The abundance and composition of genes involved in the catabolism of aromatic compounds provide important information on the biodegradation potential of organic pollutants and naturally occurring compounds in the environment. We studied catechol 2, 3 dioxygenase (C23O) and benzylsuccinate synthase (bssA) genes coding for key enzymes of aerobic and anaerobic degradation of aromatic compounds in experimental incubations with sediments from two contrasting lakes; humic lake Svarttjärn and eutrophic Vallentunasjön, respectively. Sediment cores from both lakes were incubated continuously for 5 months at constant temperatures ranging from 1.0 to 21.0 °C. The difference in C23O gene composition of the sediment analyzed at the end of the experiment was larger between lakes, than among temperature treatments within each lake. The abundance of C23O gene copies and measured respiration was positively correlated with temperature in Vallentunasjön, whereas putative C23O genes were present in lower concentrations in Svarttjärn sediments. Putative bssA genes were only detected in Svarttjärn. For both lakes, the two catabolic genes were most abundant in the surface sediment. The results emphasize the important role of temperature and nutrient availability in controlling the functional potential of sediment microorganisms and reveal differences between systems with contrasting trophic status. A better understanding of catabolic pathways and enzymes will enable more accurate forecasting of the functional properties of ecosystems under various scenarios of environmental change.

Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large non-coding fraction, functional non-coding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional non-coding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favourable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (α) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element (TE) insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on non-coding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.

Robinow syndrome (RS) is a genetically heterogeneous disorder characterized by skeletal dysplasia and a distinctive facial appearance. Previous studies have revealed locus heterogeneity with rare variants in DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A underlying the etiology of RS. The aforementioned "Robinow-associated genes" and their gene products all play a role in the WNT/planar cell polarity signaling pathway. We performed gene-targeted Sanger sequencing, exome sequencing, genome sequencing, and array comparative genomic hybridization on four subjects with a clinical diagnosis of RS who had not had prior DNA testing. Individuals in our cohort were found to carry pathogenic or likely pathogenic variants in three RS related genes: DVL1, ROR2, and NXN. One subject was found to have a nonsense variant (c.817C > T [p.Gln273*]) in NXN in trans with an ~1 Mb telomeric deletion on chromosome 17p containing NXN, which supports our contention that biallelic NXN variant alleles are responsible for a novel autosomal recessive RS locus. These findings provide increased understanding of the role of WNT signaling in skeletal development and maintenance. These data further support the hypothesis that dysregulation of the noncanonical WNT pathway in humans gives rise to RS.

The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.

Autumn phenology traits are likely to be essential for the adaptation of apple to boreal climate. However, the genetic control of these traits is not well understood, and, for example, growth cessation does not appear to be controlled by day length as in many other boreal tree species. Here, I combine a quantitative genetic and population genomic approach to study autumn senescence in apple. I phenotyped a diverse germplasm collection for the timing of autumn senescence, performed quantitative trait loci (QTL) mapping in a multiparental population (MPP), and investigated genomic signals of selection to identify candidate genes. The timing of 50% autumn senescence was negatively correlated with adaptation to higher (boreal) climate zones. Two QTL were found to control the timing of autumn senescence in the MPP, exhibiting both dominance and epistatic interactions. The QTL on linkage group (LG) 17 was also variable in the diversity germplasm, while the QTL on LG11 was not. Cultivars adapted to boreal climate showed weak signals of selection at two loci within the genomic region of chromosome 17 corresponding to the LG17 QTL interval, consistent with a recent expansion to northern Sweden. These loci coincide with two predicted UGT85 genes and a possible copy number variation in PHYC, respectively. Thus, this study provides valuable information for further research and breeding of apple in light of the ongoing climate change.

Maintaining postnatal bone growth is crucial for humans to reach their final height. To determine transcriptional networks coordinating this process, we applied spatially resolved transcriptomics to growth plate biopsies obtained from healthy adolescents who underwent epiphysiodesis surgery for idiopathic tall stature. Spatial profiling revealed new markers for each zone of the human growth plate and identified genes associated with poorly understood growth disorders, including the novel hypertrophic zone marker SGMS2. We elaborated on this finding and established that Sgms2 is present in growth plate-derived matrix vesicles, and its activity facilitates mineralization - a process impaired in patients with SGMS2 mutations. By exploring the low transcriptional activity of resting zone chondrocytes, we found that a subset of these cells exists in a functionally quiescent state in vivo, as determined by their predominantly nuclear mRNA, abundant heterochromatin, and ability to exit the G0 phase under specific conditions - features shared with skeletal stem cells in mouse growth plates. Additionally, we identified distinct sub-populations of human resting zone chondrocytes; an exploration of their hierarchy determined that CHRDL2 and/or SFRP5-positive sub-populations were among the least quiescent resting zone cells. In summary, we generated a comprehensive map of gene expression within the human growth plate, revealing novel zone-specific markers, new primary growth disorders, candidate pharmacological targets, and sub-populations of resting zone chondrocytes with features of quiescent stem cells. These results contribute to a better understanding of the cellular and molecular mechanisms governing human height and can facilitate improved diagnosis and treatment strategies for patients with skeletal growth disorders.

The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.