DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome‐wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome‐wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome‐wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution

Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum

The Triticum/Aegilops complex includes hybrid species resulting from homoploid hybrid speciation and allopolyploid speciation. Sequential allotetra- and allohexaploidy events presumably result in two challenges for the hybrids, which involve 1) cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar donor; and 2) incompatibility of chimeric protein complexes with diverged subunits from nuclear and cytoplasmic genomes. Here, we describe coevolution of nuclear rbcS genes encoding the small subunits of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) and nuclear genes encoding plastid translocons, which mediate recognition and translocation of nuclear-encoded proteins into plastids, in allopolyploid wheat species. We demonstrate that intergenomic paternal-to-maternal gene conversion specifically occurred in the genic region of the homoeologous rbcS3 gene from the D-genome progenitor of wheat (abbreviated as rbcS3D) such that it encodes a maternal-like or B-subgenome-like SSU3D transit peptide in allohexaploid wheat but not in allotetraploid wheat. Divergent and limited interaction between SSU3D and the D-subgenomic TOC90D translocon subunit is implicated to underpin SSU3D targeting into the chloroplast of hexaploid wheat. This implicates early selection favoring individuals harboring optimal maternal-like organellar SSU3D targeting in hexaploid wheat. These data represent a novel dimension of cytonuclear evolution mediated by organellar targeting and transportation of nuclear proteins

The Function of MoGlk1 in Integration of Glucose and Ammonium Utilization in Magnaporthe oryzae

Hexokinases are conserved proteins functioning in glucose sensing and signaling. The rice blast fungus Magnaporthe oryzae contains several hexokinases, including MoHxk1 (hexokinase) and MoGlk1 (glucokinase) encoded respectively by MoHXK1 and MoGLK1 genes. The heterologous expression of MoGlk1 and MoHxk1 in Saccharomyces cerevisiae confirmed their conserved functions. Disruption of MoHXK1 resulted in growth reduction in medium containing fructose as the sole carbon source, whereas disruption of MoGLK1 did not cause the similar defect. However, the ΔMoglk1 mutant displayed decreased proton extrusion and a lower biomass in the presence of ammonium, suggesting a decline in the utilization of ammonium. Additionally, the MoGLK1 allele lacking catalytic activity restored growth to the ΔMoglk1 mutant. Moreover, the expression of MoPMA1 encoding a plasma membrane H+-ATPase decreased in the ΔMoglk1 mutant that can be suppressed by glucose and G-6-P. Thus, MoGlk1, but not MoHxk1, regulates ammonium utilization through a mechanism that is independent from its catalytic activity

Neodactylariales, Neodactylariaceae (Dothideomycetes, Ascomycota): new order and family, with a new species from China

During a mycological survey of aquatic hyphomycetes on submerged decaying leaves in southwest China, a distinct new fungus was collected. The collection was cultured and sequenced and a BLAST search of its ITS and LSU sequence against data in GenBank revealed a dothideomycetous affiliation, with the closest related taxa in the genus Neodactylaria. Phylogenetic analyses of a multigene matrix containing sequences from four genes (LSU, SSU, rpb2, and tef1), representing broad groups of Dothideomycetes, revealed its placement within Dothideomycetes, but without a supported familial or ordinal affiliation. Based on further phylogenetic analyses and morphological investigations, the new fungus is described here as a new species of Neodactylaria, N. simaoensis sp. nov., and placed in a new family Neodactylariaceae fam. nov. and a new order Neodactylariales ord. nov

Extremely low-frequency magnetic exposure appears to have no effect on pathogenesis of Alzheimer's disease in aluminum-overloaded rat.

OBJECTIVE: Extremely low-frequency magnetic field (ELF-MF) has been reported to be of potential pathogenetic relevance to Alzheimer's disease (AD) for years. However, evidence confirming this function remains inconclusive. Chronic Al treatment has been identified as a contributing factor to cognitive function impairment in AD. This study aims to examine whether or not ELF-MF and Al have synergistic effects toward AD pathogenesis by investigating the effects of ELF-MF with or without chronic Al treatment on SD rats. METHODS: Sprague-Dawley (SD) rats were subjected one of the following treatments: sham (control group), oral Al (Al group), ELF-MF (100 µT at 50 Hz) with oral Al (MF+Al group), or ELF-MF (100 µT at 50 Hz) without oral Al (MF group). RESULTS: After 12 wk of treatment, oral Al treatment groups (Al and MF+Al groups) showed learning and memory impairment as well as morphological hallmarks, including neuronal cell loss and high density of amyloid-β (Aβ) in the hippocampus and cerebral cortex. ELF-MF without Al treatment showed no significant effect on AD pathogenesis. ELF-MF+Al treatment induced no more damage than Al treatment did. CONCLUSIONS: Our results showed no evidence of any association between ELF-MF exposure (100 µT at 50 Hz) and AD, and ELF-MF exposure does not influence the pathogenesis of AD induced by Al overload

Exophiala yunnanensis and Exophiala yuxiensis (Chaetothyriales, Herpotrichiellaceae), two new species of soil-inhabiting Exophiala from Yunnan Province, China

During a survey of soil fungi collected from Yunnan Province, China, two new species of Exophiala, E. yunnanensis and E. yuxiensis, were isolated from the soil of karst rocky desertification (KRD). The DNA sequences of these respective strains, including internal transcribed spacers (ITS), large subunit nuclear ribosomal RNA (LSU rRNA), partial small subunit (SSU) and β-tubulin (tub2) were sequenced and compared with those from species closely-related to Exophiala. Exophiala yunnanensis differs from the phylogenetically closely related E. nagquensis and E. brunnea by its smaller aseptate conidia. Exophiala yuxiensis is phylogenetically related to E. lecanii-corni, E. lavatrina and E. mali, but can be distinguished from them by its larger conidia. Full descriptions, illustrations and phylogenetic positions of E. yunnanensis and E. yuxiensis were provided

Developmental Instability and Gene Dysregulation in an Extracted Tetraploid from Hexaploid Wheat

The BBAA subgenomes of hexaploid common wheat can be ‘extracted’ to constitute a viable and self-reproducing novel tetraploid wheat, termed extracted tetraploid wheat (ETW). Prior studies have shown ETW manifesting phenotypic abnormalities and alteration in gene expression and epigenetic modifications. No population level investigation has been conducted, leaving the issue unclear regarding whether developmental stability, an essential property evolved in all natural organisms, might have been undermined in ETW. Here, we measured variations in five morphological traits and somatic chromosomal stability in populations of ETW and of its hexaploid donor, a resynthesized hexaploid and a natural tetraploid wheat. We observed phenotypic defects in ETW. Meanwhile, we documented much greater within-population variations in ETW than in the other wheat genotypes, most probably due to disrupted developmental stability in ETW. Also, somatic structural chromosome variations were detected only in ETW. Comparative transcriptome analyses indicated that the disrupted developmental stability of ETW is likely linked to massive dysregulation of genome-wide gene expression rather than to genetic mutations. Population network analysis of gene expression implicated intrinsic connectivity among the variable traits, while gene set enrichment analysis provided possible links between dysregulated gene expression and interlaced trait variation

Effects of ELF-MF on escape latency and total distance as measured by the MWM test.

<p>In the spatial acquisition phase, four trials per animal per day were performed for 5 d. Two-way ANOVA with repeated measures using the day and group as variable was conducted, and the performances of 5 d among groups were compared. A. Effects of ELF-MF on the escape latency of each rat in each of five training days. B. Effects of ELF-MF on the total distance travelled by each rat in each of five training days. Statistical results of two-way ANOVA with repeated measures showed no significant differences between the control and MF groups as well as between the Al and MF+Al groups. **<i>P</i><0.01 <i>vs.</i> control group, ^##<i>P</i><0.01 <i>vs.</i> MF group, n = 10 per group.</p

Platform crossings for each rat by group during the probe test.

<p>During the probe test at the sixth day after finishing the acquisition task, each rat was allowed to swim freely for 30 s, the number of crossings through the target position was recorded for each rat by group (10 rats per group). Rank sum tests revealed no significant differences in platform crossings between the Al and MF+Al groups and between the control and MF groups.</p>*<p><i>P</i><0.05 vs. Control group,</p>#<p><i>P</i><0.05 vs. MF group, n = 10 per group.</p