The anchor cell (AC) of the Caenorhabditis elegans hermaphrodite somatic gonad primordium is a signaling nexus that regulates uterine and vulval development. As the somatic gonad primordium is forming, four cells, two α and two β cells, are born with the potential to be the AC. This potential becomes restricted to the α cells, which undergo the LIN-12/Notch-mediated AC/VU decision to resolve which α cell will become the AC. The transcription factor HLH-2, the sole E/Daughterless protein ortholog in C. elegans, is critical for this process, and dynamic regulation of hlh-2 transcription contributes to the robust specification of a single AC. The hlh-2prox regulatory element mediates the dynamic pattern of hlh-2 transcription: the initial expression in the parents of the α and β cells, which is briefly sustained in the α and β cells after they are born; its subsequent restriction to the α cells during the AC/VU decision; and its continued expression in the AC. In this study, we identify the cis-acting sequences within hlh-2prox and transcription factors required for the initial expression of hlh-2 in the α and β cells and their parents, demonstrate that the Wnt/β-catenin Asymmetry Pathway (WβA) regulates restriction of hlh-2 transcription to the α cells, and show that the maintenance of hlh-2 transcription in α cells requires distinct elements and the chromatin factor LSY-12. This analysis extends our understanding of regulatory mechanisms that operate during a precise and robust Notch-mediated lateral specification paradigm.

Phenotypic plasticity allows organisms to express different traits in response to different environmental or genetic conditions. Understanding the evolution of conditional phenotypes is challenging because they are not expressed by all members of a population, which allows for the accumulation of deleterious variation due to a reduced efficacy of purifying selection. Theory suggests pleiotropic effects help prevent the decay of conditional phenotypes by exposing the variation accrued in one context to the effects of purifying selection in an alternative context. However, existing frameworks for describing the evolutionary dynamics of conditional phenotypes are limited in their ability to flexibly model the complex pleiotropic architectures that often underlie conditional phenotypes. To help improve our understanding of the evolutionary stability of conditional phenotypes, here we describe a geometric model that allows for explicit modeling of different fitness optima for conditional and alternative phenotypes, as well as their underlying pleiotropic associations. Using stochastic simulations and mathematical analyses, we show that this model recapitulates and elaborates on existing predictions regarding the role of pleiotropy in maintaining conditional phenotypes. Specifically, we found that more pleiotropic conditional phenotypes experience decreased rates of decay in fitness over periods of inexpression, the effects of which are comparable for phenotypes that are spatially and temporally conditional. Furthermore, the functional form of the relationship between conditional phenotype expression pattern and decay rate is mediated by pleiotropic effect, which provides more explicit hypotheses of when pleiotropic constraint is expected to play a significant role in the evolutionary maintenance of conditional phenotypes. Finally, we found that when pleiotropic architectures evolve over periods of conditional phenotype inexpression, decoupling from other phenotypes readily evolves and facilitates decay in fitness.

Ansell's mole-rat (Fukomys anselli) is an African rodent known for its subterranean lifestyle and unique phenotypic traits, including extreme longevity, magnetoreception, and a cooperative breeding social structure. Efforts to dissect the genetic architecture of these traits and to decipher their phylogenetic relationships within the broader African mole-rat family would greatly benefit from a reference-grade genome. Here, we report a first genome assembly of a male Ansell's mole-rat. By combining Oxford Nanopore Technologies (ONT) long-reads and Illumina short-reads with Hi-C data, we generated a chromosome level assembly with a total length of 2.27 Gb, 412 scaffolds and a scaffold N50 of 72.4 Mb. We identified 99.54% of expected genes and annotated 29,094 transcripts using RNA sequencing data. This high-quality de novo genome of Fukomys anselli lays the foundation for dissecting the genetic and evolutionary basis of its extraordinary traits and resolving African mole-rat phylogeny.

The wild blueberry relative Vaccinium stamineum offers a rich source of diversity for expanding the genetic pool of cultivated blueberries, and it has also potential for breeding as a crop on its own. Understanding the genetic architecture of fruit quality traits in this wild species can facilitate and speed up future breeding efforts for introgression and de novo domestication. Therefore, in this study, we developed a biparental population of 147 progenies from V. stamineum, which were phenotyped and genotyped for quantitative trait loci (QTL) mapping. Phenotypic data for acidity (TTA and pH) and sweetness (soluble solids content) were collected over three years. Genotypic data were obtained through targeted sequencing using 6,000 probes developed for blueberry. A linkage map was crafted containing a total of 3,797 markers spanning a cumulative distance of 1,801 cM across 12 linkage groups. Composite interval mapping revealed a total of 20 significant QTL considering the three traits and years of evaluation. Two consistent overlapping QTL interval across two years were found for TTA and soluble solids in linkage groups 8 and 9, respectively. We also found a QTL for TTA that has been previously reported for cultivated blueberry. Low to moderate heritability was observed, indicating the complex genetic architecture of these traits. Overall, the newly developed high-density genetic map provides a valuable resource for trait mapping efforts in this species, and the QTL identified for fruit quality can guide future molecular breeding strategies.

With this special issue on the Genetics of Bacteria, the authors shine new light on selections and screens from the past (and on the people that carried these out) while also pointing towards many future directions for bacterial genetics. Their goal is to highlight the GSA journals as a welcome home for reporting discoveries across bacterial systems building on their rich history.

Biological control is a sustainable strategy to combat agricultural pests. Yet, legislation increasingly restricts importing non-native biocontrol agents. Thus, selective breeding of biocontrol traits is suggested to enhance performance of existing biocontrol agents. Genomic prediction, where genomic data is used to estimate the genetic merit of an individual for specific traits, is an alternative to exploit genetic variation for the improvement of native biocontrol agents. This study aims to establish proof-of-principle for genomic prediction in insect biocontrol agents, using wing morphology traits in the model parasitoid Nasonia vitripennis Walker (Pteromalidae). We performed genomic prediction using a Genomic Best Linear Unbiased Prediction (GBLUP) model, using 1,230 individuals with 8,639 SNPs generated by genotyping-by-sequencing (GBS). We used individuals from two generations from the outbred HVRx population, 717 individuals from generation G169 and 513 from generation G172. To assess genomic prediction accuracy, we used across-generation validation: forward validation for G172 from G169, backward validation for G169 from G172, and also 5-fold cross-validation. For size-related traits, including tibia length, wing length, width, and second moment wing area, the accuracy of genomic prediction was close to zero in both across-generation validations, but much higher in 5-fold cross-validation (ranging 0.54-0.68). For the shape-related trait wing aspect ratio, a high accuracy was found for all three validation strategies, with 0.47 for across-generation forward validation, 0.65 for across-generation backward validation, and 0.54 for 5-fold cross-validation. Overall, genomic selection in insect biocontrol agents with a relative small effective population size seems promising. However, factors such as the biology of insects, phenotyping techniques, and large-scale genotyping costs still challenge the application of genomic selection to biocontrol agents.

Common bean (Phaseolus vulgaris L.) is a vital crop for direct human consumption, with essential nutrients and valuable protein that provides food security in developing countries. However, its cultivation faces significant threats from Meloidogyne incognita, a root-knot nematode, resulting in considerable yield loss. Developing crop resistance remains a key strategy for mitigating nematode infections. To investigate the genetic architecture of common bean responses to root-knot nematode (specifically, race 3 of M. incognita), we performed controlled crosses between the genotypes "IAC-Tybatã" and "Branquinho" with contrasting resistance. The resulting segregating population (F2) of 333 individuals was genotyped using genotyping-by-sequencing. We used a phenotyping approach, already optimized in the lab, to collect trait data for a subset of 200 F2:3 families. Evaluations of egg mass, root-galling index, and root dry mass (RM) were conducted 30 d after root-knot nematode inoculation under greenhouse conditions, in a completely randomized design with 10 replicates. Linkage and quantitative trait loci mapping were performed, while functional mapping of associated regions facilitated identification of candidate genes. A linkage map encompassing 954 SNPs assigned to 11 linkage groups totaling 1,687 cM formed the basis for Interval Mapping, Composite Interval Mapping, and Multiple Interval Mapping, revealing four major quantitative trait locis (on Pv03, Pv05, Pv08, and Pv10) and epistasis between quantitative trait loci on Pv08 and on Pv10 associated with the root-galling index trait. No significant quantitative trait loci were identified for egg mass and RM. The model enabled calculation of genotypic values through marker-assisted selection. The high correlation between observed and predicted values (0.72) underscores the model's significance. Candidate genes previously associated with nematode resistance were also identified within the quantitative trait loci interval on chromosome Pv10. Our results will be valuable for future selection of varieties resistant to this important crop disease.

To exploit allelic variation in Hordeum vulgare subsp. spontaneum, the Wild Barley Diversity Collection was subjected to paired-end Illumina sequencing at ∼9X depth and evaluated for several agronomic traits. We discovered 240.2 million single nucleotide polymorphisms (SNPs) after alignment to the Morex V3 assembly and 24.4 million short (1-50 bp) insertions and deletions. A genome-wide association study of lemma color identified one marker-trait association (MTA) on chromosome 1H close to HvBlp, the cloned gene controlling black lemma. Four MTAs were identified for seedling stem rust resistance, including two novel loci on chromosomes 1H and 6H and one co-locating to the complex RMRL1-RMRL2 locus on 5H. The whole-genome sequence data described herein will facilitate the identification and utilization of new alleles for barley improvement.

Plants adapt to diverse environments through complex gene regulatory networks, with the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) gene family playing a crucial role. This research identified and examined the AHL gene family within Brachypodium distachyon, a model plant for Pooideae grasses including essential cereal crops. AHL proteins are conserved across land plants, suggesting an ancient origin and fundamental importance in plant development and adaptation. Brachypodium distachyon is an efficient research model for monocot studies due to its compact genome, short life cycle, and genetic manipulation compatibility. While Arabidopsis thaliana has consistently served as a valuable model for studying the AHL gene family, understanding their function in monocots, particularly grasses, is essential for crop improvement. The conserved evolutionary history of AHL proteins makes them an excellent target for comparative genomic research across eudicots and monocots systems. Although AHL functions have been studied in Arabidopsis thaliana, their roles in Pooideae grasses remain largely unknown. This research identified 22 BdAHL genes classified into two monophyletic clades and three protein types based on conserved domains. By characterizing BdAHL gene structure, phylogeny, expression, and potential protein interactions, this study lays the groundwork for future functional analyses of Pooideae grasses. BdAHL expression profiles across different tissues and global coexpression patterns were also examined. These findings provide a foundation for future research into specific AHL gene functions in Brachypodium distachyon growth, development, and stress responses, potentially enhancing our understanding of AHL function in other Pooideae grasses and aiding crop improvement strategies.

The white-cheeked goby (Rhinogobius duospilus) is a small stream-dwelling fish endemic to southern China and Vietnam. With a sucker-like modified pelvic fin that helps it cling to substrate in fast-flowing water and vibrant breeding colors in males, R. duospilus is particularly appealing to aquarium enthusiasts. To investigate its distribution patterns, evolutionary history, and molecular adaptations to local environments, a high-quality genome assembly is critically needed. By employing PacBio HiFi sequencing combined with Hi-C-assisted assembly technology, we successfully obtained a chromosome-level genome assembly of R. duospilus. The final assembly yielded a genome size of 1031.61 Mb with a scaffold N50 of 45.55 MB. Approximately 991.84 Mb of genomic sequence was anchored onto 22 chromosome pairs. BUSCO assessment indicated high genome completeness at 96.14%. Through gene prediction and functional annotation, we identified 24,418 protein-coding genes, with 23,660 (96.8%) successfully annotated. This work presents the first high-quality reference genome for R. duospilus, creating an essential genomic resource for investigating population differentiation and adaptive evolution through comparative genomics. Additionally, this dataset provides valuable support for taxonomy, evolution and conservation genetics of genus Rhinogobius.

Ribosomal DNA (rDNA) occurs as tandem arrays of a repeat unit containing the genes encoding 18S, 5.8S and 28S rRNA separated by spacers. These rRNAs form the catalytic core of ribosomes and thus play a crucial role in protein synthesis. Due to its repetitive nature, rDNA copy number varies within and between eukaryotic species through recombination, which also results in homogenization of repeat sequences within species (concerted evolution). However, the recombination rate within rDNA has not been extensively estimated. Despite concerted evolution and strong selection to maintain the sequence of rRNA genes, some transposons insert into specific sequences in the 28S gene. We used short-read whole genome sequences to examine the dynamics of change in rDNA copy number and sequence variation in 90 samples from clonally propagated Daphnia obtusa mutation accumulation (MA) lines over ∼95 generations. We also tracked the number of Pokey elements, a DNA transposon that inserts into the 28S gene of species in the subgenus Daphnia. We observed an overall decline in rDNA copy number across MA lines between generations 5 and ∼87, although both increases and decreases were observed over short intervals. The diploid 28S copy number ranged from 144 to 1,274, with a mean of 425.2. Diploid Pokey number varied from 65 to 537 and was significantly positively correlated with 28S copy number. Moreover, the element persisted in all lines even after large reductions in 28S copy number. We found that estimating rates of rDNA copy number change over long intervals resulted in substantial underestimates, as shorter intervals revealed that large copy number changes could occur in as few as five generations. We identified five rDNA haplotypes based on 58 single nucleotide polymorphisms (SNPs) that were distributed across the 18S and 28S genes, and the three non-repetitive intergenic spacer regions. We also identified six Pokey haplotypes based on 113 SNPs. The number of these haplotypes was strongly correlated with the number of the three most common rDNA haplotypes. By tracking changes in haplotype frequency and copy number within four MA lines over short time intervals, we estimated the mean rDNA recombination rate to be 0.094 events/generation. These results reveal that rapid changes can occur in rDNA over short timescales and show that Pokey transposon dynamics are tightly linked to rDNA structure.

Anurans possess complex genomes, making molecular research challenging, particularly in non-model species. Transcriptomics offers a powerful tool for uncovering genomic responses to environmental changes through distinct transcriptional patterns. A sizeable portion of the transcriptome consists of non-coding RNAs, with long non-coding RNAs (lncRNAs) playing key roles in gene regulation. Here, we performed de novo transcriptome assembly from brain samples of Dryophytes arenicolor across three life stages: Pre-metamorphic, Metamorphic Climax, and Adults. By aligning our transcriptomes to LNCipedia, we identified 4,557 previously annotated lncRNAs with potential roles in gene regulation, macromolecule biosynthesis, and chromatin organization. To detect novel lncRNAs, we implemented a bioinformatic pipeline to filter out known mRNAs, small ncRNAs, sequences with coding potential, conserved protein domains, and previously identified D. arenicolor mRNAs, identifying 4,836 putative novel lncRNAs. To explore their functional roles, we performed Weighted Gene Correlation Analysis and gene enrichment analysis, revealing that these lncRNAs may be involved in protein heterodimerization, nucleosome assembly, and post-transcriptional regulation of gene expression. To our knowledge, this is the first study to characterize lncRNAs across multiple life stages in D. arenicolor, highlighting their potential regulatory functions.

RAD52 is a conserved member of the homologous recombination repair (HRR) apparatus from yeast to humans. Mutating conserved amino acids in the internal and external DNA binding domains of the human RAD52 protein (HsRAD52) has discrete effects in vitro. Previous studies have shown that HsRAD52 supports multiple mechanisms of HRR in budding yeast, suggesting the utility of this model system for exploring the correspondence between losses of HsRAD52 function in vitro and their impact in vivo. We report that disrupting the internal and external DNA binding domains of HsRAD52 produced distinct effects on the repair of genomic DNA double-strand breaks (DSB) by conservative and non-conservative HRR in budding yeast, suggesting that these domains contribute to separate mechanisms in vivo. The further elucidation of the effects of perturbations in the structure and biochemical function of HsRAD52 in living systems will provide new insight into its ability to support DSB repair, cancer susceptibility as well as new avenues for targeting HRR-deficient cancers.

The bumble bee wax moth, Aphomia sociella, is an important lepidopteran pest impacting bee colonies essential for pollination and apiculture. Like other moths, this species has been reported to ingest plastics. Although specific enzymes have been proposed to facilitate plastic catabolism in some moths, with controversial results, this remains entirely unexplored in A. sociella. Despite the biological and ecological relevance of A. sociella, sequence efforts aimed at understanding the genetic makeup of this species have not yet been undertaken. In this work, we successfully achieved a high-quality de novo genome assembly of A. sociella and comprehensive gene annotations generated from long-read DNA and RNA sequencing with Oxford Nanopore technology. The haploid assembly includes 347 contigs, with an N50 of 4.96 Mb, and contains 12,618 protein-coding genes. Benchmarking Universal Single Copy Orthologs (BUSCO) analyses indicates that the assembly has a high level of completeness (98.8%) and low level of fragmentation (4.1%) and duplication (0.2%). Phylogenomic analyses with other members of the Lepidoptera order placed A. sociella in the same clade as Aphomia cephalonica and indicates close evolutionary relationships with the other two species in the subfamily Galleriinae, namely Achroia grisella and Galleria mellonella. This new high-quality genome assembly, and associated annotations, represents a valuable resource for investigating the genomic basis of ecological specialization of this species, including wax and possibly plastic utilization, while offering critical support for research aimed at developing sustainable and effective pest management strategies.

Combined Annotation Dependent Depletion (CADD) is a machine learning approach used to predict the deleteriousness of genetic variants across a genome. By integrating diverse genomic features, CADD assigns a PHRED-like rank score to each potential variant. Unlike other methods, CADD does not rely on limited datasets of known pathogenic or benign variants but uses larger and less biased training sets. The rapid increase in high-quality genomes and functional annotations across species highlights the need for an automated, non-species-specific pipeline to generate CADD scores. Here, we introduce such a pipeline, facilitating the generation of CADD scores for various species using only a high-quality genome with gene annotation and a multi-species alignment. Additionally, we present updated chickenCADD scores and newly generated turkeyCADD scores, both generated with the pipeline.

The ability of oocytes to maintain their quality is essential for successful reproduction. One critical aspect of oocyte quality and successful embryogenesis after fertilization is the proper regulation of the stores of maternal mRNA by RNA-binding proteins. Many RNA-binding proteins undergo regulated phase transitions during oogenesis, and alterations of the protein phase can disrupt its ability to regulate mRNA stability and translation. In C. elegans, regulators of RNA-binding protein phase transitions in maturing oocytes of young adult hermaphrodites remain poorly characterized. However, a few recently identified genes are also required for the clearance of damaged proteins during maturation, suggesting coordination between these processes. To explore this relationship and gain insight into the regulation of phase transitions, we conducted a targeted RNAi screen of genes required for removal of protein aggregates in maturing oocytes. Here, we identify six novel regulators of phase transitions of the KH-domain protein MEX-3. We present strong evidence that the regulation of MEX-3 phase transitions in the oocyte overlaps with, but is distinct from, the regulatory network of protein aggregate clearance.

Anxiety is the most prevalent form of mental illness in the US. We aimed to identify genetic variation underlying anxiety in diverse ancestral populations through integrating genomic and brain transcriptomic data. We analyzed genome-wide association study (GWAS) summary statistics, using "Worrier/Anxious Feelings" phenotype from Pan-UK Biobank. We identified 67 independent significant loci in the combined population META-GWAS and 1 locus in the African (AFR) GWAS (P<5.0e-08). We performed transcriptome-wide association studies (TWAS) and identified 683 significantly associated genes in the META-TWAS, and 1 gene in the AFR-TWAS (P<3.85e-6). Namely, we identified CADM2 in the META-TWAS and its predicted paralog SMAGP in the AFR-TWAS. The genes identified in TWAS were enriched for variants associated with autism, neuroticism, and schizophrenia, highlighting shared genetic architecture among neuropsychiatric traits. In this study, we present these loci and genes as potential targets for future research on anxiety-related phenotypes.

By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution. However, the widespread adoption of ChIP-exo has been hindered by several technical challenges, including lengthy protocols, the need for multiple custom reactions, and incompatibilities with recent Illumina sequencing platforms. To address these barriers, we systematically optimized and adapted the ChIP-exo library construction protocol for the unique requirements of mammalian cells and current sequencing technologies. We introduce a Mammalian-Optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. We validate MO-ChIP-exo by comparing it to previously published ChIP-exo protocols and demonstrate its adaptability to both suspension (K562) and adherent (HepG2, mESC) cell lines. This improved protocol provides a more robust and efficient method for generating high-quality ChIP-exo libraries from mammalian cells.

Disease resistance is one of the main targets of animal breeding programs. In recent years, incorporating genomic information to accelerate genetic progress has become one of the priorities of the industry. Here, we combined population scale whole-genome sequencing with differential gene expression and functional annotation analyses to study resistance to Tilapia Lake Virus (TiLV) in a breeding Nile tilapia (Oreochromis niloticus) GIFT population. Fish with survival data from a natural TiLV outbreak were sampled and genotyped for 6.7M SNPs using whole-genome resequencing and imputation. Our results confirmed a QTL located in the proximal end of Oni22, identifying 74 out of the top 99 markers associated to binary survival (BS) within a 10 Mb window. The marker explaining the highest genetic variance of TiLV resistance is located at 1.7 Mb, and presents a substitution effect of 0.15. Additionally, other SNPs in several other chromosomes explained a high percentage of the genetic variance, with an important number located in two separate regions of Oni09. These results suggest an oligogenic architecture underlying resistance to TiLV, with several QTLs with moderate effect and many with small effect. Host transcriptomic analyses identified genes differentially expressed between resistant and susceptible genotypes according to the QTL in Oni22, highlighting psmb9a. and ha1f as potential causal genes. This is the first study combining whole genome sequencing at population scale with genomic approaches to assess the underlying genomic basis for TiLV resistance. Our results confirm and narrow down a QTL underlying this key trait in a major aquaculture species worldwide and found novel QTLs in other chromosomes. The identified markers and genes have the potential to improve resistance to TiLV in Nile tilapia, significantly improving animal health and welfare.

Meiotic recombination ensures the fidelity of chromosome segregation in most organisms with sexual reproduction. The distribution of crossovers along chromosomes is governed in part by interference, which prevents multiple crossovers from occurring in close proximity, though not all crossovers are subject to interference. Neither the factors that control the strength of interference, nor the extent to which they vary within and between species, are well understood. Here I confirm that crossover interference is stronger in male than in female meiosis in house mice (Mus musculus), provide the first estimate of the proportion of non-interfering crossovers in female mice, and show that this proportion is lower than in males. Interference is stronger on shorter chromosomes in both sexes, but the frequency of non-interfering crossovers is similar across the range of chromosome size. Together with evidence that interference varies across strains and subspecies, my results provide a foundation for studying the evolution and sexual dimorphism in this important feature of meiosis in mice.

Pork is the most widely consumed meat globally, and the industry has achieved substantial genetic advancements for several traits using genomic selection. However, traditional linear genomic prediction models may be inadequate for predicting complex traits, such as feed efficiency, as they primarily capture additive genetic effects and overlook non-additive effects, including dominance and epistasis. Deep learning (DL) has the potential to address this limitation due to its ability to model non-linear patterns inherent in genomic data. The objectives of this study were to compare the predictive ability of DL models to the linear models for predicting feed efficiency (FE) trait in two boar populations, estimate the non-additive genetic variance captured by DL, and assess its effect on predictive ability. Our results showed that the DL models using the averaged-prediction method had the highest predictive ability in the sire line test population (0.381 for MLP and 0.377 for CNN), compared to 0.366 for linear models. DL models also showed higher abilities in the dam line test population, with MLP achieving a predictive ability of 0.364. Additionally, we showed that DL models captured non-additive variance; however, this did not significantly improve predictive ability. In conclusion, DL models, particularly MLP, demonstrated the highest predictive ability for FE, improving performance by approximately 4.1% for the sire line and 2.8% for the dam line compared to the traditional linear models. Therefore, DL models are recommended for predicting phenotypes and for estimating total genetic effects, including non-additive components. However, this comes at a significant increase of computational cost.