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The Plant Cell Jul 2022Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated...
Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.
Topics: Bread; Diploidy; Evolution, Molecular; Genome, Plant; Hybridization, Genetic; Polyploidy; Tetraploidy; Triticum
PubMed: 35512194
DOI: 10.1093/plcell/koac130 -
Cell May 2023Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in...
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
Topics: Diploidy; Mutation; Phylogeny; Plant Breeding; Solanum tuberosum
PubMed: 37146612
DOI: 10.1016/j.cell.2023.04.008 -
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 -
Developmental Cell Jun 2017Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there... (Review)
Review
Although haploidy has not been observed in vertebrates, its natural occurrence in various eukaryotic species that had diverged from diploid ancestors suggests that there is an innate capacity for an organism to regain haploidy and that haploidy may confer evolutionary benefits. Haploid embryonic stem cells have been experimentally generated from mouse, rat, monkey, and humans. Haploidy results in major differences in cell size and gene expression levels while also affecting parental imprinting, X chromosome inactivation, and mitochondrial metabolism genes. We discuss here haploidy in evolution and the barriers to haploidy, in particular in the human context.
Topics: Animals; Diploidy; Embryonic Stem Cells; Genomic Imprinting; Haploidy; Humans; Pluripotent Stem Cells; X Chromosome Inactivation
PubMed: 28633015
DOI: 10.1016/j.devcel.2017.04.019 -
International Journal of Molecular... Jul 2022Populus ussuriensis Kom. is a valuable forest regeneration tree species in the eastern mountainous region of Northeast China. It is known that diploid P. ussuriensis...
Populus ussuriensis Kom. is a valuable forest regeneration tree species in the eastern mountainous region of Northeast China. It is known that diploid P. ussuriensis (CK) performed barely satisfactorily under salt stress, but the salt stress tolerance of polyploid (i.e., triploid (T12) and tetraploid (F20)) P. ussuriensis is still unknown. In order to compare the salt stress tolerance and salt stress response mechanism between diploid and polyploid P. ussuriensis, phenotypic observation, biological and biochemistry index detections, and transcriptome sequencing (RNA-seq) were performed on CK, T12, and F20. Phenotypic observation and leaf salt injury index analysis indicated CK suffered more severe salt injury than T12 and F20. SOD and POD activity detections indicated the salt stress response capacity of T12 was stronger than that of CK and F20. MDA content, proline content and relative electric conductivity detections indicated CK suffered the most severe cell-membrane damage, and T12 exhibited the strongest osmoprotective capacity under salt stress. Transcriptome analysis indicated the DEGs of CK, T12, and F20 under salt stress were different in category and change trend, and there were abundant WRKY, NAM, MYB and AP2/ERF genes among the DEGs in CK, T12, and F20 under salt stress. GO term enrichment indicated the basic growth progresses of CK, and F20 was obviously influenced, while T12 immediately launched more salt stress response processes in 36 h after salt stress. KEGG enrichment indicated the DEGs of CK mainly involved in plant−pathogen interaction, ribosome biogenesis in eukaryotes, protein processing in endoplasmic reticulum, degradation of aromatic compounds, plant hormone signal transduction, photosynthesis, and carbon metabolism pathways. The DEGs of T12 were mainly involved in plant−pathogen interaction, cysteine and methionine metabolism, phagosomes, biosynthesis of amino acids, phenylalanine, tyrosine and tryptophan biosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. The DEGs of F20 were mainly involved in plant hormone signal transduction, plant−pathogen interaction, zeatin biosynthesis, and glutathione metabolism pathways. In conclusion, triploid exhibited stronger salt stress tolerance than tetraploid and diploid P. ussuriensis (i.e., T12 > F20 > CK). The differences between the DEGs of CK, T12, and F20 probably are the key clues for discovering the salt stress response signal transduction network in P. Ussuriensis.
Topics: Diploidy; Gene Expression Profiling; Gene Expression Regulation, Plant; Plant Growth Regulators; Populus; Salt Stress; Stress, Physiological; Tetraploidy; Transcriptome; Triploidy
PubMed: 35886879
DOI: 10.3390/ijms23147529 -
Nature Communications Mar 2023High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers)...
High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers) mainly comprising chromosomal gains. In this study, we investigate how aneuploidy in HeH ALL arises. Single cell whole genome sequencing of 2847 cells from nine primary cases and one normal bone marrow reveals that HeH ALL generally display low chromosomal heterogeneity, indicating that they are not characterized by chromosomal instability and showing that aneuploidy-driven malignancies are not necessarily chromosomally heterogeneous. Furthermore, most chromosomal gains are present in all leukemic cells, suggesting that they arose early during leukemogenesis. Copy number data from 577 primary cases reveals selective pressures that were used for in silico modeling of aneuploidy development. This shows that the aneuploidy in HeH ALL likely arises by an initial tripolar mitosis in a diploid cell followed by clonal evolution, in line with a punctuated evolution model.
Topics: Humans; Aneuploidy; Chromosome Aberrations; Precursor Cell Lymphoblastic Leukemia-Lymphoma; Diploidy; Chromosomal Instability
PubMed: 36966135
DOI: 10.1038/s41467-023-37356-5 -
Trends in Neurosciences Dec 2018The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence... (Review)
Review
The benefits of diploidy are considered to involve masking partially recessive mutations and increasing genetic diversity. Here, we review new studies showing evidence for diverse allele-specific expression and epigenetic states in mammalian brain cells, which suggest that diploidy expands the landscape of gene regulatory and expression programs in cells. Allele-specific expression has been thought to be restricted to a few specific classes of genes. However, new studies show novel genomic imprinting effects that are brain-region-, cell-type- and age-dependent. In addition, novel forms of random monoallelic expression that impact many autosomal genes have been described in vitro and in vivo. We discuss the implications for understanding the benefits of diploidy, and the mechanisms shaping brain development, function, and disease.
Topics: Alleles; Animals; Brain; Diploidy; Epigenomics; Gene Expression Regulation; Humans
PubMed: 30098802
DOI: 10.1016/j.tins.2018.07.005 -
Vaccine Aug 2022Shorter rabies pre-exposure prophylaxis (PrEP) regimens may offer improved convenience and feasibility over classic 3-week regimens, for example in regions with poor... (Randomized Controlled Trial)
Randomized Controlled Trial
One-week intramuscular or intradermal pre-exposure prophylaxis with human diploid cell vaccine or Vero cell rabies vaccine, followed by simulated post-exposure prophylaxis at one year: A phase III, open-label, randomized, controlled trial to assess immunogenicity and safety.
Shorter rabies pre-exposure prophylaxis (PrEP) regimens may offer improved convenience and feasibility over classic 3-week regimens, for example in regions with poor access to vaccines or for travelers to rabies-endemic regions. In this multicenter, open-label, controlled trial, 570 healthy participants aged 2-64 years were randomized to receive: 1-week PrEP (vaccination days [D]0 and 7; Group 1) or classic 3-week PrEP regimen (D0, D7, and D21; Group 2) with one 1.0 mL intramuscular [IM] dose of human diploid cell culture rabies vaccine (HDCV) at each visit; 1-week PrEP with two 0.1 mL intradermal (ID) HDCV doses at each visit (Group 3); or 1-week PrEP with one 0.5 mL IM dose (Group 4) or two 0.1 mL ID doses (Group 5) of Vero cell rabies vaccine (PVRV) at each visit. Participants received simulated post-exposure prophylactic (PEP) vaccination (two IM or ID doses of HDCV or PVRV three days apart) one year later. Rabies virus neutralizing antibody titers and seroconversion (titers ≥ 0.5 IU/mL) rates were assessed 14 days and up to 1 year post-PrEP, and pre- and post-PEP. Safety was assessed throughout the study. Seroconversion rates were high 14 days post-last PrEP injection (ranging from 96.7 % to 97.2 % across groups 1, 3-5; 1-week PrEP) and reached 100 % in Group 2 (3-week PrEP). Non-inferiority of Group 1 versus Group 2 in terms of seroconversion rates 14 days post-last PrEP injection (primary objective) was not demonstrated. After simulated PEP, all groups showed rapid and robust immune responses, with all but one participant achieving seroconversion (titers ≥ 0.5 IU/mL). There were no safety concerns, and the tolerability profiles of the vaccines were similar across the groups. A 1-week, IM or ID PrEP regimen with HDCV or PVRV provided efficacious priming, enabling rapid robust anamnestic responses to simulated PEP 1 year later across age groups. ClinicalTrials.gov number: NCT03700242. WHO Universal Trial Number (UTN): U1111-1183-5743.
Topics: Animals; Antibodies, Viral; Chlorocebus aethiops; Diploidy; Humans; Injections, Intradermal; Post-Exposure Prophylaxis; Pre-Exposure Prophylaxis; Rabies; Rabies Vaccines; Rabies virus; Vaccination; Vero Cells
PubMed: 35933278
DOI: 10.1016/j.vaccine.2022.07.037 -
Bioinformatics (Oxford, England) Jul 2023Diploid assembly, or determining sequences of homologous chromosomes separately, is essential to elucidate genetic differences between haplotypes. One approach is to...
MOTIVATION
Diploid assembly, or determining sequences of homologous chromosomes separately, is essential to elucidate genetic differences between haplotypes. One approach is to call and phase single nucleotide variants (SNVs) on a reference sequence. However, this approach becomes unstable on large segmental duplications (SDs) or structural variations (SVs) because the alignments of reads deriving from these regions tend to be unreliable. Another approach is to use highly accurate PacBio HiFi reads to output diploid assembly directly. Nonetheless, HiFi reads cannot phase homozygous regions longer than their length and require oxford nanopore technology (ONT) reads or Hi-C to produce a fully phased assembly. Is a single long-read sequencing technology sufficient to create an accurate diploid assembly?
RESULTS
Here, we present JTK, a megabase-scale diploid genome assembler. It first randomly samples kilobase-scale sequences (called 'chunks') from the long reads, phases variants found on them, and produces two haplotypes. The novel idea of JTK is to utilize chunks to capture SNVs and SVs simultaneously. From 60-fold ONT reads on the HG002 and a Japanese sample, it fully assembled two haplotypes with approximately 99.9% accuracy on the histocompatibility complex (MHC) and the leukocyte receptor complex (LRC) regions, which was impossible by the reference-based approach. In addition, in the LRC region on a Japanese sample, JTK output an assembly of better contiguity than those built from high-coverage HiFi+Hi-C. In the coming age of pan-genomics, JTK would complement the reference-based phasing method to assemble the difficult-to-assemble but medically important regions.
AVAILABILITY AND IMPLEMENTATION
JTK is available at https://github.com/ban-m/jtk, and the datasets are available at https://doi.org/10.5281/zenodo.7790310 or JGAS000580 in DDBJ.
Topics: Diploidy; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing; Genome; Genomics; Haplotypes
PubMed: 37354526
DOI: 10.1093/bioinformatics/btad398 -
Microbiology Spectrum Aug 2023Within Eukaryotes, fungi are the typical representatives of haplontic life cycles. Basidiomycota fungi are dikaryotic in extensive parts of their life cycle, but diploid...
Within Eukaryotes, fungi are the typical representatives of haplontic life cycles. Basidiomycota fungi are dikaryotic in extensive parts of their life cycle, but diploid nuclei are known to form only in basidia. Among Basidiomycota, the Pucciniales are notorious for presenting the most complex life cycles, with high host specialization, and for their expanded genomes. Using cytogenomic (flow cytometry and cell sorting on propidium iodide-stained nuclei) and cytogenetic (FISH with rDNA probe) approaches, we report the widespread occurrence of replicating haploid and diploid nuclei (i.e., 1C, 2C and a small proportion of 4C nuclei) in diverse life cycle stages (pycnial, aecial, uredinial, and telial) of all 35 Pucciniales species analyzed, but not in sister taxa. These results suggest that the Pucciniales life cycle is distinct from any cycle known, i.e., neither haplontic, diplontic nor haplodiplontic, corroborating patchy and disregarded previous evidence. However, the biological basis and significance of this phenomenon remain undisclosed. Within Eukaryotes, fungi are the typical representatives of haplontic life cycles, contrasting with plants and animals. As such, fungi thus contain haploid nuclei throughout their life cycles, with sexual reproduction generating a single diploid cell upon karyogamy that immediately undergoes meiosis, thus resuming the haploid cycle. In this work, using cytogenetic and cytogenomic tools, we demonstrate that a vast group of fungi presents diploid nuclei throughout their life cycles, along with haploid nuclei, and that both types of nuclei replicate. Moreover, haploid nuclei are absent from urediniospores. The phenomenon appears to be transversal to the organisms in the order Pucciniales (rust fungi) and it does not occur in neighboring taxa, but a biological explanation or function for it remains elusive.
Topics: Animals; Diploidy; Basidiomycota; Fungi; Life Cycle Stages; Meiosis
PubMed: 37289058
DOI: 10.1128/spectrum.01532-23