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BMC Bioinformatics Feb 2022Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that...
BACKGROUND
Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemblers that can only tackle genomes of low complexity.
RESULTS
Here, Using robust programs, we build a diploid genome assembly pipeline called gcaPDA (gamete cells assisted Phased Diploid Assembler), which exploits haploid gamete cells to assist in resolving haplotypes. We demonstrate the effectiveness of gcaPDA based on simulated HiFi reads of maize genome which is highly heterozygous and repetitive, and real data from rice.
CONCLUSIONS
With applicability of coping with complex genomes and fewer restrictions on application than most of diploid assemblers, gcaPDA is likely to find broad applications in studies of eukaryotic genomes.
Topics: Alleles; Chromosomes; Diploidy; Haploidy; Haplotypes; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA
PubMed: 35164674
DOI: 10.1186/s12859-022-04591-4 -
International Journal of Molecular... Feb 2024Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches... (Review)
Review
Organisms with three or more complete sets of chromosomes are designated as polyploids. Polyploidy serves as a crucial pathway in biological evolution and enriches species diversity, which is demonstrated to have significant advantages in coping with both biotic stressors (such as diseases and pests) and abiotic stressors (like extreme temperatures, drought, and salinity), particularly in the context of ongoing global climate deterioration, increased agrochemical use, and industrialization. Polyploid cultivars have been developed to achieve higher yields and improved product quality. Numerous studies have shown that polyploids exhibit substantial enhancements in cell size and structure, physiological and biochemical traits, gene expression, and epigenetic modifications compared to their diploid counterparts. However, some research also suggested that increased stress tolerance might not always be associated with polyploidy. Therefore, a more comprehensive and detailed investigation is essential to complete the underlying stress tolerance mechanisms of polyploids. Thus, this review summarizes the mechanism of polyploid formation, the polyploid biochemical tolerance mechanism of abiotic and biotic stressors, and molecular regulatory networks that confer polyploidy stress tolerance, which can shed light on the theoretical foundation for future research.
Topics: Humans; Biological Evolution; Polyploidy; Phenotype; Diploidy
PubMed: 38396636
DOI: 10.3390/ijms25041957 -
Current Biology : CB Nov 2003
Review
Topics: Animal Communication; Animals; Biological Evolution; Diploidy; Haploidy; Insecta; Selection, Genetic; Social Behavior
PubMed: 14614837
DOI: 10.1016/j.cub.2003.10.043 -
BioTechniques Sep 2023Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to... (Review)
Review
Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including species. Most species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future genome projects were developed. Knowledge gained from genomic studies of species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.
Topics: Armillaria; Basidiomycota; Algorithms; Databases, Factual; Diploidy
PubMed: 37681497
DOI: 10.2144/btn-2023-0023 -
Cells Aug 2022Non-celiac wheat sensitivity (NCWS) is a clinical entity induced by the ingestion of gluten that leads to intestinal and/or extraintestinal symptoms, and is diagnosed... (Review)
Review
Non-celiac wheat sensitivity (NCWS) is a clinical entity induced by the ingestion of gluten that leads to intestinal and/or extraintestinal symptoms, and is diagnosed when celiac disease and wheat allergy have been ruled out. In addition to gluten, other grains' components, including amylase trypsin inhibitors (ATIs) and fermentable short-chain carbohydrates (FODMAPs), may trigger symptoms in NCWS subjects. Several studies suggest that, compared with tetraploid and hexaploid modern wheats, ancient diploid wheats species could possess a lower immunogenicity for subjects suffering from NCWS. This review aims to discuss available evidence related to the immunological features of diploid wheats compared to common wheats, and at outlining new dietary opportunities for NCWS subjects.
Topics: Celiac Disease; Diploidy; Glutens; Humans; Intestines; Wheat Hypersensitivity
PubMed: 35954233
DOI: 10.3390/cells11152389 -
Biology Letters Dec 2022Whole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects, the resulting morphological and fitness consequences and how they... (Meta-Analysis)
Meta-Analysis
Whole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects, the resulting morphological and fitness consequences and how they affect the survival of polyploid lineages are intensively studied. Another important factor may also determine the probability of establishment and success of polyploid lineages: inbreeding depression. Inbreeding depression is expected to play an important role in the establishment of neopolyploid lineages, their capacity to colonize new environments, and in the simultaneous evolution of ploidy and other life-history traits such as self-fertilization. Both theoretically and empirically, there is no consensus on the consequences of polyploidy on inbreeding depression. In this meta-analysis, we investigated the effect of polyploidy on the evolution of inbreeding depression, by performing a meta-analysis within angiosperm species. The main results of our study are that the consequences of polyploidy on inbreeding depression are complex and depend on the time since polyploidization. We found that young polyploid lineages have a much lower amount of inbreeding depression than their diploid relatives and their established counterparts. Natural polyploid lineages are intermediate and have a higher amount of inbreeding depression than synthetic neopolyploids, and a smaller amount than diploids, suggesting that the negative effect of polyploidy on inbreeding depression decreases with time since polyploidization.
Topics: Inbreeding Depression; Polyploidy; Diploidy; Inbreeding; Magnoliopsida
PubMed: 36514955
DOI: 10.1098/rsbl.2022.0477 -
Cellular and Molecular Gastroenterology... 2020
Topics: Diploidy; Gene Expression Profiling; Hepatocytes; Humans; Ploidies; Polyploidy; Stem Cells; Transcriptome
PubMed: 31654613
DOI: 10.1016/j.jcmgh.2019.09.008 -
G3 (Bethesda, Md.) Jul 2022De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain...
De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosync's correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.
Topics: Animals; Chromosomes; Diploidy; Genome; Genomics; Haplotypes; Sequence Analysis, DNA
PubMed: 35686922
DOI: 10.1093/g3journal/jkac143 -
Proceedings of the National Academy of... Nov 2022Whole genome duplications (WGDs) are one of the most dramatic mutations that can be found in nature. The effects of WGD vary dramatically but can have profound impacts...
Whole genome duplications (WGDs) are one of the most dramatic mutations that can be found in nature. The effects of WGD vary dramatically but can have profound impacts on an organism's expression, cytotype, and phenotype, altering their evolutionary trajectory as a result. Despite the growing appreciation for the contribution of WGDs in animal evolution, the significant factors influencing how polyploid animal lineages are established and maintained are still not well understood. Many hypotheses have been proposed which predict how climate and environment may influence polyploid incidence and evolution. To test and distinguish between these hypotheses, I assembled a global dataset of polyploid occurrences in three animal clades (Amphibia, Actinopterygii, and Insecta). The dataset encompasses chromosomal, phylogenetic, environmental, and climatic data across 57,905 species in 2,223 terrestrial, freshwater, and marine ecoregions. My analysis reveals a strong latitudinal gradient in all three clades, with the tendency for polyploid taxa to occur more frequently at higher latitudes. Many variables were significant (phylogenetic ANOVA < 0.05 after Bonferroni correction) between polyploids and diploids across taxa, notably those pertaining to temperature dynamics and glaciation. Glaciation in particular appears to be the most significant driver of polyploidy in animals, as these models had the highest relative likelihoods consistently across clades. These results contribute to a model of evolution wherein the broader genomic toolkit of polyploids facilitates adaptation and ecological resilience, enabling polyploids to colonize new or rapidly changing environments.
Topics: Animals; Phylogeny; Polyploidy; Diploidy; Insecta; Adaptation, Physiological
PubMed: 36409908
DOI: 10.1073/pnas.2214070119 -
Journal of Visualized Experiments : JoVE Dec 2022Saccharomyces cerevisiae is a widely used model organism in genetics, evolution, and molecular biology. In recent years, it has also become a popular model organism to...
Saccharomyces cerevisiae is a widely used model organism in genetics, evolution, and molecular biology. In recent years, it has also become a popular model organism to study problems related to speciation. The life cycle of yeast involves both asexual and sexual reproductive phases. The ease of performing evolution experiments and the short generation time of the organism allow for the study of the evolution of reproductive barriers. The efficiency with which the two mating types (a and α) mate to form the a/α diploid is referred to as the mating efficiency. Any decrease in the mating efficiency between haploids indicates a pre-zygotic barrier. Thus, to quantify the extent of reproductive isolation between two haploids, a robust method to quantify the mating efficiency is required. To this end, a simple and highly reproducible protocol is presented here. The protocol involves four main steps, which include patching the haploids on a YPD plate, mixing the haploids in equal numbers, diluting and plating for single colonies, and finally, calculating the efficiency based on the number of colonies on a drop-out plate. Auxotrophic markers are employed to clearly make the distinction between haploids and diploids.
Topics: Saccharomyces cerevisiae; Haploidy; Diploidy; Reproduction
PubMed: 36533830
DOI: 10.3791/64596