Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant

Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in Northern Chile, are highly similar to Antarctic cyanobacteria

The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments

Prevalence and incidence of iron deficiency in European community-dwelling older adults : An observational analysis of the DO-HEALTH trial

Background and aim Iron deficiency is associated with increased morbidity and mortality in older adults. However, data on its prevalence and incidence among older adults is limited. The aim of this study was to investigate the prevalence and incidence of iron deficiency in European community-dwelling older adults aged ≥ 70 years. Methods Secondary analysis of the DO-HEALTH trial, a 3-year clinical trial including 2157 community-dwelling adults aged ≥ 70 years from Austria, France, Germany, Portugal and Switzerland. Iron deficiency was defined as soluble transferrin receptor (sTfR) > 28.1 nmol/L. Prevalence and incidence rate (IR) of iron deficiency per 100 person-years were examined overall and stratified by sex, age group, and country. Sensitivity analysis for three commonly used definitions of iron deficiency (ferritin  1.5) were also performed. Results Out of 2157 participants, 2141 had sTfR measured at baseline (mean age 74.9 years; 61.5% women). The prevalence of iron deficiency at baseline was 26.8%, and did not differ by sex, but by age (35.6% in age group ≥ 80, 29.3% in age group 75–79, 23.2% in age group 70–74); P  1.5. Occurrences of iron deficiency were observed with IR per 100 person-years of 9.2 (95% CI 8.3–10.1) and did not significantly differ by sex or age group. The highest IR per 100 person-years was observed in Austria (20.8, 95% CI 16.1–26.9), the lowest in Germany (6.1, 95% CI 4.7–8.0). Regarding the other definitions of iron deficiency, the IR per 100 person-years was 4.5 (95% CI 4.0–4.9) for ferritin  1.5. Conclusions Iron deficiency is frequent among relatively healthy European older adults, with people aged ≥ 80 years and residence in Austria and Portugal associated with the highest risk

A community resource for paired genomic and metabolomic data mining

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.Peer reviewe

Climatically stable landscapes predict patterns of genetic structure and admixture in the Californian canyon live oak

[Aim]: We studied which factors shape contemporary patterns of genetic structure, diversity and admixture in the canyon live oak (Quercus chrysolepis). Specifically, we tested two alternative hypotheses: (1) that areas with high habitat suitability and stability since the Last Glacial Maximum (LGM) sustain higher effective population sizes, resulting in increased levels of genetic diversity; and (2) that populations from areas with lower habitat stability show higher levels of genetic admixture due to their recurrent colonization by individuals originating from genetically differentiated populations. Furthermore, we analysed the relative importance of past and current habitat suitability and their additive effects on contemporary patterns of genetic structure. [Location]: California, USA. [Methods]: We sampled 160 individuals from 33 localities across the distribution range of the canyon live oak in California and then combined information from 13 nuclear microsatellite DNA markers and climate niche modelling to study patterns of genetic variation in this species. We used Bayesian clustering analyses to analyse geographical patterns of genetic structure and admixture, and circuit theory to generate isolation-by-resistance (IBR) distance matrices. [Results]: We found that the degree of genetic admixture was higher in localities with lower inferred population stability, but that genetic diversity was not associated with habitat suitability or stability. Landscape genetic analyses identified habitat stability as the primary driver of population genetic differentiation. [Main conclusions]: This study shows that habitat stability can be a major factor shaping genetic variation in wind-pollinated trees and supports the idea that stable regions contribute to genetic connectivity across different climatic periods. To our knowledge, this study is the first to report an association between patterns of genetic admixture and stability of local habitat.During this work J.O. was supported by Juan de la Cierva (MICINN), José Castillejo (ME) and Severo Ochoa (EBD) research fellowships. P.F.G. received post-doctoral support from a UCLA research award to V.L.S. This workreceived financial support from grants CGL2011-25053(MICINN) and UNCM08-1E-018 (FEDER).Peer reviewe

SNP calls for all samples, final in table format

SNP calls in tab-separated format with rows as individual samples and columns as loci as inferred from Stacks. These are the final data that were filtered such that the minor allele frequency is greater than 0.05 and there is no more than 30% missing data at a locus. This file contains both Acacia koa and A. koaia samples

Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions

SNP calls for island of Hawaii, final in table format

SNP calls in tab-separated format with rows as individual samples and columns as loci as inferred from Stacks. These are the final data that were filtered such that the minor allele frequency is greater than 0.05 and there is no more than 30% missing data at a locus. This file contains both Acacia koa and A. koaia samples; the latter were removed prior to environmental association analyses

SNP calls for all samples in VCF format (before filtering)

SNP call data for all samples across all Hawaiian islands, produced by Stacks in VCF format, before final filtering steps