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Tuberculosis (TB), the leading cause of death from bacterial infections worldwide, results from infection with Mycobacterium tuberculosis (Mtb). The antitubercular agents delamanid (DLM) and pretomanid (PMD) are nitroimidazole prodrugs that require activation by an enzyme intrinsic to Mtb; however, the mechanism(s) of action and the associated metabolic pathways are largely unclear. Profiling of the chemical‐genetic interactions of PMD and DLM in Mtb using combined CRISPR screening reveals that the mutation of rv2073c increases susceptibility of Mtb to these nitroimidazole drugs both in vitro and in infected mice, whereas mutation of rv0078 increases drug resistance. Further assays show that Rv2073c might confer intrinsic resistance to DLM/PMD by interfering with inhibition of the drug target, decaprenylphophoryl‐2‐keto‐b‐D‐erythro‐pentose reductase (DprE2), by active nicotinamide adenine dinucleotide (NAD) adducts. Characterization of the metabolic pathways of DLM/PMD in Mtb using a combination of chemical genetics and comparative liquid chromatography‐mass spectrometry (LC‐MS) analysis of DLM/PMD metabolites reveals that Rv0077c, which is negatively regulated by Rv0078, mediates drug resistance by metabolizing activated DLM/PMD. These results might guide development of new nitroimidazole prodrugs and new regimens for TB treatment. [ABSTRACT FROM AUTHOR]

Histiocytic sarcoma (HS) is a rare and highly aggressive cancer in humans and dogs. In dogs, it has a high prevalence in certain breeds, such as Bernese mountain dogs (BMDs) and flat-coated retrievers. Hemophagocytic histiocytic sarcoma (HHS) is a unique form of HS that presents with erythrophagocytosis. Due to its rareness, the study of HHS is very limited, and mutations in canine HHS patients have not been studied to date. In previous work, our research group identified two major PTPN11/SHP2 driver mutations, E76K and G503V, in HS in dogs. Here, we report additional mutations located in exon 3 of PTPN11/SHP2 in both HS and HHS cases, further supporting that this area is a mutational hotspot in dogs and that mutations in tumors and liquid biopsies should be evaluated utilizing comprehensive methods such as Sanger and NextGen sequencing. The overall prevalence of PTPN11/SHP2 mutations was 55.8% in HS and 46.2% in HHS. In addition, we identified mutations in KRAS, in about 3% of HS and 4% of HHS cases. These findings point to the shared molecular pathology of activation of the MAPK pathway in HS and HHS cases. We evaluated the efficacy of the highly specific MEK inhibitor, cobimetinib, in canine HS and HHS cell lines. We found that the IC50 values ranged from 74 to 372 nM, which are within the achievable and tolerable ranges for cobimetinib. This finding positions cobimetinib as a promising potential candidate for future canine clinical trials and enhances our understanding of the molecular defects in these challenging cancers. [ABSTRACT FROM AUTHOR]

Nested within the vast genetic landscape of the major histocompatibility complex (MHC), a cluster of genes assumes a pivotal role in pathogen recognition and orchestrating mechanisms for disease resistance. This investigation successfully cloned and sequenced the complete 786 bp cDNA entity corresponding to the MHC-DQB gene in yaks. A comprehensive analysis of the sequence unveiled distinct features, including highly conserved peptide binding sites (PBS) spanning 8 amino acids and specific nucleotide-binding regions at designated positions (–1, –28, 2, 3, 29, 64, 93, and 108). The pronounced uniformity and remarkable preservation demonstrated by the yak MHC-DQB gene underscore its potential in providing protection against pathogens and the inherent stability within the DQB genetic framework. Moreover, a comparison across six distinct domains of the Yak-DQB gene revealed notable similarities with closely related species. Particularly significant is the identification of a conserved peptide-binding region consisting of 16 amino acids, alongside the detection of multiple conserved nucleotide-binding regions. When conducting a comparative analysis of amino acid lengths in the Yak-DQB orthologous sequence, a substantial homology with cattle was observed, registering at 91.2%. Interestingly, however, the DQB gene in yaks exhibited discrepancies in 23 amino acids compared to the bovine sequence. Specifically, a detailed examination revealed that 15 of these variable amino acids were clustered within the Beta 1 (в1) domain. These insights provide valuable information about the distinct characteristics of the MHC gene in both ruminant and non-ruminant species, unraveling the complexities of their comparative molecular genetics. [ABSTRACT FROM AUTHOR]

Gene duplication is an important substrate for the evolution of new gene functions, but the impacts of gene duplicates on their own activities and on the developmental networks in which they act are poorly understood. Here, we use a natural experiment of lin-12 /Notch gene duplication within the nematode genus Caenorhabditis , combined with characterization of loss- and gain-of-function mutations, to uncover functional distinctions between the duplicate genes in 1 species (Caenorhabditis briggsae) and their single-copy ortholog in Caenorhabditis elegans. First, using improved genomic sequence and gene model characterization, we confirm that the C. briggsae genome includes 2 complete lin-12 genes, whereas most other genes encoding proteins that participate in the LIN-12 signaling pathway retain a one-to-one orthology with C. elegans. We use CRISPR-mediated genome editing to introduce alleles predicted to cause gain-of-function (gf) or loss-of-function (lf) into each C. briggsae gene and find that the gf mutations uncover functional distinctions not apparent from the lf alleles. Specifically, Cbr-lin-12.1 (gf) , but not Cbr-lin-12.2 (gf) , causes developmental defects similar to those observed in Cel-lin-12 (gf). In contrast to Cel-lin-12 (gf) , however, the Cbr-lin-12.1 (gf) alleles do not cause dominant phenotypes as compared to the wild type, and the mutant phenotype is observed only when 2 gf alleles are present. Our results demonstrate that gene duplicates can exhibit differential capacities to compensate for each other and to interfere with normal development, and uncover coincident gene duplication and evolution of developmental sensitivity to LIN-12 /Notch activity. [ABSTRACT FROM AUTHOR]

Comparative landscape genetics studies provide insights on the impact of landscape elements on gene flow patterns of different species inhabiting the same geographic area. We investigated the population genetic structure of two sympatric ungulates, roe deer Capreolus capreolus and Northern chamois Rupicapra rupicapra, in a mountain area of the central Italian Alps (Trentino, northern Italy). A total of 122 chamois and 72 roe deer samples were genotyped by two species-specific panels of 11 polymorphic microsatellite loci and analyzed by aspatial and spatially explicit analyses. While the roe deer population resulted unstructured, a clear population structure was detected in chamois, with two main groups, one inhabiting the eastern and the other spread in the western part of the study area. Landscape genetics analysis confirmed these scenarios and revealed a different effect of landscape on gene flow. An IBD (Isolation-By-Distance) model best explained genetic variation in roe deer, while IBR (Isolation-By-Resistance) was found as the process underlying genetic variation patterns in chamois, suggesting arable lands, coniferous forests, watercourses, and main roads as potential barriers. Species distribution and landscape use might explain these results: roe deer mostly occupy valley floors relatively connected to each other, and their spatial behavior may promote gene flow across areas. On the other hand, chamois prefer higher elevations and their movements may be hindered by valleys, rivers, and road networks. This study highlights the different impacts of natural and anthropic landscape elements on gene flow in two sympatric species, resulting from their different ecological requirements. [ABSTRACT FROM AUTHOR]

Understanding and predicting the evolutionary responses of complex morphological traits to selection remains a major challenge in evolutionary biology. Because traits are genetically correlated, selection on a particular trait produces both direct effects on the distribution of that trait and indirect effects on other traits in the population. The correlations between traits can strongly impact evolutionary responses to selection and may thus impose constraints on adaptation. Here, we used museum specimens and comparative quantitative genetic approaches to investigate whether the covariation among cranial traits facilitated or constrained the response to selection during the major dietary transitions in one of the world's most ecologically diverse mammalian families—the phyllostomid bats. We reconstructed the set of net selection gradients that would have acted on each cranial trait during the major transitions to feeding specializations and decomposed the selection responses into their direct and indirect components. We found that for all transitions, most traits capturing craniofacial length evolved toward adaptive directions owing to direct selection. Additionally, we showed instances of dietary transitions in which the complex interaction between the patterns of covariation among traits and the strength and direction of selection either constrained or facilitated evolution. Our work highlights the importance of considering the within-species covariation estimates to quantify evolvability and to disentangle the relative contribution of variational constraints versus selective causes for observed patterns. [ABSTRACT FROM AUTHOR]

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Current efforts to halt the decline of biodiversity are based primarily on protecting species richness. This narrow focus overlooks key components of biological diversity, particularly the infra-species genetic diversity, which is critical to consider with respect to genetic adaptation in changing environments. While comparative population genetics is recognized as a relevant approach to improve biodiversity management, it is still barely considered in practice. Here, a comparative population genetics study was conducted on two key habitat-forming octocoral species, Corallium rubrum and Paramuricea clavata, to contribute to management of two Marine Protected Areas (MPAs) in the northwestern Mediterranean. Contrasting patterns of genetic diversity and structure were observed in the two species, although they share many common biological features and live in similar habitats. Differential genetic drift effects induced by species-specific reproductive strategies and demographic histories most likely explain these differences. The translation of our results into management strategies supports the definition of four management units. We identified a coldspot of genetic diversity, with genetically isolated populations, and a hotspot of genetic diversity that has a central role in the system's connectivity. Interestingly, they corresponded to the most recent and the oldest protected areas, respectively. This case study shows how moving from a "species pattern" perspective to an "eco-evolutionary processes" perspective can help assess and contribute to the effectiveness of biodiversity management plans. [ABSTRACT FROM AUTHOR]

Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry vari-ation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use. [ABSTRACT FROM AUTHOR]

Maize(Zea mays. L) is a globally important crop, and understanding its genetic diversity is crucial for plant breeding phylogenetic analyses and comparative genetics. While nuclear markers have been extensively used for mapping agriculturally important genes, they are limited in recognizing characteristics, such as cytoplasmic male sterility and reciprocal cross hybrids. In this study, we performed next-generation sequencing of 176samples, and the maize cultivars represented five distinct groups. A total of 89 single nucleotide polymorphisms (SNPs) and 11 insertion/deletion polymorphisms (InDels) were identified. To enable high-throughput detection, we successfully amplified and confirmed 49 SNP and InDel markers, which were defined as a Varietal Chloroplast Panel (VCP) using the Kompetitive Allele Specific PCR (KASP). The specific markers provided a valuable tool for identifying chloroplast groups. The verification experiment, focusing on the identification of reciprocal cross hybrids and cytoplasmic male sterility hybrids, demonstrated the significant advantages of VCP markers in maternal inheritance characterization. Furthermore, only a small subset of these markers is needed to provide useful information, showcasing the effectiveness of these markers in elucidating the artificial selection process of elite maize lines. [ABSTRACT FROM AUTHOR]

In the face of rapid urbanization, species confront various challenges, and the consequences of limited gene flow become evident. One such illustration is the Endangered salamander Hynobius yangi inhabiting a restricted region in South Korea under a mounting urbanization pressure. The species' metapopulation dynamics is consequently characterized by lack of sufficient gene flow. We compared the landscape genetic results between the two H. yangi metapopulations, one divided by an urbanized area or the other included within a forested area, using previously developed 14 species-specific genetic markers. We hypothesized that the population in the urbanized area will show signs of impact by the urbanization, while the population in the forested area will not. We analyzed the genetic diversity, population genetic structure, contemporary gene flow rate, and estimated the resistance values of land cover classes to assess landscape connectivity of each metapopulation. The urbanized area showed subdivided population structure, with higher inbreeding level, which was clearly distinguished from that of the forested area. The gene flow rates were consistently lower in the urbanized area. The estimated resistance values were generally higher, and the highest connectivity was confined to the peripheries in the urbanized area, in contrast to the forested area. We found the population in the urbanized area has been clearly impacted by urbanization with two times higher resistance than the forest counterpart. We recommend to establish management plans based on our result. This study will be a valuable addition to urban landscape genetic studies, especially for underrepresented taxon and region. [ABSTRACT FROM AUTHOR]

Estimates of gene flow resulting from landscape resistance inferences frequently inform conservation management decision‐making processes. Therefore, results must be robust across approaches and reflect real‐world gene flow instead of methodological artefacts. Here, we tested the impact of 32 individual‐based genetic distance metrics on the robustness and accuracy of landscape resistance modelling results. We analysed three empirical microsatellite datasets and 36 simulated datasets that varied in landscape resistance and genetic spatial autocorrelation. We used ResistanceGA to generate optimised multi‐feature resistance surfaces for each of these datasets using 32 different genetic distance metrics. Results of the empirical dataset demonstrated that the choice of genetic distance metric can have strong impacts on inferred optimised resistance surfaces. Simulations showed accurate parametrisation of resistance surfaces across most genetic distance metrics only when a small number of environmental features was impacting gene flow. Landscape scenarios with many features impacting gene flow led to a generally poor recovery of true resistance surfaces. Simulation results also emphasise that choosing a genetic distance metric should not be based on marginal R2‐based model fit. Until more robust methods are available, resistance surfaces can be optimised with different genetic distance metrics and the convergence of results needs to be assessed via pairwise matrix correlations. Based on the results presented here, high correlation coefficients across different genetic distance categories likely indicate accurate inference of true landscape resistance. Most importantly, empirical results should be interpreted with great caution, especially when they appear counter‐intuitive in light of the ecology of a species. see also the Perspective by William E. Peterman [ABSTRACT FROM AUTHOR]

The heterochronic genes of Caenorhabditis elegans comprise the best-studied pathway controlling the timing of tissue and organ formation in an animal. To begin to understand the evolution of this pathway and the significance of the relationships among its components, we characterized 11 Caenorhabditis briggsae orthologs of C. elegans heterochronic genes. Using CRISPR/Cas9, we made a variety of alleles and found that several mutant phenotypes differ in significant ways from those of C. elegans. Although most mutant orthologs displayed defects in developmental timing, their phenotypes could differ in which stages were affected, the penetrance and expressivity of the phenotypes, or by having additional pleiotropies that were not obviously connected to developmental timing. However, when examining pairwise epistasis and synergistic relationships, we found those paralleled the known relationships between their C. elegans orthologs, suggesting that the arrangements of these genes in functional modules are conserved, but the modules’ relationships to each other and/or to their targets has drifted since the time of the species’ last common ancestor. Furthermore, our investigation has revealed a relationship between this pathway to other aspects of the animal’s growth and development, including gonad development, which is relevant to both species. [ABSTRACT FROM AUTHOR]

Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust. Among all wheat rust resistance genes, SR9 has the largest number of alleles. Here, the authors use gene cloning, complementation and comparative genetics to resolve the relationship among Sr9 alleles, confirm their allelic identities, and show that a single amino acid change leads to resistance to Ug99. [ABSTRACT FROM AUTHOR]

1.We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedent rate of decline.2.However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remains challenging.3.We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex.4.We found that the three sky‐island taxa formed three independently evolving units without detectable post‐divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid‐Pleistocene, have experienced episodes of demographic decline in the past.5.More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesised to impact the recent demographic history (<100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa.6.We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans. [ABSTRACT FROM AUTHOR]

Ceramide biosynthesis and its connection to iso‐fatty acid metabolism in the model organism Caenorhabditis elegans was investigated using a combination of reverse genetics and comparative ESI‐(+)‐HR‐MSe ceramide profiling along with incorporation experiments with bacterial mutants specifically enriched with isotopically labeled branched‐chain amino acids or branched‐chain fatty acids. Incorporation of a l‐leucine‐derived isovalerate unit into the conserved d17 : 1iso sphingosine building block proceeds through elo‐5 dependent chain elongation and depends on peroxisomal β‐oxidation by the 3‐ketoacyl‐CoA thiolase daf‐22, although ceramide profiles of N2 wildtype and daf‐22(ok693) are indistinguishable. Biosynthesis of the homologous N‐iso‐acyl moieties also depends on l‐leucine and isovalerate chain elongation but proceeds independently of elo‐5 and daf‐22. Biosynthesis of the dominating N‐docosanoyl moiety depends on elo‐3‐catalyzed chain elongation of bacteria‐derived palmitic acid, whereas the N‐tetracosanoyl moiety is derived from de novo lipogenesis. [ABSTRACT FROM AUTHOR]

Abstract Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease.

Domestic dogs display a wide array of heritable behaviors that have intermediate genetic complexity thanks to a long history of human-influenced selection. Comparative genetics in dogs could address the scarcity of non-human neurogenetic systems relevant to human neuropsychiatric disorders, which are characterized by mental, emotional, and behavioral symptoms and involve vastly complex genetic and non-genetic risk factors. Our review describes the diverse behavioral "phenome" of domestic dogs, past and ongoing sources of behavioral selection, and the state of canine behavioral genetics. We highlight two naturally disordered behavioral domains that illustrate how dogs may prove useful as a comparative, forward neurogenetic system: canine age-related cognitive dysfunction, which can be examined more rapidly given the attenuated lifespan of dogs, and compulsive disorders, which may have genetic roots in purpose-bred behaviors. Growing community science initiatives aimed at the companion dog population will be well suited to investigating such complex behavioral phenotypes and offer a comparative resource that parallels human genomic initiatives in scale and dimensionality. [ABSTRACT FROM AUTHOR]

The distribution of genetic diversity is often heterogeneous in space, and it usually correlates with environmental transitions or historical processes that affect demography. The coast of Chile encompasses two biogeographic provinces and spans a broad environmental gradient together with oceanographic processes linked to coastal topography that can affect species' genetic diversity. Here, we evaluated the genetic connectivity and historical demography of four Scurria limpets, S. scurra, S. variabilis, S. ceciliana and S. araucana, between ca. 19° S and 53° S in the Chilean coast using genome‐wide SNPs markers. Genetic structure varied among species which was evidenced by species‐specific breaks together with two shared breaks. One of the shared breaks was located at 22–25° S and was observed in S. araucana and S. variabilis, while the second break around 31–34° S was shared by three Scurria species. Interestingly, the identified genetic breaks are also shared with other low‐disperser invertebrates. Demographic histories show bottlenecks in S. scurra and S. araucana populations and recent population expansion in all species. The shared genetic breaks can be linked to oceanographic features acting as soft barriers to dispersal and also to historical climate, evidencing the utility of comparing multiple and sympatric species to understand the influence of a particular seascape on genetic diversity. [ABSTRACT FROM AUTHOR]

Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease. [ABSTRACT FROM AUTHOR]

Interestingly, in DRB1*03:01 group all HLA-B*08 positive donors showed DRB3*01:01:02 allele, while all HLA-B*08 negative donors and 77.3% of HLA-B*18 positive donors carried DRB3*02:02:01 allele. Our results showed that three HLA alleles were associated with AIN only for patients with anti-HNA-1a specific antibodies; DRB1*01 (OR = 2.63 (1.65-4.21), DRB1*04 (OR = 0.29 (0.15-0.57)) and DQB1*03 (OR = 0.37 (0.23-0.59)), while DRB1*10 (OR = 8.74 (3.29-23.23)) was specific for the remaining group of anti-Fc IIIb antibody positive patients. The minor alleles were significantly over-represented in the subgroup of patients with EIM: 31.2% versus 7.5% in patients without EIM, I p i = 0.001, OR 5.54 for 308*A and 9.3% versus 0.7% in patients without EIM, I p i = 0.04, OR 13.55 for 238*A. No other associations were found in the studied group. A couple of HLA-B alleles showed significant differences when compared between the patient and control groups: HLA-B*15 was increased in patients, while surprisingly, HLA-B*35 showed a significant decrease in people suffering from migraines. The rare HLA-B*39:06:02:01 association with both HLA-C alleles and subsequent haplotype comparison between patient and mother, led to suspicions of possible HLA-C allele dropout in both samples. [Extracted from the article]

Summary: The roles of SHORT‐ROOT (SHR) and SCARECROW (SCR) in ground tissue patterning and differentiation have been well established in the root of Arabidopsis thaliana. Recently, work in additional organs and species revealed the extensive functional diversification of these genes, including regulation of cortical divisions essential for nodule organogenesis in legume roots, bundle sheath specification in the Arabidopsis leaf, patterning of inner leaf cell layers in maize, and stomatal development in rice. The co‐option of distinct functions and cell types is attributed to different mechanisms, including paralog retention, spatiotemporal changes in gene expression, and novel protein functions. Elaborating our knowledge of the SHR–SCR module further unravels the developmental regulation that controls diverse forms and functions within and between species. [ABSTRACT FROM AUTHOR]

As an important seedling source, monospores closely associate with yields in nori farming. However, the molecular mechanism underlying differences in monospore production for different strains remains unknown. Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain (WT) and spore deficient mutant (Y1) of Pyropia chauhanii. The WT strain that produces monospores in abundance exhibited more differentially expressed genes (DEGs) in both number and higher fold-changes than the Y1 strain incapable of producing monospores, indicating that the specific regulation of genes is involved in monospore production. Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram: one expressed only in WT strain, another expressed only in Y1 strain, and the third shared in both strains. DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website. Gene regulatory networks of WT were functionally enriched in the processing, proteolysis, and transport of proteins, especially within the small GTPase protein family, which might be account for the monospore production ability, whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy, which might be account for the rapid growth of blades. We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits. These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities, which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production. [ABSTRACT FROM AUTHOR]

Picrorhiza kurroa Royle ex Benth is a valuable medicinal herb of North-Western Himalayas due to presence of two major bioactive compounds, picroside-I and picroside-II used in the preparation of several hepatoprotective herbal drugs. These compounds accumulate in stolons/rhizomes; however, biosynthesized in different organs, viz., picroside-I in shoots and picroside-II in roots. As of today, no information exists on what transporters are transporting these metabolites from shoots and roots to the final storage organ, stolon, which ultimately transforms into rhizome. The ATP-binding cassette (ABC) transporters are reported to transport majority of secondary metabolites, including terpenoids in plants, therefore, we mined P. kurroa transcriptomes to identify and shortlist potential candidates. A total of 99 ABC transporter-encoding transcripts were identified in 3 differential transcriptomes, PKSS (shoots), PKSTS (stolons), and PKSR (roots) of P. kurroa, based on in silico comparative analysis and transcript abundance. 15 of these transcripts were further validated for their association using qRT-PCR in shoots, roots and stolon tissues in P. kurroa accessions varying for picroside-I and picroside-II contents. Organ-specific expression analysis revealed that PkABCA1, PkABCG1, and PkABCB5 had comparatively elevated expression in shoots; PkABCB2 and PkABCC2 in roots; PkABCB3 and PkABCC1 in stolon tissues of P. kurroa. Co-expression network analysis using ABC genes as hubs further unravelled important interactions with additional components of biosynthetic machinery. Our study has provided leads, first to our knowledge as of today, on putative ABC transporters possibly involved in long distance and local transport of picrosides in P. kurroa organs, thus opening avenues for designing a suitable genetic intervention strategy. [ABSTRACT FROM AUTHOR]

Dietary variation within and across species drives the eco-evolutionary responsiveness of genes necessary to metabolize nutrients and other components. Recent evidence from humans and other mammals suggests that sugar-rich diets of floral nectar and ripe fruit have favoured mutations in, and functional preservation of, the ADH7 gene, which encodes the ADH class 4 enzyme responsible for metabolizing ethanol. Here we interrogate a large, comparative dataset of ADH7 gene sequence variation, including that underlying the amino acid residue located at the key site (294) that regulates the affinity of ADH7 for ethanol. Our analyses span 171 mammal species, including 59 newly sequenced. We report extensive variation, especially among frugivorous and nectarivorous bats, with potential for functional impact. We also report widespread variation in the retention and probable pseudogenization of ADH7. However, we find little statistical evidence of an overarching impact of dietary behaviour on putative ADH7 function or presence of derived alleles at site 294 across mammals, which suggests that the evolution of ADH7 is shaped by complex factors. Our study reports extensive new diversity in a gene of longstanding ecological interest, offers new sources of variation to be explored in functional assays in future study, and advances our understanding of the processes of molecular evolution.

The article focuses on examining the genetic mechanisms associated with the p53 pathway that contribute to cancer resistance and extended lifespan in cetaceans, particularly large and long-lived marine mammals. Topics discussed include the identification of positively selected genes related to the p53 pathway, the role of gene duplications in apoptosis regulation, and the potential influence of angiogenesis inhibition on cancer resistance in cetaceans.

Recent years have seen an emergence of the field of comparative cancer genomics. However, the advancements in this field are held back by the hesitation to use knowledge obtained from human studies to study cancer in other animals, and vice versa. Since cancer is an ancient disease that arose with multicellularity, oncogenes and tumour‐suppressor genes are amongst the oldest gene classes, shared by most animal species. Acknowledging that other animals are, in terms of cancer genetics, ecology, and evolution, rather similar to humans, creates huge potential for advancing the fields of human and animal oncology, but also biodiversity conservation. Also see the video abstract here: https://youtu.be/UFqyMx5HETY [ABSTRACT FROM AUTHOR]

A precise description of traits is essential in genetics and genomics studies to facilitate comparative genetics and meta-analyses. It is an ongoing challenge in research and production environments to unambiguously and consistently compare traits of interest from data collected under various conditions. Despite previous efforts to standardize trait nomenclature, it remains a challenge to fully and accurately capture trait nomenclature granularity in a way that ensures long-term data sustainability in terms of the data curation processes, data management logistics and the ability to make meaningful comparisons across studies. In the Animal Quantitative Trait Loci Database and the Animal Trait Correlation Database, we have recently introduced a new method to extend livestock trait ontologies by using trait modifiers and qualifiers to define traits that differ slightly in how they are measured, examined or combined with other traits or factors. Here, we describe the implementation of a system in which the extended trait data, with modifiers, are managed at the experiment level as 'trait variants'. This has helped us to streamline the management and curation of such trait information in our database environment. Database URLhttps://www.animalgenome.org/PGNET/ [ABSTRACT FROM AUTHOR]

The facultative intracellular pathogen Brucella and the free-living bacteria Ochrobactrum are both α-proteobacteria and very close to each other. A group of researchers recently clustered Ochrobactrum strains into the genus Brucella according to a BLAST distance approach. Thus, we performed a deeper comparative genetic analysis for eleven Ochrobactrum strains and twelve different Brucella isolates to demonstrate important differences between these bacteria. In addition to the clear differences between Brucella and Ochrobactrum, like the differences in genes contents, and different genome sizes, the Brucella-specific gene bscp31 was not found in Ochrobactrum, as well as other important Brucella-specific proteins and virulence factors. Differences in antimicrobial resistance genes content and the presence or absence of plasmids were obvious between Brucella and Ochrobactrum spp. Genome alignment of Brucella spp. and Ochrobactrum spp. revealed a genome similarity of 85.7% maximum, whereas all analyzed Brucella spp. in this study had a similarity of 97.6-99.9%, and all compared Ochrobactrum spp. 82.6-98.0%. Because of these facts mentioned in this work, Brucella and Ochrobactrum should be considered separate genera. [ABSTRACT FROM AUTHOR]

Liver preneoplastic and neoplastic lesions of the genetically susceptible F344 and resistant BN rats cluster, respectively, with human HCC with better (HCCB) and poorer prognosis (HCCP); therefore, they represent a valid model to study the molecular alterations determining the genetic predisposition to HCC and the response to therapy. The ubiquitin-mediated proteolysis of ERK-inhibitor DUSP1, which characterizes HCC progression, favors the unrestrained ERK activity. DUSP1 represents a valuable prognostic marker, and ERK, CKS1, or SKP2 are potential therapeutic targets for human HCC. In DN (dysplastic nodule) and HCC of F344 rats and human HCCP, DUSP1 downregulation and ERK1/2 overexpression sustain SKP2-CKS1 activity through FOXM1, the expression of which is associated with a susceptible phenotype. SAM-methyl-transferase reactions and SAM/SAH ratio are regulated by GNMT. In addition, GNMT binds to CYP1A, PARP1, and NFKB and PREX2 gene promoters. MYBL2 upregulation deregulates cell cycle and induces the progression of premalignant and malignant liver. During HCC progression, the MYBL2 transcription factor positively correlates with cells proliferation and microvessel density, while it is negatively correlated to apoptosis. Hierarchical supervised analysis, regarding 6132 genes common to human and rat liver, showed a gene expression pattern common to normal liver of both strains and BN nodules, and a second pattern is observed in F344 nodules and HCC of both strains. Comparative genetics studies showed that DNs of BN rats cluster with human HCCB, while F344 DNs and HCCs cluster with HCCP. [ABSTRACT FROM AUTHOR]

Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species. [ABSTRACT FROM AUTHOR]

This article describes new algorithms that allow for viewing genetic sequences in the form of their multispectral images. We presented examples of the construction of such mappings with a demonstration of the practical problems of comparative genomics. New DNA visualization tools seem promising, thanks to their informativeness and representativeness. The research illustrates how a novel sort of multispectral mapping, based on decomposition in several parametric spaces, can be created for comparative genetics. This appears to be a crucial step in the investigation of the genetic coding phenomenon and in practical activities, such as forensics, genetic testing, genealogical analysis, etc. The article gives examples of multispectral parametric sets for various types of coordinate systems. We build mappings using binary sub-alphabets of purine/pyrimidine and keto/amino. We presented 2D and 3D renderings in different characteristic spaces: structural, integral, cyclic, spherical, and third-order spherical. This research is based on the method previously developed by the author for visualizing genetic information based on new molecular genetic algorithms. One of the types of mappings, namely two-dimensional, is an object of discrete geometry, a symmetrical square matrix of high dimension. The fundamental properties of symmetry, which are traced on these mappings, allow us to speak about the close connection between the phenomenon of genetic coding and symmetry when using the developed mathematical apparatus for representing large volumes of complexly organized molecular genetic information. [ABSTRACT FROM AUTHOR]

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The article presents a study on genetic and chemical-genetic interaction profiling in Mycobacterium tuberculosis using combined CRISPR screening. Topics discussed include performance comparison between CRISPR interference and CRISPR-knockout screenings, and genes associated with resistance/susceptibility to the antitubercular drug bedaquiline that were identified by subsequent screening.

Background: Plasmodium vivax apical membrane antigen-1 (pvama-1) is an important vaccine candidate against Malaria. The genetic composition assessment of pvama-1 from wide-range geography is vital to plan the antigen based vaccine designing against Malaria.Methods: The blood samples were collected from 84 P. vivax positive malaria patients from different districts of Khyber Pakhtunkhwa (KP) province of Pakistan. The highly polymorphic and immunogenic domain-I (DI) region of pvama-1 was PCR amplified and DNA sequenced. The QC based sequences raw data filtration was done using DNASTAR package. The downstream population genetic analyses were performed using MEGA4, DnaSP, Arlequin v3.5 and Network.5 resources.Results: The analyses unveiled total 57 haplotypes of pvama-1 (DI) in KP samples with majorly prevalent H-14 and H-5 haplotypes. Pairwise comparative population genetics analyses identified limited to moderate genetic distinctions among the samples collected from different districts of KP, Pakistan. In context of worldwide available data, the KP samples depicted major genetic differentiation against the Korean samples with Fst = 0.40915 (P-value = 0.0001), while least distinction was observed against Indian and Iranian samples. The statistically significant negative values of Fu and Li's D* and F* tests indicate the evidence of population expansion and directional positive selection signature. The slow LD decay across the nucleotide distance in KP isolates indicates low nucleotide diversity. In context of reference pvama-1 sequence, the KP samples were identified to have 09 novel non-synonymous single nucleotide polymorphisms (nsSNPs), including several trimorphic and tetramorphic substitutions. Few of these nsSNPs are mapped within the B-cell predicted epitopic motifs of the pvama-1, and possibly modulate the immune response mechanism.Conclusion: Low genetic differentiation was observed across the pvama-1 DI among the P. vivax isolates acquired from widespread regions of KP province of Pakistan. The information may implicate in future vaccine designing strategies based on antigenic features of pvama-1. [ABSTRACT FROM AUTHOR]

Bernese mountain dogs (BMDs), have an overall cancer incidence of 50%, half of which is comprised of an otherwise rare tumor, histiocytic sarcoma (HS). While recent studies have identified driver mutations in the MAPK pathway, identification of key predisposing genes has been elusive. Studies have identified several loci to be associated with predisposition to HS in BMDs, including near the MTAP/CDKN2A region, but no causative coding variant has been identified. Here we report the presence of a coding polymorphism in the gene encoding FANCG, near the MTAP/CDKN2A locus. This variant is in a conserved region of the protein and appears to be specific to BMDs. Canine fibroblasts derived from dogs homozygous for this variant are hypersensitive to cisplatin. We show this canine FANCG variant and a previously defined hypomorphic FANCG allele in humans impart similar defects in DNA repair. However, our data also indicate that this variant is neither necessary nor sufficient for the development of HS. Furthermore, BMDs homozygous for this FANCG allele display none of the characteristic phenotypes associated with Fanconi anemia (FA) such as anemia, short stature, infertility, or an earlier age of onset for HS. This is similar to findings in FA deficient mice, which do not develop overt FA without secondary genetic mutations that exacerbate the FA deficit. In sum, our data suggest that dogs with deficits in the FA pathway are, like mice, innately resistant to the development of FA. [ABSTRACT FROM AUTHOR]

Background: Although many pathological mechanisms and etiological hypotheses of acute unilateral vestibulopathy (AUVP) have been reported, but the actual etiology remains to be elucidated. Objective: This study was based on comprehensive bioinformatics to identify the critical genes of AUVP and explore its pathological mechanism. Methods: Gene expression profiles of AUVP and normal samples were collected from GSE146230 datasets of the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was constructed, and the WGCNA R-package extracted significant modules. The limma R-package was applied to identify differentially expressed genes (DEGs). The common genes of practical modules and DEGs were screened for GO and KEGG pathways analysis. The protein--protein interaction (PPI) layout and hub genes validation was created by Cytoscape software using the link from the STRING database. The functions of hub genes were predicted through the CTD (comparative genetics database). Results: A total of 332 common genes were screened from practical modules and DEGs. Functional enrichment analysis revealed that these genes were predominantly associated with inflammation and infection. After construction of PPI, expressions of hub genes, and drawing ROC curves, LILRB2, FPR1, AQP9, and LILRA1 are highly expressed in AUVP (p < 0.05) and have a certain diagnostic efficacy for AUVP (AUC > 0.7), so they were selected as hub genes. The functions of hub genes suggested that the occurrence of AUVP may be related to inflammation, necrosis, hepatomegaly, and other conditions in CTD. Conclusion: LILRB2, FPR1, AQP9, and LILRA1 may play essential roles in developing AUVP, providing new ideas for diagnosing and treating AUVP. [ABSTRACT FROM AUTHOR]

Reproductive isolation (RI) is often considered an essential component of speciation; however, its definition varies, and it is challenging to measure, making it difficult to compare across studies. While our model suggests that RI produced by epigenetic loci will generally be weaker than that produced by genetic loci, epigenetic barriers to gene flow are not necessarily negligible. As per the definition of RI proposed by Westram et al. (2022), the measurement of RI by introgression of neutral loci among populations attributes all RI to genetic differences. We can, therefore, imagine an epigenetic locus whose state (in this example methylated or unmethylated) encodes a phenotype and a neutral genetic locus that is linked with such epigenetic locus (Figure 1a), similar to a genetic locus (Figure 1b). [Extracted from the article]

The coronavirus disease 19 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a coronavirus that spilled over from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus-host interfaces. We performed high-throughput evolutionary analyses of 334 SARS-CoV-2-interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates, and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus-host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus-host arms race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified adaptations involved in SARS-CoV-2 infection in bats and primates, enlightening modern genetic determinants of virus susceptibility and severity. [ABSTRACT FROM AUTHOR]

Northern reindeer breeding is the basis of the cultural and economic complex of the indigenous peoples and ethnic groups of the north of Russia. The study of breeds and intrabreed types of domestic reindeer and their genetic structure to a large extent helps to solve the problem of supporting the traditional way of life of this part of the population of our country. To study the genetic differentiation and phylogeny of populations of the Nenets breed of reindeer (Rangifer tarandus L.), we used a test system based on multiplex PCR analysis of 16 highly polymorphic STR markers: Rt6, BMS1788, Rt30, Rt1, Rt9, FCB193, Rt7, BMS745, C143, Rt24, OheQ, C217, C32, NVHRT16, T40, and C276. Using the developed test system based on the Laboratory of Comparative Animal Genetics of the Institute of General Genetics, 228 animals from four samples of the same breed from different farms of the Russian Federation were examined. For 16 microsatellite loci, 132 alleles were identified, ranging from 2 alleles (locus C217) to 16 alleles (locus OheQ). The average number of alleles per locus for all samples was 8.25. No significant deviations from the Hardy–Weinberg equilibrium (p-value < 7.8 × 10–4 with Bonferroni correction) were observed for the "sample–locus" combinations. For four populations of the Nenets breed of reindeer, 85 alleles for microsatellite loci are common. In total, 16 unique alleles were found: KhMAO–Yugra, Beloyarsk district, village of Nunto (Nen.HMAO)—7; YaNAO, Salekhard and Priuralsky district (Nen.YamSHOS)—4; YaNAO, the upper reaches of the Hanmei River (Nen.YaNAO)—3; NAO, the western part of the Bolshezemelnaya Tundra (Nen.NAO)—2. The analysis of microsatellite variability revealed the levels of multilocus heterozygosity and allelic diversity, as well as the degree of inbreeding. According to the indicator of allelic diversity (Ar), deer from the Yamal experimental station stand out with a value of 6.25, while in animals from the SPK ERV, the value was 5.85. In general, despite the presence of inbred animals in the samples, we can talk about a low level of inbreeding depression in the studied populations of Nenets reindeer. [ABSTRACT FROM AUTHOR]

In the article, the authors present their study which examined the immune responses of wild and domestic caprid species that are essential in addressing certain zoonotic diseases. In the research, allele-specific expression and splicing analyses were used to study the blood trascriptomes of 13 Siberian ibex and domestic goat hybrids. Also mentioned are the genes showing imbalance between the ibex and goat and their relations to Toll-like receptor (TLR) and immune activation pathways.

The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the properties of statistics that combine data from multiple species, such as the fixation index (FST). The major contribution of this study is the derivation and implementation of exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size, assuming no gene flow after species divergence. We use these expressions to derive the variance in average pairwise differences within and between populations. We then derive approximations for the expectation and bias of a sequence-based estimator of FST, a commonly used genetic measurement of population differentiation, when it is applied to a non-recombining region of the genome. We show that the estimator of FST is generally biased downward. A freely available software package is provided, STCov, to calculate the mean, variances and covariances in coalescence times presented here under user-defined piecewise-constant species trees. [ABSTRACT FROM AUTHOR]

The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the properties of statistics that combine data from multiple species, such as the fixation index (FST). The major contribution of this study is the derivation and implementation of exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size, assuming no gene flow after species divergence. We use these expressions to derive the variance in average pairwise differences within and between populations. We then derive approximations for the expectation and bias of a sequence-based estimator of FST, a commonly used genetic measurement of population differentiation, when it is applied to a non-recombining region of the genome. We show that the estimator of FST is generally biased downward. A freely available software package is provided, STCov, to calculate the mean, variances and covariances in coalescence times presented here under user-defined piecewise-constant species trees. [ABSTRACT FROM AUTHOR]

The role of natural killer (NK) cells is tightly modulated by interactions of killer cell immunoglobulin-like receptors (KIR) with their ligands of the MHC class I family. Several characteristics of the KIR gene products are conserved in primate evolution, like the receptor structures and the variegated expression pattern. At the genomic level, however, the clusters encoding the KIR family display species-specific diversity, reflected by differential gene expansions and haplotype architecture. The human KIR cluster is extensively studied in large cohorts from various populations, which revealed two KIR haplotype groups, A and B, that represent more inhibitory and more activating functional profiles, respectively. So far, genomic KIR analyses in large outbred populations of non-human primate species are lacking. In this study, we roughly quadrupled the number of rhesus macaques studied for their KIR transcriptome (n = 298). Using segregation analysis, we defined 112 unique KIR region configurations, half of which display a more inhibitory profile, whereas the other half has a more activating potential. The frequencies and functional potential of these profiles might mirror the human KIR haplotype groups. However, whereas the human group A and B KIR haplotypes are confined to largely fixed organizations, the haplotypes in macaques feature highly variable gene content. Moreover, KIR homozygosity was hardly encountered in this panel of macaques. This study exhibits highly diverse haplotype architectures in humans and macaques, which nevertheless might have an equivalent effect on the modulation of NK cell activity. [ABSTRACT FROM AUTHOR]

Biodiversity is currently declining at the global scale. Apart from species declines and lowered abundances, the loss of genetic diversity is equally concerning as it may undermine fitness and the potential to adapt to future environmental change. We compared genetic diversity of historical and recent Alpine populations of two butterfly species, Lycaena helle and L. hippothoe, over a period of about 10 years. Using microsatellite markers, we found no changes over time in L. helle, while genetic diversity decreased, and differentiation increased in L. hippothoe. Lycaena helle inhabits peat bogs and wetland fallows with populations being strongly isolated, while L. hippothoe used to occur in population networks on hay meadows, with the latter being strongly exposed to agricultural intensification. We conclude that currently L. hippothoe populations are strongly declining due to changes in land use, resulting in genetic erosion potentially due to the collapse of population networks. [ABSTRACT FROM AUTHOR]

The assembled and annotated genomes for 16 inbred mouse strains (Lilue et al., Nat Genet 50:1574–1583, 2018) and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) (Thybert et al., Genome Res 28:448–459, 2018) are valuable resources for mouse genetics and comparative genomics. We developed the multiple genome viewer (MGV; http://www.informatics.jax.org/mgv) to support visualization, exploration, and comparison of genome annotations within and across these genomes. MGV displays chromosomal regions of user-selected genomes as horizontal tracks. Equivalent features across the genome tracks are highlighted using vertical 'swim lane' connectors. Navigation across the genomes is synchronized as a researcher uses the scroll and zoom functions. Researchers can generate custom sets of genes and other genome features to be displayed in MGV by entering genome coordinates, function, phenotype, disease, and/or pathway terms. MGV was developed to be genome agnostic and can be used to display homologous features across genomes of different organisms. [ABSTRACT FROM AUTHOR]

How and to what degree gene duplication events create regulatory innovation, redundancy, or neofunctionalization remain important questions in animal evolution and comparative genetics. Ankfn1 genes are single copy in most invertebrates, partially duplicated in jawed vertebrates, and only the derived copy retained in most mammals. Null mutations in the single mouse homolog have vestibular and neurological abnormalities. Null mutation of the single Drosophila homolog is typically lethal with severe sensorimotor deficits in rare survivors. The functions and potential redundancy of paralogs in species with two copies are not known. Here, we define a vestibular role for Ankfn1 homologs in zebrafish based on the simultaneous disruption of each locus. Zebrafish with both paralogs disrupted showed vestibular defects and early lethality from swim bladder inflation failure. One intact copy at either locus was sufficient to prevent major phenotypes. Our results show that vertebrate Ankfn1 genes are required for vestibular-related functions, with at least partial redundancy between ancestral and derived paralogs. [ABSTRACT FROM AUTHOR]

Genetic variation in the human gut microbiome is responsible for conferring a number of crucial phenotypes like the ability to digest food and metabolize drugs. Yet, our understanding of how this variation arises and is maintained remains relatively poor. Thus, the microbiome remains a largely untapped resource, as the large number of coexisting species in the microbiome presents a unique opportunity to compare and contrast evolutionary processes across species to identify universal trends and deviations. Here we outline features of the human gut microbiome that, while not unique in isolation, as an assemblage make it a system with unparalleled potential for comparative population genomics studies. We consciously take a broad view of comparative population genetics, emphasizing how sampling a large number of species allows researchers to identify universal evolutionary dynamics in addition to new genes, which can then be leveraged to identify exceptional species that deviate from general patterns. To highlight the potential power of comparative population genetics in the microbiome, we reanalyze patterns of purifying selection across ∼40 prevalent species in the human gut microbiome to identify intriguing trends which highlight functional categories in the microbiome that may be under more or less constraint. [ABSTRACT FROM AUTHOR]