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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 -
Origin and Evolution of Diploid and Allopolyploid Genomes Were Accompanied by Chromosome Shattering.The Plant Cell Nov 2019Complexes of diploid and polyploid species have formed frequently during the evolution of land plants. In false flax (), an important hexaploid oilseed crop closely...
Complexes of diploid and polyploid species have formed frequently during the evolution of land plants. In false flax (), an important hexaploid oilseed crop closely related to Arabidopsis (), the putative parental species as well as the origin of other species remained unknown. By using bacterial artificial chromosome-based chromosome painting, genomic in situ hybridization, and multi-gene phylogenetics, we aimed to elucidate the origin and evolution of the polyploid complex. Genomes of diploid camelinas (, = 7; , = 6; and , = 6) originated from an ancestral = 7 genome. The allotetraploid genome of ( = 13, NH) arose from hybridization between diploids related to ( = 6, N) and ( = 7, H), and the N subgenome has undergone a substantial post-polyploid fractionation. The allohexaploid genomes of and ( = 20, NNH) originated through hybridization between an auto-allotetraploid -like genome ( = 13, NN) and ( = 7, H), and the three subgenomes have remained stable overall since the genome merger. Remarkably, the ancestral and diploid genomes were shaped by complex chromosomal rearrangements, resembling those associated with human disorders and resulting in the origin of genome-specific shattered chromosomes.plantcell;31/11/2596/FX1F1fx1.
Topics: Arabidopsis; Brassicaceae; Chromosomes, Plant; Chromothripsis; Diploidy; Evolution, Molecular; Genome, Plant; Hybridization, Genetic; Phylogeny; Polyploidy
PubMed: 31451448
DOI: 10.1105/tpc.19.00366 -
Bioinformatics (Oxford, England) Jul 2018Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in...
MOTIVATION
Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse the two sequences into one haploid consensus sequence and, therefore, fail to capture the diploid nature of the organism under study. Thus, building an assembler capable of producing accurate and complete diploid assemblies, while being resource-efficient with respect to sequencing costs, is a key challenge to be addressed by the bioinformatics community.
RESULTS
We present a novel graph-based approach to diploid assembly, which combines accurate Illumina data and long-read Pacific Biosciences (PacBio) data. We demonstrate the effectiveness of our method on a pseudo-diploid yeast genome and show that we require as little as 50× coverage Illumina data and 10× PacBio data to generate accurate and complete assemblies. Additionally, we show that our approach has the ability to detect and phase structural variants.
AVAILABILITY AND IMPLEMENTATION
https://github.com/whatshap/whatshap.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Data Visualization; Diploidy; Genome, Fungal; Haplotypes; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; Yeasts
PubMed: 29949989
DOI: 10.1093/bioinformatics/bty279 -
Journal of Genetics 2021Arrhenotoky, in which females arise from fertilized eggs and males from unfertilized eggs, has evolved multiple times in animals, most prominently in the insect order...
Arrhenotoky, in which females arise from fertilized eggs and males from unfertilized eggs, has evolved multiple times in animals, most prominently in the insect order Hymenoptera. An alternative form of haplodiploidy, in which females are haploid and males diploid-here named enantiotoky-is not known to exist. An illustrated thought experiment shows that if it does evolve, it will be very unstable and is expected to disappear very quickly.
Topics: Animals; Biological Evolution; Diploidy; Female; Haploidy; Hymenoptera; Male; Pedigree; Reproduction; Sex Determination Processes
PubMed: 33764334
DOI: No ID Found -
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 -
Zoology (Jena, Germany) Dec 2022Species of planarians include both asexually reproducing individuals (reproduce through fission and regeneration) and sexually reproducing individuals (hermaphrodites...
Species of planarians include both asexually reproducing individuals (reproduce through fission and regeneration) and sexually reproducing individuals (hermaphrodites that mate to produce cocoons). While some individuals can switch between the asexual and sexual modes of reproduction. In this study, we examined the reproductive modes and ploidy of Dugesia japonica and Dugesia ryukyuensis from three spring wells in Okinawa (Japan) during two consecutive years. D. japonica are mostly asexual and triploid. In contrast, only 40 % of D. ryukyuensis are asexual and triploid; the remaining are sexual, and diploid or triploid. The sexually reproductive season of D. ryukyuensis is winter. In July, the reproductive organs disappear, and the individuals start asexual reproduction through fission and regeneration. In January of the following year, the individuals develop ovaries and necessary reproductive organs and start sexual reproduction. When these species were lab-reared for a longer period, the reproductive cycles in three strains were repeated for three years. These results confirm that D. ryukyuensis population in Okinawa switches between reproductive modes on an annual cycle, even when kept under constant temperature and no light/dark cycle.
Topics: Animals; Planarians; Triploidy; Reproduction; Seasons; Diploidy
PubMed: 36399916
DOI: 10.1016/j.zool.2022.126053 -
Scientific Reports Nov 2022Genetic drift is a basic evolutionary principle describing random changes in allelic frequencies, with far-reaching consequences in various topics ranging from species...
Genetic drift is a basic evolutionary principle describing random changes in allelic frequencies, with far-reaching consequences in various topics ranging from species conservation efforts to speciation. The conventional approach assumes that genetic drift has the same effect on all populations undergoing the same changes in size, regardless of different non-reproductive behaviors and history of the populations. However, here we reason that processes leading to a systematic increase of individuals` chances of survival, such as learning or immunological memory, can mitigate loss of genetic diversity caused by genetic drift even if the overall mortality rate in the population does not change. We further test this notion in an agent-based model with overlapping generations, monitoring allele numbers in a population of prey, either able or not able to learn from successfully escaping predators' attacks. Importantly, both these populations start with the same effective size and have the same and constant overall mortality rates. Our results demonstrate that even under these conditions, learning can mitigate loss of genetic diversity caused by drift, by creating a pool of harder-to-die individuals that protect alleles they carry from extinction. Furthermore, this effect holds regardless if the population is haploid or diploid or whether it reproduces sexually or asexually. These findings may be of importance not only for basic evolutionary theory but also for other fields using the concept of genetic drift.
Topics: Humans; Genetic Drift; Gene Frequency; Biological Evolution; Alleles; Diploidy
PubMed: 36437294
DOI: 10.1038/s41598-022-24748-8 -
American Journal of Botany Feb 2023Whole-genome duplication is considered a major mechanism of sympatric speciation due to the creation of strong and instantaneous reproductive barriers. Although...
PREMISE
Whole-genome duplication is considered a major mechanism of sympatric speciation due to the creation of strong and instantaneous reproductive barriers. Although postzygotic reproductive isolation between diploids and polyploids is often expected, the extent of reproductive incompatibility must be empirically determined and compared to patterns of genetic isolation to fully characterize the reproductive dynamics between cytotypes.
METHODS
We investigated reproductive compatibility between diploid and tetraploid Lycium australe in two mixed-cytotype populations using (1) controlled crossing experiments to evaluate fruit and seed production and (2) germination trials to test seed viability following homoploid and heteroploid crosses. We contrast these experiments with a single-nucleotide polymorphism (SNP) data set to measure genetic isolation between cytotypes and explore whether cytotype or population origin better explains patterns of genetic variation. Finally, we explore mating patterns using the observed germination rates of naturally produced seeds in each population.
RESULTS
Although homoploid and heteroploid crosses resulted in similar fruit and seed production, reproductive isolation between co-occurring diploids and tetraploids was nearly complete, due to low seed viability following heteroploid crosses. Of 191,182 total SNPs, 21,679 were present in ≥90% of individuals and replicate runs using unlinked SNPs revealed strong clustering by cytotype and differentiation of tetraploids based on population origin.
CONCLUSIONS
As often reported, diploid and tetraploid L. australe experience strong postzygotic isolation via hybrid seed inviability. Consistent with this result, cytotype explained a greater amount of variation in the SNP data set than population origin, despite some evidence of historical introgression.
Topics: Diploidy; Tetraploidy; Lycium; Reproductive Isolation; Polyploidy
PubMed: 36706341
DOI: 10.1002/ajb2.16133 -
Plant Physiology Mar 2022A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The...
A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.
Topics: Diploidy; Genome, Plant; Phylogeny; Plant Breeding; Triticum
PubMed: 35134208
DOI: 10.1093/plphys/kiac006 -
International Journal of Molecular... May 2022Saline-alkaline stress is a critical abiotic stress that negatively affects plants' growth and development. Considerably higher enhancements in plant tolerance to...
Saline-alkaline stress is a critical abiotic stress that negatively affects plants' growth and development. Considerably higher enhancements in plant tolerance to saline-alkaline stress have often been observed in polyploid plants compared to their diploid relatives, the underlying mechanism of which remains elusive. In this study, we explored the variations in morphological and physiological characteristics, phytohormones, and genome-wide gene expression between an autotetraploid rice and its diploid relative in response to alkaline stress. It was observed that the polyploidization in the autotetraploid rice imparted a higher level of alkaline tolerance than in its diploid relative. An eclectic array of physiological parameters commonly used for abiotic stress, such as proline, soluble sugars, and malondialdehyde, together with the activities of some selected antioxidant enzymes, was analyzed at five time points in the first 24 h following the alkaline stress treatment between the diploid and autotetraploid rice. Phytohormones, such as abscisic acid and indole-3-acetic acid were also comparatively evaluated between the two types of rice with different ploidy levels under alkaline stress. Transcriptomic analysis revealed that gene expression patterns were altered in accordance with the variations in the cellular levels of phytohormones between diploid and autotetraploid plants upon alkaline stress. In particular, the expression of genes related to peroxide and transcription factors was substantially upregulated in autotetraploid plants compared to diploid plants in response to the alkaline stress treatment. In essence, diploid and autotetraploid rice plants exhibited differential gene expression patterns in response to the alkaline stress, which may shed more light on the mechanism underpinning the ameliorated plant tolerance to alkaline stress following genome duplication.
Topics: Diploidy; Gene Expression; Gene Expression Regulation, Plant; Oryza; Plant Growth Regulators
PubMed: 35628377
DOI: 10.3390/ijms23105561