Evolution of plant RNA polymerase IV/V genes: evidence of subneofunctionalization of duplicated NRPD2/NRPE2-like paralogs in Viola (Violaceae)

<p>Abstract</p> <p>Background</p> <p>DNA-dependent RNA polymerase IV and V (Pol IV and V) are multi-subunit enzymes occurring in plants. The origin of Pol V, specific to angiosperms, from Pol IV, which is present in all land plants, is linked to the duplication of the gene encoding the largest subunit and the subsequent subneofunctionalization of the two paralogs (<it>NRPD1 </it>and <it>NRPE1</it>). Additional duplication of the second-largest subunit, <it>NRPD2/NRPE2</it>, has happened independently in at least some eudicot lineages, but its paralogs are often subject to concerted evolution and gene death and little is known about their evolution nor their affinity with Pol IV and Pol V.</p> <p>Results</p> <p>We sequenced a ~1500 bp <it>NRPD2/E2</it>-like fragment from 18 <it>Viola </it>species, mostly paleopolyploids, and 6 non-<it>Viola </it>Violaceae species. Incongruence between the <it>NRPD2/E2</it>-like gene phylogeny and species phylogeny indicates a first duplication of <it>NRPD2 </it>relatively basally in Violaceae, with subsequent sorting of paralogs in the descendants, followed by a second duplication in the common ancestor of <it>Viola </it>and <it>Allexis</it>. In <it>Viola</it>, the mutation pattern suggested (sub-) neofunctionalization of the two <it>NRPD2/E2</it>-like paralogs, <it>NRPD2/E2-a </it>and <it>NRPD2/E2-b</it>. The <it>d</it>_<it>N</it>/<it>d</it>_{<it>S </it>}ratios indicated that a 54 bp region exerted strong positive selection for both paralogs immediately following duplication. This 54 bp region encodes a domain that is involved in the binding of the Nrpd2 subunit with other Pol IV/V subunits, and may be important for correct recognition of subunits specific to Pol IV and Pol V. Across all <it>Viola </it>taxa 73 <it>NRPD2/E2</it>-like sequences were obtained, of which 23 (32%) were putative pseudogenes - all occurring in polyploids. The <it>NRPD2 </it>duplication was conserved in all lineages except the diploid MELVIO clade, in which <it>NRPD2/E2-b </it>was lost, and its allopolyploid derivates from hybridization with the CHAM clade, section <it>Viola </it>and section <it>Melanium</it>, in which <it>NRPD2/E2-a </it>occurred in multiple copies while <it>NRPD2/E2-b </it>paralogs were either absent or pseudogenized.</p> <p>Conclusions</p> <p>Following the relatively recent split of Pol IV and Pol V, our data indicate that these two multi-subunit enzymes are still in the process of specialization and each acquiring fully subfunctionalized copies of their subunit genes. Even after specialization, the <it>NRPD2/E2</it>-like paralogs are prone to pseudogenization and gene conversion and <it>NRPD2 </it>and <it>NRPE2 </it>copy number is a highly dynamic process modulated by allopolyploidy and gene death.</p

Osteoblast Recruitment Routes in Human Cancellous Bone Remodeling

It is commonly proposed that bone forming osteoblasts recruited during bone remodeling originate from bone marrow perivascular cells, bone remodeling compartment canopy cells, or bone lining cells. However, an assessment of osteoblast recruitment during adult human cancellous bone remodeling is lacking. We addressed this question by quantifying cell densities, cell proliferation, osteoblast differentiation markers, and capillaries in human iliac crest biopsy specimens. We found that recruitment occurs on both reversal and bone-forming surfaces, as shown by the cell density and osterix levels on these respective surfaces, and that bone formation occurs only above a given cell density. Canopies appeared an important source of osteoprogenitors, because (i) canopy cells proved to be more proliferative and less differentiated than bone surface cells, as shown by the inverse levels of Ki-67 and procollagen-3 N-terminal peptide versus osterix, and (ii) canopy cell densities, found to decline with age, and canopy-capillary contacts above eroded surfaces correlated positively with osteoblast density on bone-forming surfaces. Furthermore, we showed that bone remodeling compartment canopies arise from a mesenchymal envelope surrounding the red bone marrow, which is lifted and hypertrophied on initiation of bone resorption. This study, together with earlier reports, led to a model in which canopies and nearby capillaries are critical for reaching the osteoblast density required for bone formation

Research Notes : United States : Superoxide dismutase (SOD) in soybean

We are using vertical polyacrylamide gel electrophoresis (Davis, 1964) and a staining system modified after Beauchamp and Fridovich (1971) to study superoxide dismutase polymorphisms in the subgenus soja. This staining system generates superoxide radical; hence, it is specific for SOD activity. We re-solve up to 9 SOD bands in dry or germinating soybean cotyledons, and in leaves

A satellite-based Standardized Antecedent Precipitation Index (SAPI) for mapping extreme rainfall risk in Myanmar

In recent decades, substantial efforts have been devoted in flood monitoring, prediction, and risk analysis for aiding flood event preparedness plans and mitigation measures. Introducing an initial framework of spatially probabilistic analysis of flood research, this study highlights an integrated statistical copula and satellite data-based approach to modelling the complex dependence structures between flood event characteristics, i.e., duration (D), volume (V) and peak (Q). The study uses Global daily satellite-based Climate Hazards Group InfraRed Precipitation with Station data (CHIRPS) (spatial resolution of ∼5 km) during 1981–2019 to derive a Standardized Antecedence Precipitation Index (SAPI) and its characteristics through a time-dependent reduction function for Myanmar. An advanced vine copula model was applied to model joint distributions between flood characteristics for each grid cell. The southwest (Rakhine, Bago, Yangon, and Ayeyarwady) and south (Kayin, Mon, and Tanintharyi) regions are found to be at high risk, with a probability of up to 40% of flood occurrence in August and September in the south (Kayin, Mon, and Tanintharyi) and southwest regions (Rakhine, Bago, Yangon, and Ayeyarwady). The results indicate a strong correlation among flood characteristics; however, their mean and standard deviation are spatially different. The findings reveal significant differences in the spatial patterns of the joint exceedance probability of flood event characteristics in different combined scenarios. The probability that duration, volume, and peak concurrently exceed 50th-quantile (median) values are about 60–70% in the regions along the administrative borders of Chin, Sagaing, Mandalay, Shan, Nay Pyi Taw, and Keyan. In the worst case and highest risk areas, the probability that duration, volume, and peak exceed the extreme values, i.e., the 90th-quantile, about 10–15% in the southwest of Sagaing, southeast of Chin, Nay Pyi Taw, Mon and areas around these states and up to 30% in the southeast of Dekkhinathiri township (Nay Pyi Taw). The proposed approach could improve the evaluation of exceedance probabilities used for flood early warning and risk assessment and management. The proposed framework is also applicable at larger scales (e.g., regions, continents and globally) and in different hydrological design events and for risk assessments (e.g., insurance)

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress

Stem rust resistance in wheat is suppressed by a subunit of the mediator complex

Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar 'Canthatch' suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat. Stem rust is an important disease of wheat and resistance present in some cultivars can be suppressed by the SuSr-D1 locus. Here the authors show that SuSr-D1 encodes a subunit of the Mediator Complex and that nonsense mutations are sufficient to abolish suppression and confer stem rust resistance

Imaging the Impact of Prenatal Alcohol Exposure on the Structure of the Developing Human Brain

Prenatal alcohol exposure has numerous effects on the developing brain, including damage to selective brain structure. We review structural magnetic resonance imaging (MRI) studies of brain abnormalities in subjects prenatally exposed to alcohol. The most common findings include reduced brain volume and malformations of the corpus callosum. Advanced methods have been able to detect shape, thickness and displacement changes throughout multiple brain regions. The teratogenic effects of alcohol appear to be widespread, affecting almost the entire brain. The only region that appears to be relatively spared is the occipital lobe. More recent studies have linked cognition to the underlying brain structure in alcohol-exposed subjects, and several report patterns in the severity of brain damage as it relates to facial dysmorphology or to extent of alcohol exposure. Future studies exploring relationships between brain structure, cognitive measures, dysmorphology, age, and other variables will be valuable for further comprehending the vast effects of prenatal alcohol exposure and for evaluating possible interventions

The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification

acceptedVersio

Species-level phylogeny, fruit evolution and diversification history of Geranium (Geraniaceae)

The cosmopolitan genus Geranium L. (Geraniaceae) consists of c. 350 species distributed in temperate habitats worldwide, with most of its diversity concentrated in the Mediterranean region. Unlike other genera in Geraniaceae, the species of Geranium present contrasting seed discharge syndromes, i.e. the 'Erodium-type' (ET), the 'carpel-projection type' (CP), the 'seed-ejection type' (SE), and the 'inoperative type' (IT), which have been used to delimit major groups within the genus. However, phylogenetic relationships within Geranium are unknown and so is the evolution of the different seed discharge mechanisms. Here, we used a calibrated multispecies coalescent approach to infer the species-level phylogeny and divergence times of the genus based on chloroplast (rbcL, trnL-trnF) and nuclear (ITS) DNA sequences. Our sampling represents most of the morphological variation described in the genus. We reconstruct the evolution of the seed discharge mechanism using ancestral state reconstruction (ASR) techniques on the multispecies coalescent tree, and assess the association between fruit type evolution and species diversification using stochastic birth-death and trait-dependent diversification models. Finally, we reconstruct the early biogeographic history of the genus using discrete and continuous biogeographic analyses of species distribution centroids, including fossil evidence and tip dates. Our results show that fruit type is homoplasious and that the classification based on fruit type in Geranium is artificial. The taxonomy and putative apomorphic characters for Geranium are discussed. ASR of the fruit characters suggests that ET may represent the ancestral state in Geranium and from which CP originated twice, IT presumably once, and SE twice. The independent appearance of the SE syndrome is in both cases associated with increases in diversification rates in the genus. The biogeographic analysis centers the origin and early 10 Ma diversification of Geranium on the Mediterranean region. The evolution of seed discharge mechanism about 5 Ma might have allowed the species of Geranium to increase in geographic range and to ultimately, diversify