Recognition of the untapped potential of photosynthesis to improve crop yields has spurred research to identify targets for breeding. The CO2-fixing enzyme Rubisco is characterised by a number of inefficiencies and frequently limits carbon assimilation at the top of the canopy, representing a clear target for wheat improvement. Two bread wheat lines with similar genetic backgrounds and contrasting in vivo maximum carboxylation activity of Rubisco per unit leaf nitrogen (Vc,max,25/Narea) determined using high throughput phenotyping methods were selected for detailed study from a panel of 80 spring wheat lines. Detailed phenotyping of photosynthetic traits in the two lines using glasshouse-grown plants showed no difference in Vc,max,25/Narea determined directly via in vivo and in vitro methods. Detailed phenotyping of glasshouse-grown plants of the 80 wheat lines also showed no correlation between photosynthetic traits measured via high throughput phenotyping of field-grown plants. Our findings suggest that the complex interplay between traits determining crop productivity and the dynamic environments experienced by field-grown plants needs to be considered when designing strategies for effective wheat crop yield improvement when breeding for particular environments.

Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms? A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species ( Pseudomonas aeruginosa , Staphylococcus aureus , and Acinetobacter baumannii ) were grown in vitro for 3 days and then challenged with respective antibiotics (ciprofloxacin, daptomycin, and tigecycline) for an additional 24 h. , ABSTRACT Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms? A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species ( Pseudomonas aeruginosa , Staphylococcus aureus , and Acinetobacter baumannii ) were grown in vitro for 3 days and then challenged with respective antibiotics (ciprofloxacin, daptomycin, and tigecycline) for an additional 24 h. All three microorganisms displayed reduced susceptibility in biofilms compared to planktonic cultures. Global transcriptomic profiling of gene expression comparing biofilm to planktonic and antibiotic-treated biofilm to untreated biofilm was performed. Extracellular metabolites were measured to characterize the utilization of carbon sources between biofilms, treated biofilms, and planktonic cells. While all three bacteria exhibited a species-specific signature of stationary phase, no conserved gene, gene set, or common functional pathway could be identified that changed consistently across the three microorganisms. Across the three species, glucose consumption was increased in biofilms compared to planktonic cells, and alanine and aspartic acid utilization were decreased in biofilms compared to planktonic cells. The reasons for these changes were not readily apparent in the transcriptomes. No common shift in the utilization pattern of carbon sources was discerned when comparing untreated to antibiotic-exposed biofilms. Overall, our measurements do not support the existence of a common genetic or biochemical basis for biofilm tolerance against antibiotics. Rather, there are likely myriad genes, proteins, and metabolic pathways that influence the physiological state of individual microorganisms in biofilms and contribute to antibiotic tolerance.

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

Abstract We investigate the species-level taxonomy and evolutionary history of Nearctic ants in the Crematogaster scutellaris group (Hymenoptera: Formicidae), drawing on evidence from morphology and UCE (ultraconserved element) phylogenomics. The New World species in this group form a well-supported clade that originated in the Late Miocene (~7.3 Mya) and subsequently diverged into three major lineages: the C. coarctata clade (south-western Nearctic), the C. opaca clade (south-western Nearctic and northern Neotropics) and the C. lineolata clade (eastern Nearctic and Caribbean, with four isolated south-west endemics). We hypothesize trans-Beringian dispersal into the New World, west-to-east movement within North America and restriction of mesophilic species to the east with increasing aridification of the west. The ancestral nesting behaviour of these ants is inferred to be ground-dwelling, and this is still the predominant condition in the arid west, whereas most species in the eastern United States are arboreal. We resurrect from synonymy nine species and describe three new species: C. detecta sp. nov. (from Nevada), C. parapilosa sp. nov. (Florida) and C. vetusta sp. nov. (Arizona). We provide a worker-based key to the 34 species of Crematogaster occurring in America north of Mexico, but emphasize that there are still ongoing taxonomic issues that need to be resolved.

Cultivated sweetpotato (Ipomoea batatas (L.) Lam.) from the family Convolvulaceae is a hexaploid species with 2n = 6x = 90, and has been controversial regarding its nature as an autopolyploid arising within a species or allopolyploid forming between species. Here, we developed oligonucleotide-based painting probes for two chromosomes of I.nil, a model diploid Ipomoea species. Using these probes, we revealed pairing behavior of homoeologous chromosomes in I. batatas and its two possible polyploid ancestral species, tetraploid I. tabascana (2n = 4x = 60) and hexaploid I. trifida (2n = 6x = 90). Chromosome painting analysis revealed a high percentage of quadrivalent formation in zygotene-pachytene cells of I. tabascana, which supported that I. tabascana was an autotetraploid likely derived by doubling of structurally similar and homologous genomes rather than a hybrid between I. batatas and I. trifida (2x). The high frequency of hexavalent/bivalent and tetravalent pairing was observed in I. trifida (6x) and I. batatas. However, the percentage of hexavalent pairing in I. trifida (6x) was far higher than that in I. batatas. Thus, present results tended to support that I. trifida (6x) was an autohexaploid, while I. batatas was more likely to be a segmental allohexaploid.

Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones.

The emergence of West Nile virus (WNV) and Usutu virus (USUV) in Europe resulted in significant outbreaks leading to avifauna mortality and human infections. Both viruses have overlapping geographical, host and vector ranges, and are often co-circulating in Europe. In Germany, a nationwide bird surveillance network was established to monitor these zoonotic arthropod-borne viruses in migratory and resident birds. In this framework, co-infections with WNV and USUV were detected in six dead birds collected in 2018 and 2019. Genomic sequencing and phylogenetic analyses classified the detected WNV strains as lineage 2 and the USUV strains as lineages Africa 2 (n=2), Africa 3 (n=3), and Europe 2 (n=1). Preliminary attempts to co-propagate both viruses in-vitro failed. However, we successfully cultivated WNV from two animals. Further evidence for WNV-USUV co-infection was obtained by sampling live birds in four zoological gardens with confirmed WNV cases. Three snowy owls had high neutralizing antibody titers against both WNV and USUV, of which two were also positive for USUV-RNA. In conclusion, further reports of co-infections in animals as well as in humans are expected in the future, particularly in areas where both viruses are present in the vector population.

Enrichment panel targeting 94,752 human SNPs for assessment of kinship out to 4th-degree relatives, particularly for highly degraded samples. Gorden et al. (2022) demonstrated this panel on a set of World War II-era highly degraded samples and a pool of family references genotyped on the Illumina CytoSNP-850K chip. The panel is designed for use with Parabon’s Fx software for extended kinship from very low-coverage sequencing data.


Reference: Gorden, E.M., E.M. Greytak, K. Sturk-Andreaggi, J. Cady, T.P. McMahon, S. Armentrout, & C. Marshall. (2022). Extended kinship analysis of historical remains using SNP capture. Forensic Science International: Genetics, 57, 102636.