Pangenomic context reveals the extent of intraspecific plant NLR evolution.

Nucleotide-binding leucine-rich repeat (NLR) proteins are major components of the plant immune system, recognizing pathogen effectors and triggering defense responses. Because of the diversity of pathogen effector repertoires, NLRs have extraordinary sequence, structural, and regulatory variability. Although processes contributing to NLR diversity have been identified, the precise evolution of NLRs in their genomic context and along the multiple axes of diversity has been difficult to trace.

The genetic architecture of repeated local adaptation to climate in distantly related plants.

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses.

Landscape drivers of genomic diversity and divergence in woodland Eucalyptus.

Spatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L'Héritier 1789; the "eucalypts") are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole-genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon.

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate.

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing.

RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes in SAL1-PAP-XRN Retrograde Signaling.

In plants, the molecular function(s) of the nucleus-localized 5'-3' EXORIBONUCLEASES (XRNs) are unclear; however, their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using parallel analysis of RNA ends, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both and mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3' read-through.

Axe: rapid, competitive sequence read demultiplexing using a trie.

Summary: We describe a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial indexing, indices of differing length and several mismatches per index sequence.

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples.

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.

Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery.

Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture.

The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA.

The khmer software package: enabling efficient nucleotide sequence analysis.

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.

A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation.

Thigmomorphogenesis is viewed as being a response process of acclimation to short repetitive bursts of mechanical stimulation or touch. The underlying molecular mechanisms that coordinate changes in how touch signals lead to long-term morphological changes are enigmatic. Touch responsive gene expression is rapid and transient, and no transcription factor or DNA regulatory motif has been reported that could confer a genome wide mechanical stimulus.

TraitCapture: genomic and environment modelling of plant phenomic data.

Agriculture requires a second green revolution to provide increased food, fodder, fiber, fuel and soil fertility for a growing population while being more resilient to extreme weather on finite land, water, and nutrient resources. Advances in phenomics, genomics and environmental control/sensing can now be used to directly select yield and resilience traits from large collections of germplasm if software can integrate among the technologies. Traits could be Captured throughout development and across environments from multi-dimensional phenotypes, by applying Genome Wide Association Studies (GWAS) to identify causal genes and background variation and functional structural plant models (FSPMs) to predict plant growth and reproduction in target environments.

Dynamic interface pressure distributions of two transtibial prosthetic socket concepts.

In this study, we investigated and compared the dynamic interface pressure distribution of hands-off and hands-on transtibial prosthetic systems by means of pressure mapping. Of the 48 established unilateral amputees recruited, half (n = 24) had been wearing pressure-cast prostheses (IceCast Compact) and the other half (n = 24) had been wearing hand-cast sockets of the patellar tendon bearing design. We measured the dynamic pressure profile of more than 90% of the area within each prosthetic socket by means of four Tekscan F-Scan socket transducer arrays.

The influence of pulmonary staple line reinforcement on air leaks.

Objectives: Although uncommon, prolonged postoperative air leaks are a troublesome complication of lung surgery. This study was performed to determine if buttressing pulmonary staple lines would reduce air leakage at varying airway pressures, and if there was a difference between buttressing materials.

Methods: Using cadaver lungs, the development of air leak from staple lines was evaluated at incremental airway pressures.