microalgae (Chlorophyta) is generally poorly known and likely underestimated because of their morphological poverty and crypticity. The use of molecular tools has revolutionized algal diversity research, including the discovery of numerous new taxa. On the basis of light microscopy, we isolated Chlorochytrium-like strain ACSSI 023 from gray forest soil (Moscow region, Russia), but with spongy rather than network chloroplast. This strain was evaluated by means of 18S rRNA gene and ITS2 sequences analyses and ultrastructural observations. Morphology, comparing the ITS2 secondary structure, compensatory base changes, intron lacking and percent similarity of the 18S rRNA gene of the isolated strain allowed us to propose a new genus and species for it, Spongiosarcinopsis terrestris gen. et sp. nov. The genus forms a separate independent branch within the Stephanosphaerinia clade (Chlorophyta, Chlorophyceae) with type species—Spongiosarcinopsis terrestris ACSSI 023.

Four new species of Bacidia s.s. (Ramalinaceae, Lecanorales) in the Russian Far East

The molecular phylogeny of Bacidia s.s. in the Russian Far East was investigated using 62 nucleotide sequences from the ITS nrDNA region, 22 of which were newly obtained. Phylogenetic reconstructions employed Bayesian inference and maximum likelihood searches using MrBayes and RAxML. In addition, ITS2 secondary structures added further support using Compensatory Base Changes. As a result of morphological and phylogenetic studies, four new species of Bacidia are described. Bacidia areolata sp. nov. belongs to the suffusa group. It was collected once in Khabarovskiy Krai, the Russian Far East, on the bark of Acer tegmentosum and is closely related to B. suffusa but differs in having a smooth, cracked to areolate thallus and shorter spores. Bacidia elongata sp. nov. is a member of the fraxinea group and is similar to B. fraxinea but differs in having a wide zone of cells with enlarged lumina along the edge of the exciple. In fact, this zone of enlarged cells, in combination with its overall habit, places it morphologically close to B. suffusa, B. millegrana and B. campalea. Bacidia kurilensis sp. nov. is a basal member of the laurocerasi group and closely related to B. biatorina, B. heterochroa, B. laurocerasi and B. salazarensis. However, the combination of a granular thallus, large black apothecia and a green hue in the upper part of the exciple edge as well as in the epihymenium sets it apart from the species mentioned above. Bacidia sachalinensis sp. nov. resolves as a strongly supported member of the polychroa group and is known from a single locality in Sakhalin, the Russian Far East. Its thallus structure and apothecium colour are variable, which is typical for the polychroa group, but it differs from B. polychroa by having shorter spores with fewer septa and a mainly smooth to areolate thallus.

A new freshwater alga, Ulvella shanxiensis (Chlorophyta) described from China

A new freshwater alga species of Ulvella shanxiensis, is found in the circulating neutral water spring in China (Shanxi Province), growing epilithic and epiphytic on other substrates. This new species is characterized by olive-green, disc-shaped hollow thallus with irregularly vesicular morphology, which composed of 2–3 layers cells. Most characteristics were in agreement with Ulvella, but distinguished from the other freshwater members by thalli dimensions and cell diameter. In addition to describing the morphological structures of U. shanxiensis in detail, phylogenetic analysis based on sequences of the rbcL and 18S rDNA gene placed the algae in single clade with two samples, and demonstrated the separation between U. shanxiensis and other Ulvella species with a considerable sequence distance. Comparing with U. bullata, the internal transcribed spacer secondary structure of the new species has some compensatory base changes in 1 Helix and hemi-CBCs in 2–3 Helix, differed in several ways from that of other Ulvella algae. Consequently, these results of morphological observation and phylogenetic analysis suggest this alga as a new species, and bring a new record in the total number of recognized freshwater Ulvella species in China.