-
BMC Plant Biology Nov 2019Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the...
BACKGROUND
Intergenomic gene transfer (IGT) between nuclear and organellar genomes is a common phenomenon during plant evolution. Gossypium is a useful model to evaluate the genomic consequences of IGT for both diploid and polyploid species. Here, we explore IGT among nuclear, mitochondrial, and plastid genomes of four cotton species, including two allopolyploids and their model diploid progenitors (genome donors, G. arboreum: A and G. raimondii: D).
RESULTS
Extensive IGT events exist for both diploid and allotetraploid cotton (Gossypium) species, with the nuclear genome being the predominant recipient of transferred DNA followed by the mitochondrial genome. The nuclear genome has integrated 100 times more foreign sequences than the mitochondrial genome has in total length. In the nucleus, the integrated length of chloroplast DNA (cpDNA) was between 1.87 times (in diploids) to nearly four times (in allopolyploids) greater than that of mitochondrial DNA (mtDNA). In the mitochondrion, the length of nuclear DNA (nuDNA) was typically three times than that of cpDNA. Gossypium mitochondrial genomes integrated three nuclear retrotransposons and eight chloroplast tRNA genes, and incorporated chloroplast DNA prior to divergence between the diploids and allopolyploid formation. For mitochondrial chloroplast-tRNA genes, there were 2-6 bp conserved microhomologies flanking their insertion sites across distantly related genera, which increased to 10 bp microhomologies for the four cotton species studied. For organellar DNA sequences, there are source hotspots, e.g., the atp6-trnW intergenic region in the mitochondrion and the inverted repeat region in the chloroplast. Organellar DNAs in the nucleus were rarely expressed, and at low levels. Surprisingly, there was asymmetry in the survivorship of ancestral insertions following allopolyploidy, with most numts (nuclear mitochondrial insertions) decaying or being lost whereas most nupts (nuclear plastidial insertions) were retained.
CONCLUSIONS
This study characterized and compared intracellular transfer among nuclear and organellar genomes within two cultivated allopolyploids and their ancestral diploid cotton species. A striking asymmetry in the fate of IGTs in allopolyploid cotton was discovered, with numts being preferentially lost relative to nupts. Our results connect intergenomic gene transfer with allotetraploidy and provide new insight into intracellular genome evolution.
Topics: Cell Nucleus; DNA, Plant; Diploidy; Evolution, Molecular; Genome, Chloroplast; Genome, Mitochondrial; Genome, Plant; Genome, Plastid; Gossypium; Recombination, Genetic; Tetraploidy
PubMed: 31718541
DOI: 10.1186/s12870-019-2041-2 -
The Science of the Total Environment Dec 2018The effects of different concentrations of copper sulfate on diploid and triploid fin cell lines (named DIMF and TRMF, respectively) in Misgurnus anguillicaudatus were...
The effects of different concentrations of copper sulfate on diploid and triploid fin cell lines (named DIMF and TRMF, respectively) in Misgurnus anguillicaudatus were studied. The LC of copper sulfate estimated by an MTT assay was 268.39 in DIMF cells, and 311.54 μmol/L in TRMF cells, respectively. Activity of superoxide dismutase (SOD) in DIMF cells gradually increased as the concentration of copper sulfate increased (up to 200 μmol/L), and then gradually decreased. SOD activity in triploid loach fin cells, as well as glutathione peroxidase (GSH-Px) and glutathione-S-transferase (GST) activity in both diploid and triploid cells, decreased as the concentration of copper sulfate increased, which suggested that excessive copper exposure at the concentrations tested in this study was detrimental to anti-oxidative capability. In general, SOD, GST and GSH-Px activity was higher in triploid fin cells than in diploid cells. DNA breaks were observed by comet assays after 24 h exposure to 400 and 800 μM copper; DNA percent in the comet's tail was lower in TRMF than in DIMF. Ultrastructurally, there were no significant differences in the organelles of both cells, although a higher number of vesicles were observed in TRMF cells after copper exposure. Pathological changes induced by copper sulfate were similar in DIMF and TRMF cells, and were indicative of cell necrosis. Results above suggested that excessive copper sulfate exposure would lead to antioxidant enzymes activity reduction, along with antioxidant defenses disruption and superoxide radicals increasing, and then to DNA damage, ultrastructural changes and necrosis features in DIMF and TRMF M. anguillicaudatus fin cells. Triploid cell lines had higher resistance to copper than their diploid counterparts especially at higher concentrations of copper due to larger cells and higher intracellular content of detoxification enzymes to resist the toxicity of heavy metals.
Topics: Animal Fins; Animals; Cell Line; Copper; Copper Sulfate; Cypriniformes; Diploidy; Superoxide Dismutase; Toxicity Tests; Triploidy; Water Pollutants, Chemical
PubMed: 30189558
DOI: 10.1016/j.scitotenv.2018.06.315 -
Seminars in Cancer Biology Jun 2022We have presented an in vitro trackable model system, atavistic induced from conservation in our genome, which strongly is applicable to tumorigenesis start and... (Review)
Review
We have presented an in vitro trackable model system, atavistic induced from conservation in our genome, which strongly is applicable to tumorigenesis start and evolution. The inducing factor was death signals to proliferating normal human cells (primary cell strains), which respon-ded by a special type of tetraploidization, chromosomes with 4-chromatids (diplochromosomes, earlier described in cancer cells). The response included cell cycle stress, which prolonged S-period with result of mitotic slippage process, forming the special 4n cells by re-replication of diploid cells, which showed cell division capability to unexpected, genome reduced diploid cells which remarkably, showed fitness gain. This unique response through cell cycle stress and mitotic slippage process was further discovered to be linked to a rather special characteristic of the, 4n nucleus. The nucleus turned, self-inflicted, 90° perpendicular to the cell's cytoskeleton axis, importantly, before the special 4n-division system produced genome reduce diploid cells, we call "first cells", because of fitness gain. These 2n cells also showed the nuclear dependent 90° turn, which in both cases was associated with cells gaining cell shape changes, herein illustrated from normal fibroblastic cells changing to roundness cells, indistinguishable from todays' diagnostic cancer cell morphology. This 3-D ball-like cell shape, in metastasis, sque-ezing in and out between (?) endothelial cells in the lining of blood veins during disbursement, would be advantageous.
Topics: Cell Cycle; Cell Shape; Diploidy; Endothelial Cells; Humans; Mitosis; Neoplasms
PubMed: 33440246
DOI: 10.1016/j.semcancer.2020.12.023 -
Nature Genetics Nov 2022
Topics: Repetitive Sequences, Nucleic Acid; Recombination, Genetic; Diploidy; DNA Transposable Elements
PubMed: 36333505
DOI: 10.1038/s41588-022-01218-5 -
ACS Infectious Diseases Oct 2020The new multidrug-resistant pathogen was first described in 2009 in Japan and has emerged in many countries worldwide. This human fungal pathogen has long been...
The new multidrug-resistant pathogen was first described in 2009 in Japan and has emerged in many countries worldwide. This human fungal pathogen has long been considered a haploid fungus. Here, we report the discovery of the diploid form and spontaneous ploidy shifts in clinical isolates of . Haploid and diploid cells of differ in several aspects including growth rates, virulence, and global gene expression profiles. For example, diploid cells exhibit a slower growth rate than haploid cells in culture media; however, they are more virulent than haploid cells in a mouse systemic infection model. Global transcriptional expression analysis demonstrates that both haploid and diploid cells express a set of ploidy-enriched genes, which are involved in the regulation of metabolism, cell wall maintenance, translation and DNA replication, and other important biological processes. Antifungal susceptibility testing shows that haploid and diploid cells exhibit similar responses when treated with a number of antifungals. Taken together, haploid and diploid cells may have different fitness responses to diverse niches, and ploidy changes could be an adaptive strategy of to environmental changes. Our findings shed new light on the biology and pathogenesis of this emerging fungal pathogen.
Topics: Antifungal Agents; Candida; Candidiasis; Diploidy; Humans; Virulence
PubMed: 32902947
DOI: 10.1021/acsinfecdis.0c00282 -
G3 (Bethesda, Md.) Aug 2022The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals....
The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.
Topics: Animals; Carps; Cell Nucleus; Diploidy; Genes, Mitochondrial; Triploidy
PubMed: 35924985
DOI: 10.1093/g3journal/jkac197 -
Proceedings of the National Academy of... Oct 2022Sexual reproduction is widespread in eukaryotes; however, only asexual reproduction has been observed in unicellular red algae, including , which branched early in...
Sexual reproduction is widespread in eukaryotes; however, only asexual reproduction has been observed in unicellular red algae, including , which branched early in Archaeplastida. possesses a small genome; it is polyextremophile, grows either photoautotrophically, mixotrophically, or heterotrophically, and is being developed as an industrial source of vitamins and pigments because of its high biomass productivity. Here, we show that exhibits a sexual life cycle, alternating between cell-walled diploid and cell wall-less haploid, and that both phases can proliferate asexually. The haploid can move over surfaces and undergo self-diploidization or generate heterozygous diploids through mating. Further, we prepared the whole genome and a comparative transcriptome dataset between the diploid and haploid and developed genetic tools for the stable gene expression, gene disruption, and selectable marker recycling system using the cell wall-less haploid. The BELL/KNOX and MADS-box transcription factors, which function in haploid-to-diploid transition and development in plants, are specifically expressed in the haploid and diploid, respectively, and are involved in the haploid-to-diploid transition in , providing information on the missing link of the sexual life cycle evolution in Archaeplastida. Four actin genes are differently involved in motility of the haploid and cytokinesis in the diploid, both of which are myosin independent and likely reflect ancestral roles of actin. We have also generated photosynthesis-deficient mutants, such as blue-colored cells, which were depleted in chlorophyll and carotenoids, for industrial pigment production. These features of facilitate the understanding of the evolution of algae and plants and the industrial use of microalgae.
Topics: Actins; Animals; Carotenoids; Chlorophyll; Diploidy; Genomics; Haploidy; Life Cycle Stages; Plants; Rhodophyta; Transcription Factors; Vitamins
PubMed: 36194630
DOI: 10.1073/pnas.2210665119 -
Journal of Comparative Physiology. B,... Jul 2021Ploidy level affects both the cell size and metabolic rate (MR) of organisms. The present study aimed to examine whether ploidy levels cause differences in cell surface...
Ploidy level affects both the cell size and metabolic rate (MR) of organisms. The present study aimed to examine whether ploidy levels cause differences in cell surface area (SA), MR and metabolic scaling. The resting MR (RMR), red blood cell SA (SA), red blood cell count (RBCC), gill SA (GSA), and ventilation frequency (VF) were measured in diploid and triploid common carp with different body masses (M). The results showed that both M and ploidy level affected the RMR, GSA, VF, and SA, with interactions between M and ploidy level. The triploids had larger SA but lower RBCC than those of the diploids. The SA increased weakly but significantly with increasing M, by an exponent of 0.043, in the triploids but did not increase in the diploids. The RMR of the triploids and diploids scaled with M, by exponents of 0.696 and 1.007, respectively. The RMR was higher in the triploids than the diploids. The GSA scaled with M, with an exponent of 0.906 in the triploids and an exponent of 1.043 in the diploids. The VF scaled with M by an exponent of - 0.305 in the triploids but showed no correlation with M in the diploids. The larger SA and RMR and smaller scaling exponents of both the GSA and VF of the triploids were consistent with the finding that the b was smaller in the triploids than in the diploids. This suggests that the ploidy-induced changes of SA and SA scaling affect the metabolic scaling of fish.
Topics: Animals; Carps; Diploidy; Gills; Respiration; Triploidy
PubMed: 33811547
DOI: 10.1007/s00360-021-01365-x -
The Journal of Experimental Biology Jan 2021Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen...
Being composed of small cells may carry energetic costs related to maintaining ionic gradients across cell membranes as well as benefits related to diffusive oxygen uptake. Here, we test the hypothesis that these costs and benefits of cell size in ectotherms are temperature dependent. To study the consequences of cell size for whole-organism metabolic rate, we compared diploid and triploid zebrafish larvae differing in cell size. A fully factorial design was applied combining three different rearing and test temperatures that allowed us to distinguish acute from acclimated thermal effects. Individual oxygen consumption rates of diploid and triploid larvae across declining levels of oxygen availability were measured. We found that both acute and acclimated thermal effects affected the metabolic response. In comparison with triploids, diploids responded more strongly to acute temperatures, especially when reared at the highest temperature. These observations support the hypothesis that animals composed of smaller cells (i.e. diploids) are less vulnerable to oxygen limitation in warm aquatic habitats. Furthermore, we found slightly improved hypoxia tolerance in diploids. By contrast, warm-reared triploids had higher metabolic rates when they were tested at acute cold temperature, suggesting that being composed of larger cells may provide metabolic advantages in the cold. We offer two mechanisms as a potential explanation of this result, related to homeoviscous adaptation of membrane function and the mitigation of developmental noise. Our results suggest that being composed of larger cells provides metabolic advantages in cold water, while being composed of smaller cells provides metabolic advantages in warm water.
Topics: Animals; Cell Size; Diploidy; Larva; Triploidy; Zebrafish
PubMed: 33257437
DOI: 10.1242/jeb.227124 -
Human Vaccines & Immunotherapeutics 2019The large-scale production of a human diploid cell (HDC) vaccine (HDCV) for rabies is limited by several technical challenges. Kanghua Biological Products Co., Ltd., has... (Randomized Controlled Trial)
Randomized Controlled Trial
The large-scale production of a human diploid cell (HDC) vaccine (HDCV) for rabies is limited by several technical challenges. Kanghua Biological Products Co., Ltd., has successfully used microcarrier technology for the large-scale culture of HDCs in bioreactors to develop a lyophilized and purified HDCV. In this blinded, randomized, parallel-group study conducted between July and October 2014 in Mianzhu, Sichuan Province, China, we monitored the safety and immunogenicity of this vaccine in a healthy population vaccinated according to the Essen post-exposure immunization schedule. A hamster kidney cell vaccine was used as the control. Adverse reactions were monitored 0.5, 6, 24, 48, and 72 h post vaccination to assess safety. Neutralizing antibodies in venous blood were measured on day 7, 14, and 72 to evaluate the immunogenicity of the vaccine while follow-up monitoring continued for 1 month. No serious adverse reactions were observed in any volunteer. The incidence rates of systemic and local adverse reactions were, respectively, 10.6% and 2.9% in the test group and 20.0% and 13.6% in the control group. After the third injection, the positive conversion rates of antibodies in the test and control groups were 100% and 98.82%, respectively. In addition, the average antibody titers on day 7, 14, and 42, were respectively, 1.71, 2.72, and 1.29 times higher than those in the control group. These results indicate that HDCV had a better safety profile and higher immunogenicity than the hamster kidney cell rabies vaccine. Trial registration number: 20130602.
Topics: Adult; Animals; Antibodies, Neutralizing; Antibodies, Viral; Cell Culture Techniques; Cricetinae; Diploidy; Female; Freeze Drying; Humans; Immunization Schedule; Immunogenicity, Vaccine; Injections, Intramuscular; Kidney; Male; Microspheres; Middle Aged; Rabies; Rabies Vaccines; Rabies virus
PubMed: 30457436
DOI: 10.1080/21645515.2018.1549450