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Comptes Rendus Biologies Jan 2024Transferring an asexual mode of reproduction by seeds (apomixis) to cultivated plants would enable clonal reproduction of heterozygous genotypes such as F1 hybrids with...
Transferring an asexual mode of reproduction by seeds (apomixis) to cultivated plants would enable clonal reproduction of heterozygous genotypes such as F1 hybrids with hybrid vigor (heterosis), facilitating their access and multiplication by small-scale growers. Although sources of apomixis and the genetic loci controlling its constituent elements have been identified in wild species, their transfer by crossing to cultivated species has so far been unsuccessful. Here, we have introduced synthetic apomixis in hybrid rice to produce a high (95-100%) frequency of clonal seeds, via the inactivation of three meiotic genes-resulting in unreduced, non-recombined gametes-and the addition of an egg cell parthenogenesis trigger. The genotype and phenotype, including grain quality, of the F1 hybrid are reproduced identically in the clonal apomictic progenies. These results make synthetic apomixis compatible with future use in agriculture.
Topics: Oryza; Seeds; Reproduction; Agriculture; Genotype
PubMed: 38206040
DOI: 10.5802/crbiol.125 -
Ecology and Evolution Jan 2024Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid...
Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus , and hermaphroditism in . Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic , and a diploid hermaphroditic via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index ( ) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.
PubMed: 38192904
DOI: 10.1002/ece3.10831 -
ArXiv May 2024Effective connectivity estimation plays a crucial role in understanding the interactions and information flow between different brain regions. However, the functional...
Effective connectivity estimation plays a crucial role in understanding the interactions and information flow between different brain regions. However, the functional time series used for estimating effective connectivity is derived from certain software, which may lead to large computing errors because of different parameter settings and degrade the ability to model complex causal relationships between brain regions. In this paper, a brain diffuser with hierarchical transformer (BDHT) is proposed to estimate effective connectivity for mild cognitive impairment (MCI) analysis. To our best knowledge, the proposed brain diffuser is the first generative model to apply diffusion models to the application of generating and analyzing multimodal brain networks. Specifically, the BDHT leverages structural connectivity to guide the reverse processes in an efficient way. It makes the denoising process more reliable and guarantees effective connectivity estimation accuracy. To improve denoising quality, the hierarchical denoising transformer is designed to learn multi-scale features in topological space. By stacking the multi-head attention and graph convolutional network, the graph convolutional transformer (GraphConformer) module is devised to enhance structure-function complementarity and improve the ability in noise estimation. Experimental evaluations of the denoising diffusion model demonstrate its effectiveness in estimating effective connectivity. The proposed model achieves superior performance in terms of accuracy and robustness compared to existing approaches. Moreover, the proposed model can identify altered directional connections and provide a comprehensive understanding of parthenogenesis for MCI treatment.
PubMed: 38168455
DOI: No ID Found -
BioRxiv : the Preprint Server For... Dec 2023Bacteria in the genus have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing...
Bacteria in the genus have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called "parthenogenesis-induction" phenotype can be found in a number of strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 years ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex-determining factor Transformer, and a eukaryotic-like serine-threonine kinase with leucine rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model, . We suggest these proteins are parthenogenesis-inducing factors and our results indicate this would be made possible by a novel mechanism of bacterial-host interaction.
PubMed: 38076953
DOI: 10.1101/2023.12.01.569668 -
Phylloxera and Aphids Show Distinct Features of Genome Evolution Despite Similar Reproductive Modes.Molecular Biology and Evolution Dec 2023Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome...
Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared with the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with 1 sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared with their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.
Topics: Animals; Male; Aphids; X Chromosome; Parthenogenesis; Reproduction; Evolution, Molecular
PubMed: 38069672
DOI: 10.1093/molbev/msad271 -
Heredity Feb 2024From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval...
From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval brains of facultatively parthenogenetic Drosophila. We identified a background of aneuploidy in D. mercatorum strains and found increased levels of aneuploidy in the larval brain tissue of animals arising parthenogenetically versus those arising from sexual reproduction. There is also intra-individual variation in germline-derived aneuploidy within the same strain. To determine if this is a general feature of facultative parthenogenesis in drosophilids, we compared sexually reproduced and parthenogenetic offspring from an engineered facultative parthenogenetic strain of D. melanogaster. In addition to germline-derived aneuploidy, this revealed somatic aneuploidy that increased by up to fourfold in parthenogens compared to sexually reproduced offspring. Therefore, the genetic combination identified in D. mercatorum that causes facultative parthenogenesis in D. melanogaster results in aneuploidy, which indicates that the loss of mitotic control resulting in parthenogenesis causes subsequent genome variation within the parthenogenetic offspring. Our findings challenge the assumption that parthenogenetic offspring are near genetic replicas of their mothers.
Topics: Animals; Drosophila; Drosophila melanogaster; Reproduction; Sexual Behavior, Animal; Parthenogenesis
PubMed: 38017115
DOI: 10.1038/s41437-023-00664-z -
Syntenic relationship of chromosomes in species and based on the chromosome-level genome assemblies.Philosophical Transactions of the Royal... Jan 2024The clade, to which the parasitic nematode genus belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites....
The clade, to which the parasitic nematode genus belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites. Reproductive strategies are also diverse in this group of nematodes, employing not only sexual reproduction but also parthenogenesis, making it an attractive group to study genome adaptation to specific conditions. An in-depth understanding of genome evolution, however, has been hampered by fragmented genome assemblies. In this study, we generated chromosome-level genome assemblies for two species and the outgroup species using long-read sequencing and high-throughput chromosome conformation capture (Hi-C). Our synteny analyses revealed a clearer picture of chromosome evolution in this group, suggesting that a functional sex chromosome has been maintained throughout the group. We further investigated sex chromosome dynamics in the lifecycle of and found that bivalent formation in oocytes appears to be important for male production in the mitotic parthenogenesis. This article is part of the Theo Murphy meeting issue ': omics to worm-free populations'.
Topics: Animals; Male; Strongyloides; Synteny; Chromosomes; Nematoda; Life Cycle Stages; Sex Chromosomes
PubMed: 38008120
DOI: 10.1098/rstb.2022.0446 -
Annual Review of Animal Biosciences Feb 2024Cloning as it relates to the animal kingdom generally refers to the production of genetically identical individuals. Because cloning is increasingly the subject of... (Review)
Review
Cloning as it relates to the animal kingdom generally refers to the production of genetically identical individuals. Because cloning is increasingly the subject of renewed attention as a tool for rescuing endangered or extinct species, it seems timely to dissect the role of the numerous reproductive techniques encompassed by this term in animal species conservation. Although cloning is typically associated with somatic cell nuclear transfer, the recent advent of additional techniques that allow genome replication without genetic recombination demands that the use of induced pluripotent stem cells to generate gametes or embryos, as well as older methods such as embryo splitting, all be included in this discussion. Additionally, the phenomenon of natural cloning (e.g., a subset of fish, birds, invertebrates, and reptilian species that reproduce via parthenogenesis) must also be pointed out. Beyond the biology of these techniques are practical considerations and the ethics of using cloning and associated procedures in endangered or extinct species. All of these must be examined in concert to determine whether cloning has a place in species conservation. Therefore, we synthesize progress in cloning and associated techniques and dissect the practical and ethical aspects of these methods as they pertain to endangered species conservation.
Topics: Animals; Endangered Species; Cloning, Organism; Nuclear Transfer Techniques; Fishes; Cloning, Molecular
PubMed: 37988633
DOI: 10.1146/annurev-animal-071423-093523 -
International Journal of Molecular... Oct 2023Oocyte activation via dual inhibition of protein synthesis and phosphorylation has improved in vitro embryo production in different mammalian species. In this study, we...
Oocyte activation via dual inhibition of protein synthesis and phosphorylation has improved in vitro embryo production in different mammalian species. In this study, we evaluated the effects of the combination of cycloheximide (CHX), dimethyl amino purine (DMAP), and anisomycin (ANY) on the activation of bovine oocytes, particularly on dynamics of MPF and MAPKs, embryonic developmental potential, and quality. The results showed that the cleavage and blastocyst rates, as well as levels of CCNB1, CDK1, p-CDK1, and p-CDK1, were similar among groups; ANY and ANY + CHX reduced the expression of ERK1/2 compared to DMAP-combinations ( < 0.05), whereas ANY + DMAP, CHX + DMAP, and ANY + CHX + DMAP reduced p-ERK1/2 compared to ANY and ANY + CHX treatments ( < 0.05). The quality of blastocysts in terms of cell counts, their allocation, and the numbers of TUNEL-positive cells did not differ among groups. However, transcript levels of were higher in embryos derived from ANY + CHX + DMAP treatment compared to other groups, while expression levels of did not show differences. In addition, the ratio of the ANY + CHX + DMAP treatment was significantly low compared to the ANY treatment ( < 0.05) and did not differ significantly from the other treatments. In conclusion, oocyte activation by dual inhibition of protein synthesis and phosphorylation induces MPF inactivation without degradation of CCNB1, while MAPK inactivation occurs differentially between these inhibitors. Thus, although the combined use of these inhibitors does not affect early developmental competence in vitro, it positively impacts the expression of transcripts associated with embryonic quality.
Topics: Cattle; Animals; Parthenogenesis; Maturation-Promoting Factor; Mitogen-Activated Protein Kinases; Adenine; Oocytes; Cycloheximide; Blastocyst; Anisomycin; Mammals
PubMed: 37958778
DOI: 10.3390/ijms242115794 -
Nature Communications Nov 2023The formation and consequences of polyploidization in animals with clonal reproduction remain largely unknown. Clade I root-knot nematodes (RKNs), characterized by...
The formation and consequences of polyploidization in animals with clonal reproduction remain largely unknown. Clade I root-knot nematodes (RKNs), characterized by parthenogenesis and allopolyploidy, show a widespread geographical distribution and extensive agricultural destruction. Here, we generated 4 unzipped polyploid RKN genomes and identified a putative novel alternative telomeric element. Then we reconstructed 4 chromosome-level assemblies and resolved their genome structures as AAB for triploid and AABB for tetraploid. The phylogeny of subgenomes revealed polyploid RKN origin patterns as hybridization between haploid and unreduced gametes. We also observed extensive chromosomal fusions and homologous gene expression decrease after polyploidization, which might offset the disadvantages of clonal reproduction and increase fitness in polyploid RKNs. Our results reveal a rare pathway of polyploidization in parthenogenic polyploid animals and provide a large number of high-precision genetic resources that could be used for RKN prevention and control.
Topics: Animals; Polyploidy; Hybridization, Genetic; Triploidy; Germ Cells; Chromosomes; Nematoda
PubMed: 37935661
DOI: 10.1038/s41467-023-42700-w