Low Heterozygosity Research Articles

Pan-genome analysis reveals genomic variations during enoki mushroom domestication, with emphasis on genetic signatures of cap color and stipe length

IntroductionThe domestication of edible mushrooms, including Flammulina filiformis, offers valuable insights into the genetic changes driven by artificial selection. Understanding these changes is crucial for uncovering the mechanisms behind genome evolution in domesticated mushrooms. ObjectivesThis study aims to investigate the population structure, genetic diversity, and domestication-related genomic changes in F. filiformis. By comparing the genome sequences of 199 wild and cultivated strains, we aim to elucidate the impact of domestication on F. filiformis. MethodsWe performed de novo genome assembly and gene-based pan-genome analysis on the 199 strains, which included both wild and cultivated strains. We also conducted genome-wide association studies (GWAS) using presence-absence variation (PAV) and SNP data, combined with RNA sequencing, to identify genes associated with domestication traits, such as cap color and stalk length. Gene functional confirmation was achieved through genetic transformation experiments. ResultsOur analysis grouped the strains into four distinct populations, which correlated with varying intensities of artificial selection. The three cultivated populations exhibited smaller genome sizes, fewer genes, lower genetic variation, reduced gene expression diversity, and lower heterozygosity compared to the wild population. The analysis revealed the loss of genes related to the beta-lactam antibiotic catabolic process and specific MAPK pathway genes during domestication, rendering domesticated strains more susceptible to diseases. Four genes closely associated with cap color and stipe length were identified, but genetic transformation experiments confirmed the functional relevance of only two (FfB and FfD) identified through PAV-based GWAS. ConclusionThis study uncovered significant genomic variations between cultivated and wild Flammulina filiformis populations, including the loss of pathogen resistance genes during domestication. We also identified key genes linked to cap color and stipe length, demonstrating for the first time the important role of PAV variation in mushroom domestication. These insights provide a foundation for future mushroom breeding and evolutionary research.

Assessing population structure and morpho-molecular characterization of sunflower (Helianthus annuus L.) for elite germplasm identification.

Sunflower (Helianthus annuus L.), known for its adaptability and high yield potential, is vital in global edible oil production. Estimating genetic diversity is a key pre-breeding activity in crop breeding. The current study comprised of 48 genotypes which were assessed for their biometrical traits at department of Oilseeds, Tamil Nadu Agricultural University, during the rainy season of 2022. The lines were subsequently characterised using 103 simple sequence repeat (SSR) markers for molecular diversity analysis. The results indicated that the net nucleotide distances indicated varying genetic divergence, with subpopulations II and V showing the highest (0.056) and I and IV the lowest (0.014). Subpopulation IV exhibited the highest heterozygosity (0.352), while subpopulation III had the lowest heterozygosity and a low Fst (0.173). Principal components analysis (PCA) and hierarchical cluster analysis were employed for assessing the morphological diversity, facilitating genotype grouping and parent selection for breeding programs. The first four components cumulatively accounted for 86.72% of the total variation. Cluster Analysis grouped 48 sunflower genotypes into three clusters based on genetic diversity. COSF 13B stands out for its high head diameter, oil content, seed yield, and oil yield based on mean performance of morphological data. Principal coordinate analysis (PCoA) mirrored the groupings from the Neighbor Joining method, with the first three components explaining 27.24% of the total variation. Molecular data analysis identified five distinct clusters among the germplasm. By integrating morphological and molecular marker data with genetic distance analysis, substantial diversity was revealed with the genotypes RHA 273 and GMU 325 consistently demonstrated high oil yield per plant. The genotypes GMU 477, GMU 450, COSF 13B, RHA 102, CMS 1103B, and RHA GPR 58 have been identified as suitable parents for enhancing oil content in sunflower breeding programs. These findings also aid in selecting SSR markers for genotype characterization and in choosing diverse parents for breeding programs.

Chromosome-level genome assembly and functional annotation of Citrullus colocynthis: unlocking genetic resources for drought-resilient crop development

Main conclusionThe chromosome-level genome assembly of Citrullus colocynthis reveals its genetic potential for enhancing drought tolerance, paving the way for innovative crop improvement strategies.This study presents the first comprehensive genome assembly and annotation of Citrullus colocynthis, a drought-tolerant wild close relative of cultivated watermelon, highlighting its potential for enhancing agricultural resilience to climate change. The study achieved a chromosome-level assembly using advanced sequencing technologies, including PacBio HiFi and Hi-C, revealing a genome size of approximately 366 Mb with low heterozygosity and substantial repetitive content. Our analysis identified 23,327 gene models, that could encode stress response mechanisms for species’ adaptation to arid environments. Comparative genomics with closely related species illuminated the evolutionary dynamics within the Cucurbitaceae family. In addition, resequencing of 27 accessions from the United Arab Emirates (UAE) identified genetic diversity, suggesting a foundation for future breeding programs. This genomic resource opens new avenues for the de novo domestication of C. colocynthis, offering a blueprint for developing crops with enhanced drought tolerance, disease resistance, and nutritional profiles, crucial for sustaining future food security in the face of escalating climate challenges.

Demographic and genetic impacts of powdery mildew in a young oak (Quercus robur L.) cohort

Key messageBy monitoring a field experiment over nine years, we investigated the impacts of the two main pathogen species Erysiphe quercicola S. Takam. and U. Braun and Erysiphe alphitoides (Griffon and Maubl.) U. Braun and S. Takam causing powdery mildew on a young cohort of pedunculate oak (Quercus robur L.), both from a demographic and genetic point of view using SNP markers. We show that survival rate is affected by mean disease severity. But while the growth-related tolerance to infection of the oak individual seems to be more determinant than resistance against infection, no equalizing effect of the disease could be detected.ContextStudies on the effects of pathogens on the survival and population dynamics of forest trees are scarce. Yet a better understanding of these interactions could prove strategic in the challenging context of climate change.AimsOur general objective was to characterize the demographic and genetic impact of the two main pathogen species Erysiphe quercicola S. Takam. and U. Braun and Erysiphe alphitoides (Griffon and Maubl.) U. Braun and S. Takam causing powdery mildew in the early stages of a Quercus robur L. population.MethodsAn ad hoc field design with two disease exposures, natural and protected, was surveyed over nine years. This enabled a detailed phenotypic monitoring of 1733 emerging individuals from 15 progenies, and the genotyping of 68% of them.ResultsThe pathogen induced high levels of seedling mortality several years after sowing, associated with reduced growth and capacity to overwinter. Fast-growing families showed the highest survival rate under both natural and protected disease exposure. Contrary to a possible trade-off hypothesis between growth and defense, family height potential was not negatively related to disease resistance across the studied oak mother trees. While supporting a deleterious effect of very low individual heterozygosity on the probability of survival, average genomic diversity was not significantly affected by mortality associated with powdery mildew. Our study also points to a few candidate genes for several fitness-related traits.ConclusionOverall, our results suggest that in oak natural populations, infection levels (related to resistance sensu stricto) may be less determinant than growth-related tolerance to infection for the fate of seedlings. However, an equalizing effect of powdery mildew on relative oak genotype performances cannot be excluded at later stages.

Host genetic diversity and body condition influence parasite resistance and clearance in a wild marine mammal population.

Host genetic variability can modulate infection resistance, although its role in infection clearance remains unclear. Hookworm disease (Uncinaria sp.) is the leading cause of pup mortality in several otariid species, although the parasite can be cleared through immune-mediated processes. We evaluated the association of host genetic diversity, body condition and immune response with hookworm resistance and/or clearance in the South American fur seal (Arctocephalus australis). Uninfected pups had higher heterozygosity than parasitized individuals, indicating a negative relationship between heterozygosity and the chances of infection. Likewise, pups that died of hookworm infection had lower heterozygosity than those that died of non-infectious causes. Interestingly, once infected, pups that survived hookworm infection had heterozygosities similar to pups that died of hookworm disease. However, pups that cleared the infection had a higher body mass and parasite-specific immunoglobulin G levels than those that did not recover or died of hookworm disease. Thus, although heterozygosity predicted resistance to and mortality from hookworm infections, it did not affect parasite clearance, which was facilitated by better body condition and adaptive immune responses. This demonstrates that host genetic variability and host-environment interactions influence disease dynamics, acting at different, well-defined stages of infection.

Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes

Sea cucumbers, marine benthic invertebrates, play crucial roles in maintaining the stability of marine ecosystems and hold key evolutionary positions. However, information regarding their genomes remains limited. Here, we conducted genome survey analyses on seven species from four orders. Results indicated that Colochirus anceps, Colochirus quadrangularis, and Pseudocolochirus violaceus within the order Dendrochirotida have significantly larger genomes (2238–3754 Mbp) compared to conventional sea cucumber genomes, accompanied by a very high proportion of repeat sequences (69.39–72.52 %). While Holothuria edulis and Holothuria atra exhibited similar genome sizes comparable to those of other species within the order Holothuriida, heterozygosity and repeat content varied among all the six species in this order. The representative species Apostichopus californicus of the order Synallactida possesses the smallest genome size (573.45Mbp) within its order, but its heterozygosity (2.24 %) is significantly higher than that of other species. The representative species Synapta maculata of the order Apodida exhibited a normal genome size (900.97 Mbp), lower proportion of repeat sequences (42.19 %), and lower heterozygosity (0.84 %), making it the species with the least challenges for genome sequencing and assembly in the future among all surveyed species. Subsequently, we compiled genomic information from a total of 19 sea cucumber genomes, both newly sequenced and previously reported, revealing a significant linear relationship (P = 0.0001) between genome size and the proportion of repeat sequences in sea cucumbers. Additionally, phylogenetic and comparative analysis of mitochondrial genomes among them indicated extensive rearrangements within the order Apodida, leading to significant discrepancies between mitochondrial and nuclear genome phylogenies.

Genetic and telomeric variability: Insights from a tropical avian hybrid zone.

Telomere lengths and telomere dynamics can correlate with lifespan, behaviour and individual quality. Such relationships have spurred interest in understanding variation in telomere lengths and their dynamics within and between populations. Many studies have identified how environmental processes can influence telomere dynamics, but the role of genetic variation is much less well characterized. To provide a novel perspective on how telomeric variation relates to genetic variability, we longitudinally sampled individuals across a narrow hybrid zone (n = 127 samples), wherein two Manacus species characterized by contrasting genome-wide heterozygosity interbreed. We measured individual (n = 66) and population (n = 3) differences in genome-wide heterozygosity and, among hybrids, amount of genetic admixture using RADseq-generated SNPs. We tested for population differences in telomere lengths and telomere dynamics. We then examined how telomere lengths and telomere dynamics covaried with genome-wide heterozygosity within populations. Hybrid individuals exhibited longer telomeres, on average, than individuals sampled in the adjacent parental populations. No population differences in telomere dynamics were observed. Within the parental population characterized by relatively low heterozygosity, higher genome-wide heterozygosity was associated with shorter telomeres and higher rates of telomere shortening-a pattern that was less apparent in the other populations. All of these relationships were independent of sex, despite the contrasting life histories of male and female manakins. Our study highlights how population comparisons can reveal interrelationships between genetic variation and telomeres, and how naturally occurring hybridization and genome-wide heterozygosity can relate to telomere lengths and telomere dynamics.

Analysis of inbreeding depression in five S1 Cassava families of elite varieties at the seedling nursery and clonal evaluation trial stages.

Background Cassava is an outcrossing, highly heterozygous plant that is reported to suffer from inbreeding depression. However, unraveling recessive traits and exploring additive genes would require a limited level of inbreeding for the genetic improvement of cassava. Method The impact of inbreeding depression (ID) on agronomic and biotic tolerance of cassava was evaluated using the S1 progenies of five African cassava varieties (TMS 30572, TME 419, TMS 98/0505, TMS 01/1371, and TMS 98/0002) at the seedling and clonal evaluation stages. Results At both trial stages, the effects of ID were severe on average performance of fresh root yield and fresh foliage yield; moderate on harvest index, dry matter content, vigor, and tolerance to cassava mosaic disease, cassava bacterial blight, and cassava anthracnose diseases; and less severe on plant height. Further examination of S1 families using molecular markers showed varying levels of heterozygosity at several loci across the genome. In addition, the degree of heterozygosity and ID varied by the S1 family. The TMS 01/1371 family showed the lowest degree of heterozygosity and ID on the average performance of different agronomic attributes, indicating that inbreeding may be strategically explored in this family to increase genetic gain and identify useful recessive traits. Lastly, the observed depression from inbreeding was higher in seedling evaluation than in clonal evaluation trials for fresh root yield, fresh foliage yield, harvest index, and dry matter content. Conclusion S1 individuals showing relatively low heterozygosity based on SNP data were selected as parents to advance genetic gain in cassava. Generally, reduced heterozygosity was prominent in traits with severe ID impacts on average phenotypic performance. Our results highlight the relative importance of exploring non-additive genetic effects and transgressive segregations for favorable allele combinations in cassava improvement.

Individual and social heterosis act independently in honey bee (Apis mellifera) colonies.

Heterosis occurs in individuals when genetic diversity, i.e., heterozygosity, increases fitness. Many advanced eusocial insects evolved mating behaviors, including polyandry and polygyny, which increase inter-individual genetic diversity within colonies. The possibility of this structure of diversity to improve group fitness has been termed social heterosis. Neither the independence of individual and social heterosis nor their relative effect sizes have been explicitly measured. Through controlled breeding between pairs of Western honey bee queens (Apis mellifera L.; n=3 pairs) from two distinct populations, we created inbred colonies with low genetic diversity, hybrid colonies with high heterozygosity, and mixed colonies (combining inbred workers from each population) with low heterozygosity and high social diversity. We then quantified two independent traits in colonies: survival against bacterial challenge and maintenance of brood nest temperature. For both traits, we found hybrid and mixed colonies outperformed inbred colonies but did not perform differently from each other. During immune challenge assays, hybrid and mixed colonies experienced hazard ratios of 0.49 (95% CI [0.37, 0.65]) and 0.69 (95% CI [0.50, 0.96]) compared to inbred colonies. For nest temperatures, hybrid and mixed colonies experienced 1.94±0.97°C and 2.82±2.46°C less thermal error and 0.14±0.11°C2 and 0.16±0.06°C2 less thermal variance per hour than inbred lines. This suggests social and individual heterosis operate independently and may have similar effect sizes. These results highlight the importance of both inter- and intra-individual diversity to fitness, which may help explain the emergence of polyandry/polygyny in eusocial insects and inform breeding efforts in these systems.

Emerging Cases of Cat-Transmitted Sporotrichosis Driven by Sporothrix brasiliensis in Northeast Brazil.

Cat-transmitted sporotrichosis is caused by the emerging fungal pathogen Sporothrix brasiliensis and constitutes a significant public health issue that affects people living in resource-poor urban centers in Brazil. The lack of knowledge about transmission dynamics makes it difficult to propose public health policies to contain the advance of sporotrichosis. We describe the recent emergence of 1,176 cases of sporotrichosis in cats (2016 to 2021) in the metropolitan region of Recife, Brazil, leading to significant zoonotic transmission and an overwhelming occurrence of S. brasiliensis as the etiological agent. Most cases were from cats in the cities of Olinda (408/1,176; 34.70%), Jaboatão dos Guararapes (332/1,176; 28.23%), and Recife (237/1,176; 20.15%). Molecular typing using amplified fragment length polymorphism (EcoRI-GA/MseI-AG) revealed low polymorphic information content (PIC = 0.2499) and heterozygosity (H = 0.2928), typical of an outbreak scenario. Dendrogram and multivariate cluster analysis revealed that isolates from Pernambuco are closely related to Rio de Janeiro isolates. We report a substantial occurrence of MAT1-2 idiomorphs in the metropolitan region of Recife (0:60 ratio; χ2 = 60.000, P < 0.0001). The limited population differentiation and genetic diversity of the isolates from Pernambuco suggest a recent introduction, possibly via a founder effect, from the parental population in Rio de Janeiro. Our findings emphasize the critical importance of molecular surveillance of S. brasiliensis for outbreak response. A comprehensive one-health strategy is mandatory to control the spread of cat-transmitted sporotrichosis driven by S. brasiliensis, encompassing sanitary barriers, quick diagnosis, and treatment.

MAP3K1, SPEF2 and PLCZ1 genes association with fertility and semen quality traits of AI bulls in Andhra Pradesh

Bull fertility plays an important role in improving the economic value of the herd and is measured in terms of semen quality traits, which is influenced by both genetic and non-genetic factors. Polymorphism of MAP3K1/ CviQI (rs463712269), SPEF2/HpyCH4V (rs722354121) and PLCZ1/AvaII (rs208019489) and their association with scrotal circumference, sperm motility and plasma membrane integrity, respectively were studied on 239 bulls of different breeds reared in different frozen semen bull stations. The MAP3K1/CviQ1 assay revealed that T allele was more frequent in Ongole and Murrah population. RFLP at SPEF2/ HpyCH4V locus indicated fixation of T allele in both the exotic purebred cattle (Holstein Friesian and Jersey) whereas selective advantage of C allele was observed in Murrah buffaloes. Except in Holstein Friesian crossbred, other cattle genetic groups were with CC genotype for PLCZ1/AvaII assay and the Murrah population had low genetic diversity and heterozygosity excess. The PLCZ1/ AvaII genotypes had significant influence on the plasma membrane integrity of sperm in Holstein Friesian, Jersey and Ongole bulls. The plasma membrane integrity of sperm was reported to be high in heterozygotes (CG) of Jersey and Ongole cattle. The present study, concluded the importance of PLCZ1 gene as a marker for semen quality assessment and selection in bulls.

New insights into the phylogeny of Neogastropoda aided by draft genome sequencing of a volutid snail

AbstractNeogastropoda is a large order of predominantly marine gastropod molluscs, typically predatory or parasitic on other animals. It includes over 16,000 species representing a large post‐Cretaceous radiation, but the internal phylogenetic relationships of contained taxa are far from resolved, with inconsistent results from nuclear genes, mitogenomes, and morphology. One major issue in reconstructing the molecular phylogeny is the lack of high‐quality sequences for early‐diverging families and superfamilies such as Volutidae (Volutoidea). Here, we examine the superfamily‐level phylogenetic relationships in Neogastropoda, aided by newly sequenced draft genome and mitogenome of the volutid snail Fulgoraria chinoi from the deep sea off Japan. The genome of F. chinoi is relatively large at 1.54&amp;amp;#x02009;Gb but exhibits low genome heterozygosity; over 54% of this genome constitutes of repeat contents, and we find evidence for active insertion of transposable elements, particularly LINEs and SINEs. A total of 50,792 protein‐coding genes (PCGs) were predicted from the nuclear genome, and a circular mitogenome was also assembled and annotated. Our phylogenetic analyses using mitogenomes recovered each neogastropod superfamily as monophyletic, though also revealed inconsistent phylogenetic signals within superfamilies. Phylogenetic reconstructions using the PCGs resulted in a robust tree from different models and data matrices, recovering Volutoidea as the earliest diverging superfamily (among those for which comparable data is available) within a monophyletic Neogastropoda. Dated phylogenetic analysis revealed an early Cretaceous radiation of Neogastropoda, congruent with the fossil record. Our study provides a robust internal evolutionary framework for the speciose but genomically undersampled Neogastropoda, and expands the available genomic resources for this order. Genomic data for key missing lineages such as Mitroidea, Olivoidea, and Cancellariidae are much sought in the future for a full understanding of Neogastropoda evolution.

P-560 Characterization of ploidy level and parental genome inheritance abnormalities in preimplantation human embryos

Abstract Study question Can preimplantation genetic testing (PGT) platforms with integrated genotyping aid the characterization of genome-wide chromosomal abnormalities in human embryos and factors contributing to their occurrence? Summary answer Signatures detected by genotype-criteria-based models in PGT pinpoint origin of haploidy, triploidy and genome-wide uniparental disomy (gwUPD), highlighting recombination deficiencies potentially underpinning these phenomena. What is known already While there is a growing body of knowledge on the frequency and origin of individual chromosome abnormalities, very little is known about genome-wide chromosomal abnormalities in human development. Indeed, genome-wide abnormalities are incompatible with normal human development, making the preimplantation stage the ideal time to characterize them. Novel PGT technologies provide the research and clinical opportunity to characterize both known ploidy-level abnormalities (triploid/haploid) and identify theoretical genome-wide abnormalities undetectable at later stages of development. Study design, size, duration PGT genotyping data from 96660 embryos were used to assess incidence of ploidy-level abnormalities and correlation with potential predisposing clinical factors. Parental origin of putative haploidy and triploidy was assessed on 14 and 41 embryos with parental genotypes available (trios), respectively. For the 41 triploid trios, meiotic origin and recombination rates were also evaluated. A novel genotype-criteria based model to detect theoretical gwUPD and meiotic origin was developed on a semi-contemporaneous 74009 female embryo dataset. Participants/materials, setting, methods PGT was performed with targeted next-generation sequencing, including 5000 genome-wide SNPs. Informative SNPs from trios were used to identify parental origin of haploidy/triploidy. Informative SNPs within 5cM of the centromere were used to evaluate meiotic origin and extended beyond 5cM to identify maternal recombination observing shifts between single (SPH) and biparental (BPH) homologs. gwUPD was predicted when low genome-wide heterozygosity, increased homozygosity in the centromeric region, and decreased similarity to sibling embryos were observed. Main results and the role of chance Genome wide ploidy abnormalities were detected in 1.1% (n = 1.063/96.660; CI 95%: 1-1,2%) of embryos. Haploidy was mainly of paternal origin (n = 12/14), whereas triploidy was exclusively maternal in origin (n = 41/41) and prominently due to meiosis II errors (n = 30/41; 73.2%; 95% CI:57.1-85.8%). Advanced maternal age was positively associated with an increased risk of triploid conceptions (OR = 1.059 per year; p &amp;lt; 0.001). Investigation of maternal recombination rates detected by three consecutive SNPs shifting between SPH and BPH (with a calculated genotyping error of 0.16%) in triploid embryos revealed an outlier group of 7 embryos with statistically lower (P &amp;lt; 0.001) identified crossover events (0-2 events genome-wide) compared to the average 23.7 detectable events genome-wide (SD:4.3). Recombinant gwUPD was predicted in 41 out of 74009 human embryos (0.05%; 95% CI:0.04-0.07%). These embryos showed a high homozygosity in pericentromeric regions, as a proof of each pair of chromosomes being the same parental homolog resulting from a faulty meiosis II, but with detectable heterozygosity regions throughout the rest of the genome, indicating that crossovers occurred between the two parental homologs during prophase I. Multifocal biopsies from the same embryos confirmed the reproducibility of identification of the number of recombination events in triploid embryos and the gwUPD prediction. Limitations, reasons for caution This assay genotypes only a portion of the genome and underestimation of recombination events is possible. Our current detection of gwUPD is limited to recombinant uniparental isodisomy of MII origin only. Therefore, the exact prevalence of these abnormal gwUPD configurations requires further understanding and analysis. Wider implications of the findings Genotyping in routine PGT can identify severe genome-wide abnormalities with associated gestational complications that would otherwise go undiagnosed. Comprehensive characterization of these abnormalities is not possible at later stages of development. Therefore, PGT offers a unique opportunity to delve into their biological origin and identify novel biomarkers for embryo competence. Trial registration number not applicable

Cryptic diversity of shallow and mesophotic Stephanocoenia intersepta corals across Florida Keys National Marine Sanctuary.

Population genetic analyses can provide useful data on species' regional connectivity and diversity which can inform conservation and restoration efforts. In this study, we quantified the genetic connectivity and diversity of Stephanocoenia intersepta corals from shallow (<30 m) to mesophotic (30-45 m) depths across Florida Keys National Marine Sanctuary. We generated single nucleotide polymorphism (SNP) markers to identify genetic structuring of shallow and mesophotic S. intersepta corals. We uncovered four distinct, cryptic genetic lineages with varying levels of depth-specificity. Shallow-specific lineages exhibited lower heterozygosity and higher inbreeding relative to depth-generalist lineages found across both shallow and mesophotic reefs. Estimation of recent genetic migration rates demonstrated that mesophotic sites are more prolific sources than shallow sites, particularly in the Lower Keys and Upper Keys. Additionally, we compared endosymbiotic Symbiodiniaceae among sampled S. intersepta using the ITS2 region and SYMPORTAL analysis framework, identifying symbionts from the genera Symbiodinium, Breviolum, and Cladocopium. Symbiodiniaceae varied significantly across depth and location and exhibited significant, but weak correlation with host lineage and genotype. Together, these data demonstrate that despite population genetic structuring across depth, some mesophotic populations may provide refuge for shallow populations moving forward and remain important contributors to the overall genetic diversity of this species throughout the region. This study highlights the importance of including mesophotic as well as shallow corals in population genetic assessments and informs future science-based management, conservation, and restoration efforts within Florida Keys National Marine Sanctuary.

Can hair snares provide a reliable method for estimating abundance of an exotic ungulate?

Mitigating exotic species invasions requires reliable information on abundance and source-sink dynamics to evaluate effectiveness of control efforts. Despite being present in the southeastern United States for centuries, wild pigs (Sus scrofa) continue to invade new areas, including the Sam D. Hamilton Noxubee National Wildlife Refuge (NNWR) in Mississippi, a forested landscape with an emerging wild pig population. Considering the early stage of invasion, we designed and implemented a non-invasive hair sampling technique to estimate abundance and relatedness of wild pigs within the NNWR. Following 8-week sampling periods in 2021 (n = 160 samples) and 2022 (n = 159 samples), we identified 38 and 26 unique individuals, respectively, although recapture rates were too low to yield precise abundance estimates. We also identified low heterozygosity indicating high relatedness among our population which likely reflected lack of barrier features to gene flow and/or a limited number of external source populations. Finally, we observed positive trends in viable samples collected relative to sampling week, suggesting more optimal sampling period(s) may exist (e.g., autumn). We also acknowledge that use of grain in more accessible areas rather than our remote approach using scent-only attractants may increase hair snare attractiveness and wild pig encounters, while permitting increased sampling frequency. Collectively, these modifications (i.e., altered season, bait type, and access) provide viable pathways to increase precision for abundance estimates. When used concomitantly with ongoing monitoring and control efforts, non-invasive hair sampling will contribute to a more holistic understanding of this exotic species and better inform management actions.

Evolutionary relationship of moso bamboo forms and a multihormone regulatory cascade involving culm shape variation.

Moso bamboo (Phyllostachys edulis) known as Mao Zhu (MZ) in Chinese exhibits various forms with distinct morphological characteristics. However, the evolutionary relationship among MZ forms and the mechanisms of culm shape variation are still lacking. Here, the main differences among MZ forms were identified as culm shape variation, which were confirmed by analysing MZ forms (799 bamboo culms) and MZ (458 bamboo culms) populations. To unravel the genetic basis underlying the morphological variations, 20 MZ forms were subjected to whole-genome resequencing. Further analysis yielded 3 230 107 high-quality SNPs and uncovered low genetic diversity and high genotype heterozygosity associated with MZ forms' formation. By integrating the SNP data of 427 MZ individuals representing 15 geographic regions, the origins of eight MZ forms were successfully traced using the phylogenetic tree and the identified common heterozygous loci. Meanwhile, transcriptomic analysis was performed using shoots from MZ and its two forms with culm shape variation. The results, combined with genomic analyses, demonstrated that hormone signalling related genes played crucial roles in culm variation. Co-expression network analysis uncovered genes associated with multiple plant hormone signal transduction, especially auxin and cytokinin were involved in culm shape variation. Furthermore, the regulatory relationships of a specific transcription factor and their target genes associated with auxin and ethylene signalling were validated by yeast one-hybrid, electrophoretic mobility shift assays, and dual-luciferase reporter. Overall, this study provides important insights into the culm shape variation formation in bamboo, which facilitates to breed new varieties with novel culms.

Lack of Genetic Variation in Low Heterozygosity and Clonal Animals Creates Lack of Physiological Variation

Data variability frequently complicates reproducibility and interpretation of experimental results. Such variability arises from numerous sources such as differences in procedures or not accounting for key biological factors (e.g. sex, biological rhythms, prandial state). Making the situation more problematic, variation in physiological performance is often viewed as highly labile, easily and rapidly influenced by environmental stressors, development, etc., making it diffcult to pin down a source for variation. Undeniably, however, unknown (or ignored) genetic variation among and within strains/lines can also be a significant source of data variability in published physiological measurements, though surprisingly this has not been extensively investigated as a specific source of physiological variation. We hypothesized that variation in physiological performance is correlated with the intrinsic degree of genetic variability of the subject animal. To test this hypothesis, we employed two animal models: 1) Inbred lines ( e.g., NHGRI-1) derived from wild type strains of the zebrafish ( Danio rerio), with an estimated 15% of the genetic heterozygosity of wild type AB zebrafish, and 2) the parthenogenetically reproducing marbled crayfish ( Procambarus virginalis), all specimens of which are genetically identical clones. For these two animal models, we measured both physiological variables (e.g. heart rate, stroke volume, cardiac output, oxygen consumption) and morphological variables (e.g. yolk-chorion ratio, body mass, embryo mass, total length, condition factor, specific growth rate) during development. We subjected the two animal models to environmental stress in the form of both temperature and hypoxia to stimulate physiological responses that could be compared and contrasted among populations. From these data we then calculated the resultant coeffcients of variation for measured variables for wild type and low/zero heterozygosity populations and/or species. In zebrafish, both the wildtype AB and NHRGI-1 lines showed similar developmental trajectories characterized by similar mean values for physiological and morphological variables. Additionally, similar mean values for physiological and morphological variables were recorded in the face of temperature and hypoxia challenge. Yet, importantly, the coeffcient of variation for each measured variable was significantly lower in NHGRI-1 than AB larvae for &gt;90% of the assessed endpoints. In the clonal crayfish, genetically identical early stage marbled crayfish reared in different temperatures or oxygen levels show major acclimation responses, but generally showed less morphological and physiological variation about the mean than sexually-reproducing species crayfish with inherently much greater genetic variation, as evident from comparisons of calculated coeffcients of variation. A key question regarding the clonal crayfish is how can there be any morphological or physiological variation between individuals? We suggest that variability that persists may arise from microenvironmental differences during rearing (e.g. egg position during incubation on the mother’s pleon) and/or stochastic differences in gene expression (e.g. due to random epimutations) in this clonal species. In conclusion, genetic diversity clearly contributes to physiological variability. For future experiments, low heterozygosity lines and/or clonal species may be useful for decreasing inter-individual variation, thus aiding interpretation of results and enhancing reproducibility. In any event, scientific documentation of physiological studies should include as much information on (genetic) background of the experimental animals as possible. NSF IOS-2103499. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology.

The Hetian Qing donkey is an excellent local donkey breed in Xinjiang. It is of great significance to accelerate breeding and the speed of breeding and rejuvenation, as well as to understand the genetic basis of the strategies and population. This study collected a total of 4 male donkeys and 28 female donkeys. It then obtained genotype data through Simplified Genomic Sequencing (GBS) technology for data analysis. The results detected a total of 55,399 SNP loci, and the genotype detection rate of individuals was ≥90%. A total of 45,557 SNP loci were identified through quality control, of which 95.5% were polymorphic. The average minimum allele frequency was 0.250. The average observed heterozygosity was 0.347. The average expected heterozygosity was 0.340. The average IBS (state homologous) genetic distance was 0.268. ROH: 49 (homozygous fragments), with 73.47% of the length between 1 and 5 Mb. The average per-strip ROH length was 1.75 Mb. The mean inbreeding coefficient was 0.003. The 32 Hetian green donkeys could be divided into six families. The number of individuals in each family is significant. To sum up, the Hetian Qing donkey population has low heterozygosity, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the subsequent process of seed protection, seed selection should be conducted according to the divided pedigree to ensure the long-term protection of the genetic resources of Hetian green donkeys.

Low genetic variability and high isolation of a post-harvest South American pinniped population as revealed by genome-wide single nucleotide polymorphisms

Abstract Otaria flavescens has been one of the most heavily exploited pinnipeds during the last 200 years, with depletion of ~90% in some colonies. After the prohibition on sealing in South America, populations stabilized except for the Uruguayan population, which showed a constant decrease. The underlying causes of its decline are unknown. This study used genome-wide single nucleotide polymorphisms to assess the variability and connectivity of some of the most overexploited sea lion colonies in the Atlantic Ocean. Our results revealed low allelic richness, nucleotide diversity, and heterozygosity in the Uruguayan population and evidence of complete isolation from the Argentinean populations under study. In contrast, the Patagonian populations showed a high degree of connectivity, which could explain their recovery and high levels of diversity at present. Our study highlights the critical situation of the Uruguayan sea lion population, emphasizing the need for maintaining continuous conservation efforts in the region.

Chromosomal-Level Reference Genome for the Chinese Endemic Pygmy Grasshopper, Zhengitettix transpicula, Sheds Light on Tetrigidae Evolution and Advancing Conservation Efforts.

The pygmy grasshopper, Zhengitettix transpicula, is a Chinese endemic species with an exceedingly limited distribution and fragile population structure, rendering it vulnerable to extinction. We present a high-continuity, chromosome-scale reference genome assembly to elucidate this species' distinctive biology and inform conservation. Employing an integrated sequencing approach, we achieved a 970.40 Mb assembly with 96.32% coverage across seven pseudo-chromosomes and impressive continuity (N50 > 220 Mb). Genome annotation achieves identification with 99.2% BUSCO completeness, supporting quality. Comparative analyses with 14 genomes from Orthoptera-facilitated phylogenomics and revealed 549 significantly expanded gene families in Z. transpicula associated with metabolism, stress response, and development. However, genomic analysis exposed remarkably low heterozygosity (0.02%), implying a severe genetic bottleneck from small, fragmented populations, characteristic of species vulnerable to extinction from environmental disruptions. Elucidating the genetic basis of population dynamics and specialization provides an imperative guideline for habitat conservation and restoration of this rare organism. Moreover, divergent evolution analysis of the CYP305m2 gene regulating locust aggregation highlighted potential structural and hence functional variations between Acrididae and Tetrigidae. Our chromosomal genomic characterization of Z. transpicula advances Orthopteran resources, establishing a framework for evolutionary developmental explorations and applied conservation genomics, reversing the trajectory of this unique grasshopper lineage towards oblivion.