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Polyploidization and localisation of poly(A)+ RNA in the different cell types of the vitellogenic meroistic ovary of the fleshfly, Sarcophaga bullata.

The degree of polyploidization, the level of transcriptional activity and the volume of the different cell types present in the meroistic ovary of Sarcophaga bullata were measured during different vitellogenic stages. The nurse cells and the germinal vesicle exhibited very pronounced differences with regard to DNA content and mRNA synthesis, even though they are genetically identical. During the 4C stage (late vitellogenesis), we observed different degrees of polyploidy in follicle cells adjacent to the oocyte and those surrounding the nurse cells. Although the chromatin of the germinal vesicle is condensed into a karyosome, in situ hybridisation revealed the presence of transcriptional activity. The volume of the germinal vesicle, which contains only 4C DNA, is big enough to contain 2048C DNA. The meroistic ovary is a highly polarized differentiating system. Our results are discussed in the light of the fact that the polytrophic ovary is a miniature electrophoresis chamber.

Animals

Genome-wide cyclin gene evolution in Arabidopsis and Brassica reveals polyploidization-driven duplication and flowering-time associations.

Cyclin genes are plant cell cycle regulators that play essential roles in growth, development, and reproduction. However, the evolutionary dynamics and genomic organization of cyclin genes across the Brassicaceae family remain poorly understood, particularly in the context of allotetraploid genome evolution. Here, we investigated the diversity, expansion mechanisms, and potential functional diversification of cyclin genes across ten Brassicaceae genomes, including four Arabidopsis and six Brassica species. A total of 1087 cyclin genes representing 23 cyclin types were identified. Comparative genomic analyses revealed that cyclin gene expansion was strongly influenced by polyploidization in Brassica species, with 1845 duplication events involving 1063 genes. Whole-genome duplication was the predominant mechanism driving expansion, while both inter- and intra-genomic duplications contributed to gene retention in tetraploid Brassica species, with the highest duplication frequency observed in Brassica juncea. Across genomes, 120 physical gene clusters were identified, including homogeneous and heterogeneous types. Ortholog analysis between progenitor and allotetraploid species identified 852 orthologous pairs involving 366 genes, indicating extensive conservation following allotetraploid formation. Phylogenetic analysis resolved cyclins into three major clades, while expression-based clustering in Brassica napus grouped genes into four major clusters, suggesting functional diversification. Integration of pan-genomic and flowering-time QTL analyses further identified two cyclin genes, Bna21cycA2 and Bna113cycD4, which contain amino acid polymorphisms and represent putative candidate variations potentially associated with flowering-time variation across multiple genomes. These findings provide new insights into the evolutionary expansion, retention, and potential functional divergence of cyclin genes in Brassicaceae and highlight candidate loci for future functional studies and crop improvement.

Evolution, Molecular

Angiotensin evokes in polyploid rat glioma cells hyperpolarization-depolarization responses and cross-desensitization with bradykinin.

Angiotensins I, II and III induced a hyperpolarizing response of up to 1 min duration followed by a depolarizing response of up to 4 min when applied by pressure pulses or iontophoresis to polyploid rat glioma cells C6-4-2. The hyperpolarization (depolarization) was associated with a 50% decrease (no measurable change) in membrane resistance. The reversal potential (ca.-90 mV) of the hyperpolarization most likely points to an increase K+ conductance. Cells desensitized to angiotensins on application of high doses of either angiotensins or bradykinin.

Angiotensin II

A general treatment of chromosome synapsis in even-numbered polyploids.

Relationships between frequencies of fully paired pachytene configurations are examined for even-numbered polyploids, up to decaploids and beyond. Sequential association is assumed at any given number of equidistant synaptic sites showing uniform propensities for partner exchange. Only with two sites per chromosome, can each configuration represent an equal proportion of the nucleus. In the limit as the number of sites tends to infinity and the intervals between them tend to zero, pachytene multivalent frequency is seen to be a function of bivalent frequency, the minimum number of changes in pairing partner and ploidy. Each type of multivalent may represent the entire nucleus only in the lowest ploidy which can support it, thereafter becoming rare. Sets of homologous multivalents are never likely to be common and large multivalents are expected to be scarce, unless representing maximal configurations. Only bivalents can prevail at every even-numbered ploidy level. At constant bivalent frequency, the transition from discrete to continuous pairing favours the largest type of multivalent. These deductions provide a basis for investigations of the mechanics of chromosome synapsis and may lead to a comprehensive theory of genome analysis.

Cell Nucleus

Cytogenetic and molecular approaches of polyploidization in colorectal adenocarcinomas.

We present the cytogenetic analysis of 23 cases of polyploid colorectal adenocarcinomas. We took advantage of the high intratumoral heterogeneity of the karyotypes to identify clones, subclones, and cell-to-cell variations. This allowed us to reconstruct the chromosomal evolution of each tumor and to propose a schema of the chromosomal changes in relation to the endoreduplication process. All but one case were characterized by a relative deficiency of chromosomes 17p and 18. Other deficiencies affecting the late-replicating X, and to a lesser degree, 1p, 5q, 14, 15, 8p, 10, 21, and 4, and excesses affecting the early-replicating X, 8q, 13, 16, 17q, and 11 were frequently associated. This pattern of imbalances is very similar to that of the monosomic type previously described in near-diploid tumors. The pattern of the 23rd tumor corresponded to those of the trisomic type tumors. These data largely confirm the existence of two distinct processes of chromosomal evolution in colorectal adenocarcinomas, with a strong tendency to undergo endoreduplication for the monosomic type near-diploid tumors. To correlate cytogenetic and molecular data, allelic losses analyses were investigated for probes of chromosomes 17p and 18. In all 12 informative tumors, a loss of heterozygosity for probes of the short arm of chromosome 17 indicated the occurrence of a rearrangement of chromosome 17 before the endoreduplication. The same was true for allelic losses for probes of chromosome 18 found in 11 of 12 informative tumors. The correlation between cytogenetic and molecular data is thus excellent and indicates that losses of 17p and 18 are early events in the tumor process.

Adenocarcinoma

Metabolic utilization of diets by polyploid rainbow trout (Salmo gairdneri).

1. Nitrogen (NH4) excretion and oxygen consumption were measured in four groups of juvenile rainbow trout (36-40 g): triploids obtained by a heat shock treatment (3n); triploids obtained by mating diploid females with tetraploid males (3n/4n); tetraploids (4n) and a diploid control (2n). 2. No differences in daily N excretion patterns and in N excretion rate measured as a percentage of N intake were detected between groups. 3. Oxygen consumption of the 2n group was significantly inferior to that of the 3n and 4n groups but not to the 3n/4n group. 4. SDA, specific dynamic action (measured as a percentage of the energy intake), ranged from 5.6 to 8.6% and was not different between groups. 5. Protein energy catabolism measured as per cent of total energy expenditure was significantly higher in the 2n group than in polyploid groups.

Ammonia

Ribosomal RNA structure in the diploid and phylogenetically polyploid amphibian species Hyla and Odontophrynus.

Ribosomal RNA of the diploid amphibian species Hyla chrysoscelis and Odontophrynus americanus is structurally modified by hidden breaks. Phylogenetically polyploid related species like the tetraploid Hyla versicolor, the tetraploid Odontophrynus americanus and the octoploid Ceratophrys ornata do not show hidden breaks in ribosomal RNA. Structural modifications of rRNA molecules in diploid amphibians has no detectable effect on the ribosomal activity in vitro.

Amphibians

Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.

Cereal genomes have undergone repeated polyploidization and transposable element (TE) proliferation, collectively generating complex regulatory landscapes. However, the evolutionary trajectories and functional implications of these landscapes remain largely unexplored. Using chromatin-bound RNA sequencing across seven cereal species, we systematically mapped 45,952 regulatory element transcripts (RETs), including 32,867 distal RETs corresponding to enhancer RNAs (eRNAs). Our analysis revealed that 56% of lineage-specific eRNAs originated from TE expansions, indicating that TEs serve as major reservoirs of species-specific regulatory innovation in cereals. Notably, we identified remarkable conservation in defense-related functions, root-specific expression, and TE-derived origins of eRNAs across both ancient and recent evolutionary layers of Triticeae, suggesting recurrent recruitment of TE-derived, root-associated regulatory elements throughout Triticeae evolution. Furthermore, we found that young eRNA pairs in hexaploid wheat with high sequence similarity, many originating from RLG_famc8.3 and DTC_famc4.3, exhibited pronounced root specificity and coordinated expression, suggesting targeted amplification and refinement of successful ancestral regulatory strategies established after Triticeae divergence. To facilitate community access, we developed Cereal-eRNAdb (http://bioinfo.cemps.ac.cn/Cereal-eRNAdb/), a comprehensive database integrating 69,426 eRNAs with functional annotations across 296 samples. Our findings suggest that TE-mediated innovation of root-specific eRNAs may contribute to Triticeae adaptation and provide a foundational resource for exploiting regulatory variation in cereal crop breeding.

Enhancer RNAs

Placental polyploidization: a comparative study in the mouse and the guinea pig.

The trophoblastic and endodermal tissues of the guinea pig were cytophotometrically examined at two stages of development, either shortly after the primary trophoblastic giant cell layer had degenerated (Sansom and Hill, 1931) and the visceral yolk sac was starting to form (Kaufman and Davidoff, 1977) (c. 10.5 days p.c. at the egg cylinder stage) or later in gestation, when the yolk sac was well developed (c. 17.5 days p.c. at the neural tub closure stage). Subsequently, the trophoblastic and endodermal tissues of the mouse were analysed in a manner identical to those of the guinea pig. Finally, the nuclear DNA content values from the analysis of the tissues of each species were compared. The results thus obtained indicate firstly that, in the guinea pig, polyploid nuclei also appear within visceral endoderm after the primary trophoblastic giant cells degenerate and, secondly, that placental specialization in the rodents, as originally defined by Mossman (1937), apparently tends towards lower levels of polyploidy within trophoblast and higher levels within the derivatives of visceral endoderm.

Animals

Comparative transmission genetics of introgressed chromatin in reciprocal advanced backcross populations in Gossypium (cotton) polyploids.

Introgression is a potential source of valuable genetic variation and interspecific introgression lines are important resources for plant breeders to access novel alleles. Experimental advanced-generation backcross populations contain individuals with genomic compositions similar to those resulting from natural interspecific hybridization and provide opportunities to study the nature and transmission pattern of donor chromatin in recipient genomes. Here, we analyze transmission of donor chromatin in reciprocal backcrosses between G. hirsutum and G. barbadense. Across the genome, recurrent backcrossing in both backgrounds yielded donor chromatin at slightly higher frequencies than the Mendelian expectation in BC5F1 plants, while the average frequency of donor alleles in BC5F2 segregating families was less than expected. In the two subgenomes of polyploid cotton, the rate of donor chromatin introgression was similar. Although donor chromatin was tolerated over much of the recipient genomes, 21 regions recalcitrant to donor alleles were identified. Only limited correspondence is observed between the recalcitrant regions in the two backgrounds, suggesting the effect of species background on introgression of donor segments. Genetic breakdown was progressive, with floral abscission and seed inviability ongoing during backcrossing cycles. Regions of either high or low introgression tended to be in terminal chromosomal regions that are generally rich in both genes and crossover events, with long stretches around the centromere having limited crossover activity resulting in relatively constant low introgression frequencies. Constraints on fixation and selection of donor alleles highlights the challenges of utilizing introgression breeding in crop improvement.

Humans

Inhibition of DNA topoisomerase II by ICRF-193 induces polyploidization by uncoupling chromosome dynamics from other cell cycle events.

ICRF-193, a novel noncleavable, complex-stabilizing type topoisomerase (topo) II inhibitor, has been shown to target topo II in mammalian cells (Ishida, R., T. Miki, T. Narita, R. Yui, S. Sato, K. R. Utsumi, K. Tanabe, and T. Andoh. 1991. Cancer Res. 51:4909-4916). With the aim of elucidating the roles of topo II in mammalian cells, we examined the effects of ICRF-193 on the transition through the S phase, when the genome is replicated, and through the M phase, when the replicated genome is condensed and segregated. Replication of the genome did not appear to be affected by the drug because the scheduled synthesis of DNA and activation of cdc2 kinase followed by increase in mitotic index occurred normally, while VP-16, a cleavable, complex-stabilizing type topo II inhibitor, inhibited all these processes. In the M phase, however, late stages of chromosome condensation and segregation were clearly blocked by ICRF-193. Inhibition at the stage of compaction of 300-nm diameter chromatin fibers to 600-nm diameter chromatids was demonstrated using the drug during premature chromosome condensation (PCC) induced in tsBN2 baby hamster kidney cells in early S and G2 phases. In spite of interference with M phase chromosome dynamics, other mitotic events such as activation of cdc2 kinase, spindle apparatus reorganization and disassembly and reassembly of nuclear envelopes occurred, and the cells traversed an unusual M phase termed "absence of chromosome segregation" (ACS)-M phase. Cells then continued through further cell cycle rounds, becoming polyploid and losing viability. This effect of ICRF-193 on the cell cycle was shown to parallel that of inactivation of topo II on the cell cycle of the ts top2 mutant yeast. The results strongly suggest that the essential roles of topo II are confined to the M phase, when the enzyme decatenates intertwined replicated chromosomes. In other phases of the cycle, including the S phase, topo II may thus play a complementary role with topo I in controlling the torsional strain accumulated in various genetic processes.

Animals

Reduced proliferative activity of polyploid cells in primary hepatocellular carcinoma.

The proliferative activity of tumor cells differing in DNA content (ploidy) and nuclearity was investigated in primary hepatocellular carcinomas of the rat by flow cytometric analysis of collagenase-isolated cells immunostained after labelling with bromodeoxyuridine (BrdU) in vivo. The diploid cell fraction in these euploid tumours was higher than in normal liver, and the rate of binucleation as well as the proliferative activity of the binuclear cells was very low. The highest proliferative activity (BrdU labelling index) was found among the diploid tumour cells. The activity in mononuclear tetraploid and octoploid cells was reduced in inverse proportion to their increasing DNA content, possibly suggesting a loss of proliferative potential associated with polyploidization. There was a significant correlation between the proliferative activity of hepatocellular carcinoma cells and nonparenchymal liver cells in the different tumours, indicating that different cell types within a tumour may respond to common growth stimuli. Treatment of tumour-bearing rats with a promoting carcinogen (2-acetylaminofluorene) resulted in significant stimulation of tumour cell proliferation (all ploidy classes), whereas the proliferation of non-parenchymal (stromal) cells in the tumour was slightly inhibited.

2-Acetylaminofluorene

A high-quality draft genome assembly of Johnsongrass illuminates relationships between polyploidization, crop-wild hybridization, and reproductive biology.

Johnsongrass [Sorghum halepense (L.) Pers.] is an allopolyploid, rhizomatous, perennial grass species and one of the most troublesome weeds in global agriculture. We assembled the first Johnsongrass genome to clarify poorly understood genetic factors influencing variable rates of crop-wild hybridization with cultivated sorghum [S. bicolor (L.) Moench]. The draft genome assembly has a total size of 3.26 Gb and BUSCO completeness of 95.3%. We also report the first evolutionary analysis of INHIBITION OF ALIEN POLLEN (IAP), the only known cross-(in)compatibility locus in the genus. Our results reveal an evolutionary history of genome instability, including the loss of distinct parental subgenomes, and suggest that Nebraska accession 'J-37,' the genome donor, is a segmental allotetraploid that may function as a diploid or aneuploid during meiosis. Genome instability could explain observations of variable ploidies in Johnsongrass and facilitate ongoing hybridization with sorghum where gamete ploidies and IAP alleles match. Given this information, we provide a suggested research framework for studying evolution and gene expression in the Sorghum genus where crop-wild hybridization occurs and for predicting the potential for hybridization between specific crossing partners. Collectively, this work will bolster efforts to study and manage reproductive biology in other crop-wild polyploid complexes.

Sorghum

Chromosome differentiation and pairing behavior of polyploids: an assessment on preferential metaphase I associations in colchicine-induced autotetraploid hybrids within the genus Secale.

Preferential chromosome association at metaphase I has been analyzed and compared in autotetraploid cells obtained by colchicine treatment of hybrid diploid rye plants with different degrees of chromosomal divergence between homologs. The tendency to identical over homologous, but not identical, pairing preferences detected when homologous partners are contributed by less related parental lines indicates that chromosome differentiation may play an important role on preferential pairing behavior of polyploids. However, associations between more similar (identical) partners are not always favored, thus suggesting that additional factors must be considered. Other hypotheses for explaining pairing preferences in competitive situations are discussed. No clear relationship has been found between multivalent frequencies at metaphase I and chromosome differentiation between homologs or preferential pairing behavior. Therefore evolutionary divergences among related genomes should be carefully stated when evaluated from metaphase I configuration frequencies.

Chromosomes

Fine physical mapping of Ph1, a chromosome pairing regulator gene in polyploid wheat.

The diploid-like chromosome pairing in polyploid wheat is controlled by the Ph1 (pairing homoeologous) gene that is located on chromosome arm 5BL. By using a combination of cytogenetic and molecular techniques, we report the physical location of the Ph1 gene to a submicroscopic chromosome region (Ph1 gene region) that is flanked by the breakpoints of two deletions (5BL-1 and ph1c) and is marked by a DNA probe (XksuS1). The Ph1 gene region is present distal to the breakpoint of deletion 5BL-1 but proximal to the C-band 5BL2.1. Two other DNA probes (Xpsr128 and Xksu75) flank the region-Xpsr128 being proximal and Xksu75 being distal. The estimated size of the region is less than 3 Mb. The chromosome region around the Ph1 gene is high in recombination as the genetic distance of the region between 5BL-1 breakpoint and C-band 5BL2.1 (not resolved by the microscope) is at least 9.3 cM.

Chromosome Banding

Sex determination in polyploids of Caenorhabditis elegans.

In Caenorhabditis elegans triploid animals with two X chromosomes (symbolized 3A;2X) are males. However, these triploid males can be feminized by making them mutant for recessive dosage compensation mutations, by adding X chromosome duplications or by microinjecting particular DNA sequences termed feminizing elements. None of these treatments affects diploid males. This study explores several aspects of these treatments in polyploids. The dosage compensation mutants exhibit a strong maternal effect, such that reduction of any of the dosage compensation gene functions in the mother leads to sex reversal of 3A;2X animals. Likewise, all X chromosome duplications tested cause both sex reversal and intersexual development of many 3A;2X animals. Microinjected feminizing element DNA does not cause extensive sex reversal, but does result in intersexual development in 3A;2X animals. Neither X chromosome duplications nor microinjected feminizing elements show that extreme maternal effect of the dosage compensation mutants, although there is indirect evidence for a maternal effect of the feminizing elements. In particular, very little feminizing element DNA needs to be microinjected in order to feminize triploid males, far less than what is needed for stable inheritance, implying that feminizing elements can work within the mother's gonad. However, even very high concentrations of microinjected feminizing elements do not affect sex determination in diploid males, suggesting that they are not part of the numerator of the X/A ratio. In addition, no pair of X chromosome duplications feminizes diploid males, suggesting that none of these duplications contains a numerator of the X/A ratio. Instead, I infer that an X-linked locus, as yet undefined, must be present in two copies for hermaphrodite development to ensue or that the two X chromosomes might interact.

Animals

Sex determination and polyploid gigantism in the dwarf surfclam (Mulinia lateralis Say).

Mulinia lateralis, the dwarf surfclam, is a suitable model for bivalve genetics because it is hardy and has a short generation time. In this study, gynogenetic and triploid M. lateralis were successfully induced. For gynogenesis, eggs were fertilized with sperm irradiated with ultraviolet light and subsequently treated with cytochalasin B to block the release of the second polar body (PB2). Triploidy was induced by blocking PB2 in normally fertilized eggs. The survival of gynogenetic diploids was very low, only 0.7% to 8 days post-fertilization (PF), compared with 15.2% in the triploid groups and 27.5% in the normal diploid control. Larvae in all groups metamorphosed at 8-10 days PF, and there was no significant post-larval mortality. At sexual maturation (2-3 months PF), all gynogenetic diploids were female, and there was no significant difference (P > 0.05) in sex ratio between diploids and triploids. These results suggested that the dwarf surfclam may have an XX-female, XY-male sex determination with Y-domination. Compared with diploids, triploids had a relative fecundity of 59% for females and 80% for males. Eggs produced by triploid females were 53% larger (P < 0.001) in volume than those from diploid females. In both length and weight measurements at three months PF, the gynogenetic diploids were not significantly (P > 0.33) different from normal diploid females, suggesting that inbreeding depression was minimal in meiosis II gynogens. Triploid clams were significantly larger (P < 0.001) than normal diploids. We hypothesize that the increased body-size in triploids was caused by a polyploid gigantism due to the increased cell volume and a lack of cell-number compensation.

Animals

Genetic polymorphism and evolution in parthenogenetic animals. II. Diploid and polyploid Solenobia triquetrella (Lepidoptera: Psychidae).

Genic polymorphism at sixteen enzyme loci of four different chromosomal races of Solenobia triquetrella (bisexual, two diploid parthenogenetic races and tetraploid parthenogentiic) has been studied by starch gel electrophoresis. Isolated small diploid bisexual populations have rather uniform allele frequencies at all loci which we have studied. Diploid and tetraploid parthenogenetic individuals of this species are in general as heterozygous as bisexual ones. All parthenogenetic local populations are different from each other in the Alps. These parthenogenetic genotypes cannot be derived from a common ancestor through single mutations but rather bear evidence for a polyphyletic origin of parthenogenesis in Solenobia triquetrella. In the marginal distribution areas of the species in northern Europe single genotypes are spread over far larger areas than in the mountain regions of central Europe. This may be due to the old origin of parthenogenesis and polyploidy in northern Europe. No new parthenogenetic and polyploid strains have lately arisen in the regions outside of the Alps.

Alcohol Oxidoreductases