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PubMed2006

Phylogenetic networks from multi-labelled trees.

It is now quite well accepted that the evolutionary past of certain species is better represented by phylogenetic networks as opposed to trees. For example, polyploids are typically thought to have resulted through hybridization and duplication, processes that are probably not best represented as bifurcating speciation events. Based on the knowledge of a multi-labelled tree relating collection of polyploids, we present a canonical construction of a phylogenetic network that exhibits the tree. In addition, we prove that the resulting network is in some well-defined sense a minimal network having this property.

Algorithms↗
PubMed2004

An efficient mannose selection protocol for tomato that has no adverse effect on the ploidy level of transgenic plants.

A protocol for Agrobacterium-mediated transformation with mannose selection was developed for cotyledon petiole, hypocotyl and leaf explants of tomato (Lycopersicon esculentum L. Mill). More than 400 transgenic plants from three tomato varieties were selected with 1% mannose in combination with 0.1-0.5% glucose. Average transformation frequencies ranged from 2.0 to 15.5% depending on the construct, genotype and type of tissue used for transformation. The highest transformation rate was obtained for hypocotyl explants from tomato variety SG048. The ploidy levels of 264 independent transgenic events and 233 non-transgenic plants regenerated from tissue culture were assessed by flow cytometry. The incidence of polyploids within the total population of transgenic plants varied from 10 to 78% and was not significantly different from the non-transgenic population. The greatest variation in the proportion of polyploids was observed in plants derived from different explant types, both in transgenic and non-transgenic regenerants, across three studied genotypes. Transgenic and non-transgenic plants regenerated from leaves included the highest number of normal diploid plants (82-100%), followed by cotyledon petiole-derived plants (63-78%). Transgenic plants produced from hypocotyls contained 22-58% diploids depending on the genotype used in transformation. Results described in this study demonstrate that, although transformation frequencies for leaf tissue are still lower under current protocols, the high percentage of diploids obtained make leaf tissue an attractive transformation target.

Agrobacterium tumefaciens↗
PubMed1998

Segregational fidelity of chromosomes in human thyroid tumour cells.

Using fluorescence in situ hybridisation (FISH) we have analysed the segregational fidelity of all the human chromosomes during mitotic cell division. The losses and gains of chromosomes were analysed in human polyploid cell lines derived from a well-differentiated papillary thyroid cancer. These thyroid cells can be cultured for more than 300 population doublings. For the purpose of our study the polyploid nature of the cells may act as a protective buffer against the cell-lethal effects of the loss of individual chromosomes. To evaluate the role of the p53 gene product in maintaining the fidelity of chromosome segregation we compared the frequencies of chromosome loss and gain in cultures with wild-type p53 activity (K1E7neo3) and cultures transfected with plasmids expressing a mutant p53 product (K1E7scx6). Cultures were analysed for the presence of both structurally normal and rearranged chromosomes at both early and late passages. Cell cultures with defective p53 activity showed progressive chromosome loss from a median chromosome number of 87-97 to 75-86. Cell growth in cultures with wild-type p53 activity showed the loss of chromosomes 6, 7, and 8 and the gain of 17 and 20. Cultures expressing mutant p53 activity showed the loss of chromosomes 2, 5, 14 and 17 and the gain of 4 and 22. The combination of defective p53 and growth resulted in further destabilisation with the additional losses of chromosomes 3, 11, 15, 16 and 21. Chromosomes 1, 9, 10, 12, 13, 18, 19, X and Y segregated stably under all the culture conditions as did the structurally rearranged marker chromosomes. The study has demonstrated variation in the fidelity of mitotic chromosome segregation and the influence of p53 gene activity upon the segregation of individual human chromosomes.

Chromosome Segregation↗
PubMed2003

Developmental changes in the ploidy of mouse implanting trophoblast cells in vitro.

Shortly after the onset of implantation, polar mouse trophoblast cells proliferate and give rise to the ectoplacental cone, constituted by two distinct cell populations: undifferentiated, diploid cells and giant cells. Giant cells characteristically exhibit exaggerated dimensions and polyploid nuclei. In this study, we employ ectoplacental cones as a dynamic source of trophoblast giant cells to analyze cell proliferation, cell death, and ploidy under in vitro conditions. Our results show that DNA synthesis and the increase in the cell number are relevant only during the first 24 h of culture. Subsequently, DNA synthesis still occurs, mainly in the giant cell compartment, while the number of cells gradually decreases. Cell death by injury and apoptosis was also observed in the non-giant cell compartment of the ectoplacental cone. These findings suggest that the first 24 h of culture are crucial to the mitotic activity of the ectoplacental cone cells that gradually ceases, favoring the endoreduplication process. The DNA synthesis index during the subsequent experimental intervals emphasizes accumulation of DNA for the polyploidization. There was clear correlation between DNA content and nuclear dimension. The ploidy values for the trophoblast giant cells varied from 2C up to 368C in the giant cells, but were not as expressive as those known from in vivo conditions, probably due to the absence of regulatory factors specific to the embryonic-maternal interface. In situ hybridization and histochemistry for the nucleolus-organizing region showed that trophoblast nuclei have only two marker signals, indicative of a typical polytenic process. This present study elucidates important aspects of trophoblast behavior and provides new information on trophoblast physiology in vivo and in vitro.

Animals↗
PubMed1999

Tripolar acytokinetic mitosis and formation of feto-maternal syncytia in the bovine placentome: different modes of the generation of multinuclear cells.

The vast majority of trophoblast giant cells in the ruminant placenta are binuclear and are believed to derive from mononuclear trophoblastic cells by a single acytokinetic mitosis. There is no satisfactory explanation for the generation of the small proportion of trophoblast giant cells with one, three, or more nuclei. In this light-and electronmicroscopic study of bovine placentomal tissue from the second half of gestation, developmental stages of the trophoblast giant cells are investigated. Large mitotic figures indicate mitotic polyploidization, which is proposed to be due to two subsequent acytokinetic mitoses. Tripolar mitoses offer an explanation for the development of trinucleate trophoblast giant cells. Measurements of nuclear volumes in a series of semithin sections revealed that three size classes of trophoblast giant cells occur. The approximately doubling of nuclear volume between each class is thought to reflect different levels of DNA content that result from polyploidization in this cell type. Although trinuclear feto-maternal hybrid cells are the standard outcome of the fusion of binuclear trophoblast giant cells with uterine epithelial cells, some syncytia with at least five nuclei were observed in the uterine epithelium.

Animals↗
PubMed2003

Ectopic expression of the Suppressor of Underreplication gene inhibits endocycles but not the mitotic cell cycle in Drosophila melanogaster.

The Suppressor of Underreplication ( SuUR) gene contributes to the regulation of DNA replication in regions of intercalary heterochromatin in salivary gland polytene chromosomes. In the SuUR mutant these regions complete replication earlier than in wild type and, as a consequence, undergo full polytenization. Here we describe the effects of ectopic expression of SuUR using the GAL4-UAS system. We demonstrate that ectopically expressed SuUR exerts qualitatively distinct influences on polyploid and diploid tissues. Ectopic expression of SuUR inhibits DNA replication in polytene salivary gland nuclei, and reduces the degree of amplification of chorion protein genes that occurs in the follicle cell lineage. Effects caused by ectopic SuUR in diploid tissues vary considerably; there is no obvious effect on eye formation, but apoptosis is observed in the wing disc, and wing shape is distorted. The effect of ectopic SuUR expression is enhanced by mutations in the genes E2F and mus209 ( PCNA). Differential responses of polyploid and diploid cells to ectopic SuUR may reflect differences in the mechanisms underlying mitotic cell cycles and endocycles.

Animals↗
PubMed2003

Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags.

Single-nucleotide polymorphisms (SNPs) are useful markers for gene diagnosis and mapping of genes on chromosomes. However, polyploidy, which is characteristic of the evolution of higher plants, complicates the analysis of SNPs in the duplicated genes. We have developed a new method for SNP analysis in hexaploid wheat. First, we classified a large number of expressed sequence tags (ESTs) from wheat in silico. Those grouped into contigs were anticipated to correspond to transcripts from homoeologous loci. We then selected relatively abundant ESTs, and assigned these contigs to each of the homoeologous chromosomes using a nullisomic/tetrasomic series of Chinese Spring wheat strains in combination with pyrosequencing. The ninety genes assigned were almost evenly distributed into seven homologous chromosomes. We then created a virtual display of the relative expression of these genes. Expression patterns of genes from the three genomes in hexaploid wheat were classified into two major groups: (1) genes almost equally expressed from all three genomes; and (2) genes expressed with a significant preference, which changed from tissue to tissue, from certain genomes. In 11 cases, one of the three genes in the allopolyploid was found to be silenced. No preference for gene-silencing in particular genomes or chromosomes was observed, suggesting that gene-silencing occurred after polyploidization, and at the gene level, not at the chromosome or genome level. Thus, the use of this SNP method to distinguish the expression profiles of three homoeologous genes may help to elucidate the molecular basis of heterosis in polyploid plants.

Base Sequence↗
PubMed2005

Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations.

Triticeae species (including wheat, barley and rye) have huge and complex genomes due to polyploidization and a high content of transposable elements (TEs). TEs are known to play a major role in the structure and evolutionary dynamics of Triticeae genomes. During the last 5 years, substantial stretches of contiguous genomic sequence from various species of Triticeae have been generated, making it necessary to update and standardize TE annotations and nomenclature. In this study we propose standard procedures for these tasks, based on structure, nucleic acid and protein sequence homologies. We report statistical analyses of TE composition and distribution in large blocks of genomic sequences from wheat and barley. Altogether, 3.8 Mb of wheat sequence available in the databases was analyzed or re-analyzed, and compared with 1.3 Mb of re-annotated genomic sequences from barley. The wheat sequences were relatively gene-rich (one gene per 23.9 kb), although wheat gene-derived sequences represented only 7.8% (159 elements) of the total, while the remainder mainly comprised coding sequences found in TEs (54.7%, 751 elements). Class I elements [mainly long terminal repeat (LTR) retrotransposons] accounted for the major proportion of TEs, in terms of sequence length as well as element number (83.6% and 498, respectively). In addition, we show that the gene-rich sequences of wheat genome A seem to have a higher TE content than those of genomes B and D, or of barley gene-rich sequences. Moreover, among the various TE groups, MITEs were most often associated with genes: 43.1% of MITEs fell into this category. Finally, the TRIM and copia elements were shown to be the most active TEs in the wheat genome. The implications of these results for the evolution of diploid and polyploid wheat species are discussed.

DNA Transposable Elements↗
PubMed2006

Pollinator-mediated assortative mating in mixed ploidy populations of Chamerion angustifolium (Onagraceae).

Establishment of polyploid individuals within diploid populations is theoretically unlikely unless polyploids are reproductively isolated, pre-zygotically, through assortative pollination. Here, we quantify the contribution of pollinator diversity and foraging behaviour to assortative pollen deposition in three mixed-ploidy populations of Chamerion angustifolium (Onagraceae). Diploids and tetraploids were not differentiated with respect to composition of insect visitors. However, foraging patterns of the three most common insect visitors (all bees) reinforced assortative pollination. Bees visited tetraploids disproportionately often and exhibited higher constancy on tetraploids in all three populations. In total, 73% of all bee flights were between flowers of the same ploidy (2x-2x, 4x-4x); 58% of all flights to diploids and 83% to tetraploids originated from diploid and tetraploid plants, respectively. Patterns of pollen deposition on stigmas mirrored pollinator foraging behaviour; 73% of all pollen on stigmas (70 and 75% of pollen on diploid and tetraploid stigmas, respectively) came from within-ploidy pollinations. These results indicate that pollinators contribute to high rates of pre-zygotic reproductive isolation. If patterns of fertilization track pollen deposition, pollinator-plant interactions may help explain the persistence and spread of tetraploids in mixed-ploidy populations.

Alberta↗
PubMed2002

Two haplotypes of resistance gene analogs have been conserved during evolution at the leaf rust resistance locus Lr10in wild and cultivated wheat.

The isolation of genes of agronomic interest such as disease resistance genes is a central issue in wheat research. A good knowledge of the organization and evolution of the genome can greatly help in defining the best strategies for efficient gene isolation. So far, very few wheat disease resistance loci have been studied at the molecular level and little is known about their evolution during polyploidization and domestication. In this study, we have analyzed the haplotype structure at loci orthologous to the leaf rust resistance locus Lr10in hexaploid wheat which spans 350 kb in diploid wheat. Two haplotypes (H1, H2) were defined by the presence (H1) or the absence (H2) of two different resistance gene analogs ( rga1, rga2) at this locus on chromosome 1AS. Both haplotypes were found in a collection of 113 wild and cultivated diploid and polyploid wheat lines and they do not reflect phylogenetic relationships. This indicates an ancient origin for this disease resistance locus and the independent conservation of the two haplotypes throughout the evolution of the wheat genome. Finally, the coding regions of the H1 haplotype RGAs are extremely conserved in all the species. This suggests a selective pressure for maintaining the structural and functional configuration of this haplotype in wheat. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s10142-002-0051-9.

Amino Acid Sequence↗
PubMed2005

Ploidy, geographical distribution and morphological differentiation of Parasenecio auriculata (Senecioneae; Asteraceae) in Japan.

Parasenecio auriculata is a woodland perennial herb widely distributed in Northeastern Asia, constituted by a poorly understood polyploidy with a diploid (2n = 2x = 60) and a tetraploid (2n = 4x = 120). In this study, for a better understanding of the polyploidal evolution, cytogeography and morphological variation were analyzed in Japanese P. auriculata, including two varieties; var. bulbifera endemic to central Hokkaido and var. kamtschatica widely distributed in northern Honshu and Hokkaido. The occurrence of two polyploidal levels was reconfirmed. While var. bulbifera is predominantly tetraploid, var. kamtschatica is comprised of diploid and tetraploid. Morphological variation among 22 quantitative characteristics is continuous and not distinctive among cytotypes or varieties, but plant size tended to be larger in the order, diploid of var. kamtschatica, var. bulbifera, and tetraploid of var. kamtschatica. The cytotype distribution showed a conspicuous geographical pattern. Besides var. bulbifera endemic to the central Hokkaido, the diploid of var. kamtschatica is mainly found in Southern Hokkaido, and the tetraploid has a disjunct distribution in eastern and northern Hokkaido and northern Honshu. Such a geographical pattern is possibly attributable to the differentiation of climatic preference among cytotypes and varieties, and may have been established in association with the climatic cline along the Japanese archipelago.

Analysis of Variance↗
PubMed2006

Germination characteristics of native Japanese dandelion autopolyploids and their putative diploid parent species.

Germination characteristics of native Japanese Taraxacum lineages of Taraxacum platycarpum (diploid), T. venustum (triploid and tetraploid), and T. albidum (pentaploid) have been studied at different temperatures. Taraxacum platycarpum ssp. hondoense is the putative diploid parent of T. venustum. Diploid T. platycarpum ssp. hondoense and the polyploids T. venustum and T. albidum are found in different areas of Japan, and distribution differences may reflect divergent ecological and physiological traits among ploidy levels. In this study, to prevent mixing of seeds of different polyploidy we used flow cytometry to examine the ploidy level of the plants from which seeds were collected. Results from seed-germination experiments showed that dependence on temperature of final percentage germination was qualitatively similar for both autopolyploids T. venustum and diploids T. platycarpum--germination was suppressed at high and low temperatures. It was also shown that seed germination of autopolyploids was suppressed more than that of the ancestral diploid at low temperatures and that seed germination for polyploids was higher than for the diploid. Threshold variations at low temperatures might affect the distribution of native dandelions. Taraxacum venustum, which occurs in cool climates, might have developed a distinctly lower germination threshold at low temperatures whereas T. albidum, which is native to warm climates, might have developed an adaptive threshold at high temperatures.

Adaptation, Physiological↗
PubMed2005

Ploidy of micronucleated thyrocytes induced by methylnitrosourea injection.

Ploidy of thyroid parenchyma was studied in adult rats in the control and on day 9 after hemithyroidectomy; operated animals received 3 injections of N-nitroso-N-methylurea. The population of follicular thyrocytes is mainly diploid; total count of polyploid cells increased from 4.4% in the control to 8.5% in experimental rats. All thyrocytes containing micronuclei were tetraploid. No diploid micronucleated elements were detected. This suggests that genetically damaged thyrocytes divide by the mechanism of acytokinetic (polyploidizing) mitosis.

Alkylating Agents↗
PubMed2005

Ductal breast carcinomas with whole chromosome gains as a particular subset of near-diploid tumors with different metastasis free survival.

We recently proposed the existence of a subtype of slightly hyperdiploid ductal breast cancers with cytogenetic alterations differing from those usually observed in the majority of these tumors. We aimed to establish whether these tumors, which represent about 50% of those with a DNA index (DI) comprised between 1.1 and 1.3, correspond to a particular clinicopathological entity. A retrospective study of 1771 patients operated for ductal carcinomas was performed. Three classes of tumors constituted according to DI were compared for the usual clinicopathological factors and clinical outcome. About 690 tumors (39%) were diploid/hypodiploid (DI < 1.1), 134 (7.6%) were hyperdiploid (1.1 < or = DI < 1.3) and 947 (53.4%) were polyploid (DI > or = 1.3). Median follow-up time was 106 months (range 1-177). Polyploid tumors were significantly associated with large tumor size, advanced clinical stage, high histological grade and S-phase fraction (SPF), positive lymph nodes and loss of steroid receptors. Hyperdiploid and diploid/hypodiploid tumors were similar for all the variables except SPF which was significantly higher in hyperdiploid tumors (p < 0.001). Overall survival was similar in hyperdiploid and diploid/hypodiploid tumors in univariate and multivariate analysis, while hyperdiploid tumors were significantly related to a poorer metastasis free survival, both in univariate (p = 0.023) and multivariate analysis (p = 0.031). Despite very close initial clinicopathological and biological characteristics, hyperdiploid tumors differed from diploid/hypodiploid tumors by a higher risk of metastasis, possibly related to their increased SPF.

Aneuploidy↗
PubMed2005

Polyploidy, evolutionary opportunity, and crop adaptation.

The finding that even the smallest of plant genomes has incurred multiple genome-wide chromatin duplication events, some of which may predate the origins of the angiosperms and therefore shape all of flowering plant biology, adds new importance to the molecular analysis of polyploidization/diploidization cycles and their phenotypic consequences. Early clues as to the possible phenotypic consequences of polyploidy derive from recent QTL mapping efforts in a number of diverse crop plants of recent and well-defined polyploid origins. A small sampling examples of the role(s) of polyploidy in conferring crop adaptation from human needs include examples of (1) dosage effects of multiple alleles in autopolyploids, and (2) 'intergenomic heterosis' conferring novel traits or transgressive levels of existing traits, associated with merging divergent genomes in a common allopolyploid nucleus. A particularly interesting manifestation of #2 is the evolution of complementary alleles at corresponding ('homoeologous') loci in divergent polyploid taxa derived from a common ancestor. Burgeoning genomic data for both botanical models and major crops offer new avenues for investigation of the molecular and phenotypic consequences of polyploidy, promising new insights into the role of this important process in the evolution of botanical diversity.

Adaptation, Biological↗
PubMedDate not supplied

Gene mapping of 28S and 5S rDNA sites in the spined loach Cobitis taenia (Pisces, Cobitidae) from a diploid population and a diploid-tetraploid population.

We compare the chromosomal 28S and 5S rDNA patterns of the spined loach C. taenia (2n = 48) from an exclusively diploid population and from a diploid-polyploid population using 28S and 5S rDNA probe preparation and labelling, and fluorescence in situ hybridization (FISH). The 5S rDNA was located in two to three chromosome pairs, and separated from the 28S loci for the males and one female (F1) from the diploid population. Loaches from a diploid-polyploid population, and one female (F2) from the diploid population were characterized by at least one chromosome pair with 5S and 28S overlapping signals. The fishes differed mainly in their number of 28S rDNA loci, located on 3-6 chromosomes. All individuals from both populations were characterized by one acrocentric chromosome bearing a 28S rDNA signal on the telomeres of its long arm. The number of major ribosomal DNA in the karyotype of C. taenia by FISH was always higher than the number of Ag-NORs. Our data confirm the extensive polymorphism of NORs in both populations, as already has been observed in closely related Cobitis species, and less polymorphic 5S rDNA pattern. However, this preliminary result highlights the need for a wider scale study.

Animals↗
PubMed2026

Optimization of functional genetics tools for a model tetraploid Capsella bursa-pastoris, with focus on homoeolog-aware gene editing.

Capsella bursa-pastoris is a recent allotetraploid and a promising model for studying early consequences of polyploidy. One of the intriguing questions in polyploid research is how new functions arise from initially identical or nearly identical homoeologous genes. Functional genetics tools, including genetic editing, can help to understand this process, but they have not been developed for C. bursa-pastoris yet. We present here the results of our study aimed at filling this gap. In particular, we compared the efficiency of floral dip transformation in six accessions of C. bursa-pastoris representing distant populations. The Asian clade accession PGL0025 had the highest efficiency of transformation (~&#x2009;1.1%). Comparison of Agrobacterium tumefaciens strains EHA105 and GV3101 (pMP90) showed that the latter is more effective. Also, we created a genome-wide gRNA database for all pairs of homoeologs of the PGL0001 accession of C. bursa-pastoris and integrated it into publicly available genome browser: https://t2e.online/igv_capsella_bursa-pastoris/ . We assessed the possibility of differential editing for two pairs of homoeologous genes with high sequence similarity (>&#x2009;90%) both in vitro and in silico. Despite the test results that indicated off-target activity, we have succeeded in obtaining lines of plants with homozygous frameshift mutations in each of the homoeologs separately in vivo. We expect that these findings and resources will promote the use of C. bursa-pastoris as a model in functional genetics experiments, in particular, the studies of the fate of duplicated gene after polyploidization event.

Capsella↗
PubMed2026

Polyploidy Arithmetic.

Polyploidy occurs in plants and animals, and is an important force in speciation and genome evolution. The main focus of this paper is the following fundamental question that was recently posed by Huber and Maher: Given the ploidy numbers of a collection of extant species, or their ploidy profile, what is the smallest number of hybridizations needed in any evolutionary history for these species to completely represent these numbers? In this paper, we shall show that this question can be rephrased in terms of addition chains and the closely related addition sequences, which have been studied for over a century in mathematics and computer science. These are sequences of natural numbers that start with 1, so that each number in the sequence larger than 1 is the sum of two other numbers arising earlier in the sequence. In our first main result, we show that finding the smallest number of hybridization events to explain a ploidy profile, or the hybrid number, is equivalent to solving the so-called addition sequence problem. This immediately implies that computing the hybridization number is computationally intractable. Even so, it also leads to new connections to representing polyploid evolution using networks. More specifically, in our second main result we show that ploidy profiles representable by tree-child networks are exactly the addition chains, implying a polynomial-time algorithm for identifying these profiles. We then consider beaded tree-child networks, which permit the representation of autopolyploidy events, and in our third main result we provide a greedy polynomial-time algorithm to decide whether a given profile can be realized by such a network. We expect that our results can be leveraged in future work through, for example, making use of known algorithms for computing short addition sequences to give bounds for the hybrid number, and in guiding network reconstruction for polyploid species.

Polyploidy↗