Detection and identification of phytoplasma associated with witches’ broom and little leaf disease in Arundo donax: first report from India

During the survey of two successive years 2012–2013, in nearby places of Gorakhpur districts, Uttar Pradesh, India, Arundo donax plants were found to be exhibiting witches’ broom, excessive branching accompanied with little leaf symptoms with considerable disease incidence. Nested PCR carried out with universal primers pair R16F2n/R16R2 employing the PCR (P1/P7) product as a template DNA (1:20) resulted in expected size positive amplification ~1.2 kb in all symptom-bearing plants suggested the association of phytoplasma with witches’ broom disease of Narkat plants. BLASTn analysis of the 16S rRNA gene sequence showed the highest (99%) sequence identity with Candidatus phytoplasma asteris (16SrI group). In phylogenetic analysis, the sequence data showed close relationships with the members of 16SrI phytoplasma and clustered within a single clade of 16SrI group and closed to B subgroup representatives. This is a first report of 16Sr I-B group phytoplasma associated with witches’ broom accompanied with little leaf disease of Narkat in India.     

Origin of the cultivated passion fruit Passiflora edulis f. flavicarpa and genomic relationships among species of the subgenera Decaloba and Passiflora

• Passiflora edulis f. flavicarpa is the most economically important species in the genus Passiflora. However, the origin of this yellow form of passion fruit remains unclear, being suggested as a hybrid (P. edulis f. edulis × P. ligularis) or wild mutant.
• Here, the origin and genomic relationships of P. edulis f. flavicarpa with some related species in the genus Passiflora (subgenera Decaloba and Passiflora) were investigated using genomic in situ hybridization (GISH). Genomic DNA of 18 species was used as probe, which was hybridized onto chromosomes of P. edulis f. flavicarpa.
• Of all genomic DNA probes tested, none allowed us to identify a specific chromosome set in P. edulis f. flavicarpa. Conversely, probes from the subgenus Passiflora, P. edulis f. edulis, P. alata, P. cincinnata, P. coccinea, P. nitida and P. vitifolia, produced intense and uniform hybridizations on all chromosomes of P. edulis f. flavicarpa. Moreover, probes from P. ligularis, P. foetida and P. sublanceolata produced more intense hybridizations in the terminal region of four chromosomes, corresponding to the DNAr 45S locus, and also dispersed, less intense, hybridization across all chromosomes. Probes from the subgenus Decaloba, P. biflora, P. capsularis, P. cervii, P. coriacea, P. micropetala, P. morifolia, P. rubra and P. suberosa, produced hybridizations restricted to the DNAr 45S sites.
• The hybrid origin of P. edulis f. flavicarpa could not be supported based on the GISH results, and it is suggested that this species is conspecific with P. edulis f. edulis, because the probe with DNA of this form hybridized strongly throughout the target genome. The other putative parent species, P. ligularis, showed only a distant relationship with the target genome. The results also suggest that species of the subgenus Passiflora share many repetitive sequences and that the relationship between subgenera Decaloba and Passiflora is very distant.

     

Phylogenomics of the hyperdiverse daisy tribes: Anthemideae,Astereae, Calenduleae,Gnaphalieae, and Senecioneae

Asteraceae account for 10% of all flowering plant species, and 35%–40% of these are in five closely related tribes that total over 10 000 species. These tribes include Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae, which form one of two enormous clades within Subfamily Asteroideae. We took a phylogenomics approach to resolve evolutionary relationships among these five tribes. We sampled the nuclear and plastid genomes via HybSeq target enrichment and genome skimming, and recovered 74 plastid genes and nearly 1000 nuclear loci, known as Conserved Orthologous Sequences. We tested for conflicting support in both data sets and used network analyses to assess patterns of reticulation to explain the early evolutionary history of this lineage, which has experienced whole‐genome duplications and rapid radiations. We found concordance and conflicting support in both data sets and documented four ancient hybridization events. Due to the timing of the early radiation of this five‐tribe lineage, shortly before the Eocene–Oligocene extinction event (34 MYA), early lineages were likely lost, obscuring some details of their early evolutionary history.     

United in adversity: Aridity and cold influence aggregation behaviour in a social lizard,Egernia stokesii

Sociality has evolved independently many times in a diverse array of animal taxa. While sociality in some invertebrates, birds and mammals is relatively well understood, complex social behaviour in Squamate reptiles is a comparatively recent discovery. The extent to which social behaviour is phylogenetically constrained, or free to respond to environmental conditions is a key question in understanding sociality. We sampled 74 aggregations involving 137 individuals of a social lizard (Egernia stokesii) from 13 sites across a 96 250 km² area showing a wide range of environmental conditions. Over all locations, 70% of the lizards were found in aggregations, supporting the previous suggestion that aggregation in this species is phylogenetically constrained. However, the size of aggregations was negatively related to spatial variation in aridity and daily variation in maximum temperature, suggesting that social behaviour also varied in response to harsh environmental conditions. Lizards aggregated more in arid areas and on cold days. Our results show that it is overly simplistic to regard social behaviour in E. stokesii as either phylogenetically constrained or environmentally determined. A more nuanced appreciation of the extent to which social behaviour is free to vary in response to environmental conditions improves our understanding of social behaviour in Squamate reptiles.     

Agriculture erases climate constraints on soil nematode communities across large spatial scales

Anthropogenic conversion of natural to agricultural land reduces aboveground biodiversity. Yet, the overall consequences of land‐use changes on belowground biodiversity at large scales remain insufficiently explored. Furthermore, the effects of conversion on different organism groups are usually determined at the taxonomic level, while an integrated investigation that includes functional and phylogenetic levels is rare and absent for belowground organisms. Here, we studied the Earth's most abundant metazoa—nematodes—to examine the effects of conversion from natural to agricultural habitats on soil biodiversity across a large spatial scale. To this aim, we investigated the diversity and composition of nematode communities at the taxonomic, functional, and phylogenetic level in 16 assemblage pairs (32 sites in total with 16 in each habitat type) in mainland China. While the overall alpha and beta diversity did not differ between natural and agricultural systems, all three alpha diversity facets decreased with latitude in natural habitats. Both alpha and beta diversity levels were driven by climatic differences in natural habitats, while none of the diversity levels changed in agricultural systems. This indicates that land conversion affects soil biodiversity in a geographically dependent manner and that agriculture could erase climatic constraints on soil biodiversity at such a scale. Additionally, the functional composition of nematode communities was more dissimilar in agricultural than in natural habitats, while the phylogenetic composition was more similar, indicating that changes among different biodiversity facets are asynchronous. Our study deepens the understanding of land‐use effects on soil nematode diversity across large spatial scales. Moreover, the detected asynchrony of taxonomic, functional, and phylogenetic diversity highlights the necessity to monitor multiple facets of soil biodiversity in ecological studies such as those investigating environmental changes.     

Morphological,biochemical, and molecular characterization of Oscillatoria kawamurae (Oscillatoriales,Cyanobacteria) isolated from different geographical regions

Oscillatoria kawamurae is an unusual freshwater cyanobacterium because of its large trichome and ambiguous gas vacuole. Because little is known about its phenotypic or genotypic characteristics, this study conducted morphological, biochemical, and genetic characterization of O. kawamurae strains isolated from Japan, Laos, and Myanmar. All strains displayed similar morphological characteristics; however some differences were observed in vegetative cell widths, trichome colors, and the distribution patterns of their gas vacuole‐like structures. The in vivo and phycobiliprotein absorption spectra revealed the two different trichome colors found in the four representative strains of O. kawamurae (Inle1, Lao7, Biwa6, and Inba3). These different trichome colors corresponded to the different ratios of phycoerythrin and phycocyanin, the two types of phycobilin pigments: 0.25 for olive‐green strain (Inle1) and 0.65–0.73 for brown‐green strains (Biwa6, Inba3, and Lao7). Cellular fatty acid compositions of the four strains were C14:0, C15:0, C16:0, C16:1c, C17:0, C18:0, C18:1c, C18:3α and C18:4, whereas two strains (Biwa6 and Inba3) lacked C17:0. Of the fatty acids, palmitic acid (C16:0) was predominant. PCR experiments using primers targeting a gas vesicle gene (gvpA) recovered gvpA fragments from all O. kawamurae strains, suggesting that this species has true gas vacuoles. The 16S rDNA sequences of all of the strains were identical regardless of their different trichome colors and/or geographic origins. Phylogenetic analyses based on the 16S rDNA sequences indicated that O. kawamurae forms a monophyletic clade with O. princeps CCALA 1115 clB1 and O. duplisecta ETS‐06. We discuss the taxonomy of O. kawamurae based on the data obtained in this study.