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Implication of Triticum searsii as the B-genome donor to wheat using DNA hybridizations.

In vitro DNA:DNA hybridizations and hydroxyapatite thermal chromatography were employed to help identify the species ancestral to the B genome of the polyploid wheats. We hybridized 3H-Triticum aestivum DNA to the unlabeled DNAs of T. urartu, T. speltoides, T. sharonensis, T. bicorne, T. longissimum, and T. searsii, 3H-Labeled DNA of T. urartu was hybridized with the DNA of a synthetic tetraploid. AADD. The heteroduplex thermal stabilities indicated that T. searsii was most closely related to T. aestivum (ABD) and that the genome of T. urartu was more closely related to the A genome than the B genome. The degree of reassociation which may have occurred between the six diploid species and the D genome of T. aestivum was evaluated by hybridizing 3H-T. tauschii DNA with the DNAs of the diploids. The results indicated that T. urartu had the least sequence homology to T. tauschii, the D-genome donor lending additional support to the conclusion that T. urartu is related to the A genome. Thus, it is highly probable that T. searsii is the B-genome donor to the polyploid wheats or a major chromosome donor if the B genome is, in fact, polyphyletic in origin.

DNA↗

Comparison of the primary structure of waxy proteins (granule-bound starch synthase) between polyploid wheats and related diploid species.

The waxy proteins encoded by the genomes A, B, and D in polyploid wheats and related diploid species were isolated by SDS-PAGE. The N-terminal amino acid sequences of mature proteins and V8 protease-induced fragments were determined. A total of five amino acid substitutions was detected in these sequences, which represent about 10% of the whole sequences of the waxy proteins. A comparison of these sequences in polyploid wheats with those in related diploid species revealed the following: (i) waxy proteins encoded by the A genome of polyploid wheats were identical to that of Triticum monococcum, (ii) the waxy protein encoded by the B genome of T. turgidum was identical to that of T. searsii, but differed from those of T. speltoides and T. longissimum by one amino acid substitution, (iii) the waxy protein encoded by the B genome of T. aestivum differed from that encoded by the B genome of T. turgidum by one amino acid substitution, and (iv) the waxy protein encoded by the D genome of T. aestivum was identical to that of T. tauschii.

Amino Acid Sequence↗

DNA ploidy and autophagic protein degradation as determinants of hepatocellular growth and survival.

Hepatocytes have the ability to go through specialized cell cycles, which, during normal developmental liver growth, result in the formation of binuclear and polyploid cells. In the adult rat liver, the majority of the hepatocytes (about 70%) are tetraploid, 15-20% are octoploid, and only 10-15% are diploid (about 50% in humans). One-third of the hepatocytes in either rats or humans are binuclear (with two diploid or two tetraploid nuclei). Among cultured rat hepatocytes stimulated with growth factors (EGF and insulin), one-half of the mitoses are of the binucleating type (suggesting a "quantal" mechanism), causing one-third of the postmitotic cells to become binuclear. In contrast, regenerative liver growth, induced by partial hepatectomy, is predominantly nonbinucleating. During rat liver carcinogenesis, the early populations of phenotypically altered cells (foci) are predominantly diploid, as are the later neoplastic nodules and carcinomas, which can be shown to have a regeneration-like, largely nonbinucleating growth pattern. A negative correlation between growth capacity and ploidy can be demonstrated in cultured hepatocytes, regenerating livers, neoplastic nodules, and hepatocellular carcinomas, suggesting that suppression of binucleation and polyploidization may carry a growth advantage, in addition to helping to maintain a large population of diploid, potential stem cells. Since a diploid genome is less protected against mutagenic change than a polyploid genome, diploid tumor cells may, furthermore, be more prone than polyploid cells to undergo mutation-based progression toward increasing malignancy. The ability of liver tumor promoters like 2-acetylaminofluorene, cyproterone acetate, alpha-hexachlorocyclohexane and methylclofenapate to induce nonbinucleating hepatocyte growth may, therefore, cooperate with the selective growth stimulation of cancer cells and cancer cell precursors to promote liver carcinogenesis. Autophagy, a mechanism for the bulk degradation of cytoplasm, contributes to intracellular protein turnover and serves to restrict cellular growth. Rat liver carcinogenesis is accompanied by a progressive reduction of autophagic capacity, preneoplastic livers having 50% and hepatocellular carcinoma cells only 20% as much autophagy as normal hepatocytes. The ascites hepatoma cell line AH-130 has virtually no autophagy during logarithmic growth, but some autophagy is turned on when the cells become growth-arrested at high cell density. Ascitic fluid from AH-130 cells is able to completely inhibit autophagy in normal hepatocytes, suggesting that the cancer cells may improve their growth ability through an autocrine, autophagy-suppressive mechanism. Hepatocytes from preneoplastic livers similarly maintain a low autophagic activity under restrictive culture conditions, thereby surviving much better than normal hepatocytes, which switch on their autophagy. In the presence of an autophagy inhibitor (3-methyladenine), normal and preneoplastic hepatocytes survive equally well, testifying to the importance of autophagy as a determinant of cell survival and growth.

Animals↗

Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana.

Polyploidization is found frequently in plants, and species previously considered to be diploid may show remnants of earlier polyploidization events on closer inspection of their genomes. The success of polyploids may lie in increased genetic redundancy supporting subsequent genetic diversification. Although doubling the genome does not generate diversity per se, recent studies show that rapid genomic rearrangements and changes in DNA modification and gene expression patterns are associated with polyploid formation. But recessive modifications will not become phenotypically apparent in early polyploid generations. Here we show that epialleles in tetraploid plants (but not in diploids) interact in trans and lead to heritable gene silencing persisting after segregation from the inactivating allele. This mechanism, resembling paramutation, leads to the establishment of functional epigenetic homozygosity and, thus, to conversion of new recessive alleles into traits expressed in early polyploid generations. Such interactions probably contribute to rapid adaptation and evolution of polyploid plant species.

Alleles↗

PCR-mediated recombination in amplification products derived from polyploid cotton.

PCR recombination describes a process of in vitro chimera formation from non-identical templates. The key requirement of this process is the inclusion of two partially homologous templates in one reaction, a condition met when amplifying any locus from polyploid organisms and members of multigene families from diploid organisms. Because polyploids possess two or more divergent genomes ("homoeologues") in a common nucleus, intergenic chimeras can form during the PCR amplification of any gene. Here we report a high frequency of PCR-induced recombination for four low-copy genes from allotetraploid cotton ( Gossypium hirsutum). Amplification products from these genes ( Myb3, Myb5, G1262 and CesA1) range in length from 860 to 4,050 bp. Intergenomic recombinants were formed frequently, accounting for 23 of the 74 (31.1%) amplicons evaluated, with the frequency of recombination in individual reactions ranging from 0% to approximately 89%. Inspection of the putative recombination zones failed to reveal sequence-specific attributes that promote recombination. The high levels of observed in vitro recombination indicate that the tacit assumption of exclusive amplification of target templates may often be violated, particularly from polyploid genomes. This conclusion has profound implications for population and evolutionary genetic studies, where unrecognized artifactually recombinant molecules may bias results or alter interpretations.

Journal Article↗

Polyploid evolution: keeping the peace at genomic reunions.

Incompatible gene or chromosomal combinations brought together in allopolyploid genomes cannot be purged through Mendelian segregation. But recent studies suggest that the elimination of DNA sequences and alteration of DNA methylation patterns may permit the restoration of fertility in some allopolyploids.

Animals↗

Large-scale screening of genes responsible for silique length and seed size in Brassica Napus via pooled CRISPR library.

BACKGROUND: Enhancing rapeseed (Brassica napus, B. napus) yield is critical for ensuring global vegetable oil security. However, yield is heavily influenced by silique development and seed size, the enhancement of which is limited by scarce genetic resources. The CRISPR/Cas9 system has emerged as a powerful tool for constructing genome-wide mutant libraries, even in polyploid crops with complex genomes. RESULTS: The transcriptome-wide association study (TWAS) data, tissue-specific expression profiles data and reported genes were integrated to identify candidate genes regulating silique development and seed size. We constructed a sgRNA library targeting these genes and generated a CRISPR/Cas9 editing mutant library through genetic transformation. Specifically, 6124 sgRNAs were designed for 1739 candidate genes with ≦ 4 orthologues. 681 T0 plants were obtained through genetic transformation, which harbor 453 sgRNAs. Of 408 T0 plants analyzed, 151 (37.00%) exhibited successful gene editing events, targeting 84 candidate genes. Ten homozygous mutant plants were isolated and preliminary phenotypic analysis was performed in mutants targeting the BnaHRDs. The results suggest that mutations in BnaHRD.A03 and BnaHRD.C03 may modulate plant height (PH), main inflorescence length (MIL), silique length (SL), effective silique number per plant (ENS), seed number per silique (SNPS), and thousand-seed weight (TSW). CONCLUSIONS: This study harnessed the CRISPR/Cas9 technology to establish a preliminary library of gene-edited mutants in B. napus, thereby laying a robust foundation for the future screening of candidate genes pertaining to silique development and seed size. Furthermore, this study provides a methodological framework for rapid functional gene discovery in B. napus through CRISPR-based approaches.

Brassica napus↗

Intergenomic translocations of polyploid oats (genus Avena) revealed by genomic in situ hybridization.

Wild and cultivated hexaploid oats share the same genomes (AACCDD) and display a considerable level of interspecific variation in both plant and chromosome morphology. The GISH was utilized to detect the interspecific genomic compositions in four hexaploid and two tetraploid oats using total genomic DNA of Avena eriantha (a C-genome diploid) as probe. Intergenomic translocations between A/D and C-genome chromosomes were frequently observed in hexaploid and tetraploid species. In the hexaploid, two pairs of A/D genome segments on C-genome chromosome (A/D-C) translocation and four to six pairs of C-genome segments on A/D genome chromosome (C-A/D) translocation were clearly identified whilst the number of A/D-C translocations was constant among species. In the tetraploid A. maroccana (AACC), a pair of A-C and four pairs of C-A translocations were observed. Moreover, the A/D translocation segments on chromosome 5C was detected only in A. byzantina and A. maroccana, whilst A/D-C translocations were observed on the 1C and 7C of A. sativa, A. fatua and A. sterilis. A. byzantina did however also carry the 1C rearrangement. This result shows that A. byzantina has retained a similar genomic constitution to the tetraploid ancestor of hexaploid oats, A. maroccana. Three pairs of A-C translocations were detected only in A. murphyi (AACC), and two pairs of those were the 1C and 7C as well as the three hexaploid species except A. byzantina.

Avena↗

Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor.

Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species.

Base Sequence↗

A bivalent polyploid model for mapping quantitative trait loci in outcrossing tetraploids.

Two major aspects have made the genetic and genomic study of polyploids extremely difficult. First, increased allelic or nonallelic combinations due to multiple alleles result in complex gene actions and interactions for quantitative trait loci (QTL) in polyploids. Second, meiotic configurations in polyploids undergo a complex biological process including either bivalent or multivalent formation, or both. For bivalent polyploids, different degrees of preferential chromosome pairings may occur during meiosis. In this article, we develop a maximum-likelihood-based model for mapping QTL in tetraploids by considering the quantitative inheritance and meiotic mechanism of bivalent polyploids. This bivalent polyploid model is implemented with the EM algorithm to simultaneously estimate QTL position, QTL effects, and QTL-marker linkage phases by incorporating the impact of a cytological parameter determining bivalent chromosome pairings (the preferential pairing factor). Simulation studies are performed to investigate the performance and robustness of our statistical method for parameter estimation. The implication and extension of the bivalent polyploid model are discussed.

Algorithms↗

Genomic analyses of three Acanthus L. species provide insight into polyploidization-driven speciation and evolution.

Allopolyploidy fundamentally influences plant evolution, yet the genomic dynamics of allotetraploidization remain incompletely understood. We investigated Acanthus tetraploideus (2n = 4x = 96), an ecologically significant allotetraploid true mangrove from Indo-West Pacific intertidal zones. Our prior integrative investigations indicate that A. tetraploideus originated through hybridization of the diploid species A. ilicifolius and A. ebracteatus with subsequent chromosome doubling. Here, we present complete chromosome-scale genome assemblies for all three species, representing the first genomic resources for true mangrove polyploid research. Our analysis reveals that the three species have experienced at least four rounds of polyploidization events, with the most recent, approximately 53 mya, possibly an Acanthus-specific event. The allotetraploid A. tetraploideus, which emerged between 1.5 and 2.2 mya, has A. ebracteatus as its maternal progenitor and A. ilicifolius as its paternal one. Through a comprehensive genomic comparison and analysis of homoeologous gene expression, we propose a gradual evolutionary trajectory for allotetraploidy in A. tetraploideus. Despite the allotetraploidization event dating back to around 2 mya, A. tetraploideus retains a high degree of colinearity with its ancestral genomes, with the majority (76.2%) of duplicated genes retained and no significant sub-genome bias in gene expression. Furthermore, we have identified positive selection in specific genes that may facilitate the adaptation of Acanthus mangrove species to their intertidal habitats. These findings establish A. tetraploideus as a model for studying allopolyploid evolution while providing new insights into mangrove speciation processes.

Genome, Plant↗

Genome evolution in the genus Sorghum (Poaceae).

BACKGROUND AND AIMS: The roles of variation in DNA content in plant evolution and adaptation remain a major biological enigma. Chromosome number and 2C DNA content were determined for 21 of the 25 species of the genus Sorghum and analysed from a phylogenetic perspective. METHODS: DNA content was determined by flow cytometry. A Sorghum phylogeny was constructed based on combined nuclear ITS and chloroplast ndhF DNA sequences. KEY RESULTS: Chromosome counts (2n = 10, 20, 30, 40) were, with few exceptions, concordant with published numbers. New chromosome numbers were obtained for S. amplum (2n = 30) and S. leiocladum (2n = 10). 2C DNA content varies 8.1-fold (1.27-10.30 pg) among the 21 Sorghum species. 2C DNA content varies 3.6-fold from 1.27 pg to 4.60 pg among the 2n = 10 species and 5.8-fold (1.52-8.79 pg) among the 2n = 20 species. The x = 5 genome size varies over an 8.8-fold range from 0.26 pg to 2.30 pg. The mean 2C DNA content of perennial species (6.20 pg) is significantly greater than the mean (2.92 pg) of the annuals. Among the 21 species studied, the mean x = 5 genome size of annuals (1.15 pg) and of perennials (1.29 pg) is not significantly different. Statistical analysis of Australian species showed: (a) mean 2C DNA content of annual (2.89 pg) and perennial (7.73 pg) species is significantly different; (b) mean x = 5 genome size of perennials (1.66 pg) is significantly greater than that of the annuals (1.09 pg); (c) the mean maximum latitude at which perennial species grow (-25.4 degrees) is significantly greater than the mean maximum latitude (-17.6) at which annual species grow. CONCLUSIONS: The DNA sequence phylogeny splits Sorghum into two lineages, one comprising the 2n = 10 species with large genomes and their polyploid relatives, and the other with the 2n = 20, 40 species with relatively small genomes. An apparent phylogenetic reduction in genome size has occurred in the 2n = 10 lineage. Genome size evolution in the genus Sorghum apparently did not involve a 'one way ticket to genomic obesity' as has been proposed for the grasses.

Cell Nucleus↗

Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae).

Genome-wide duplication (polyploidization) is prevalent in a large number of eukaryotic organisms and is particularly widespread in flowering plants. Polyploid species appear to vary from their diploid progenitors in a variety of ecologically important traits, suggesting that genome duplications provide a mechanism for ecological diversification. Studies of nucleotide variation at duplicate genes that arise via polyploidization allow us to infer the evolutionary forces that act on these polyploid loci. In an effort to examine the evolutionary dynamics of homoeologous loci, molecular population genetic analyses were undertaken for duplicate regulatory genes in the allopolyploid Hawaiian silversword alliance, a premier example of adaptive radiation. The levels and patterns of nucleotide variation for the floral homeotic genes ASAPETALA1 (ASAP1) and ASAPETALA3/TM6 (ASAP3/TM6) were studied in two species representing different lineages within the Hawaiian silversword alliance: Argyroxiphium sandwicense ssp. macrocephalum and Dubautia ciliolata ssp. glutinosa. Homoeologueous copies of ASAP1 and ASAP3/TM6 show differing levels and patterns of nucleotide polymorphism. Duplicate ASAP1 copies have similar levels of nucleotide diversity and haplotype structure in both species; by contrast, duplicate ASAP3/TM6 genes display different levels and patterns of variation in D. ciliolata ssp. glutinosa. Additionally, D. ciliolata ssp. glutinosa appears to be segregating for a moderate frequency null allele in one ASAP3/TM6 homoeologue. These results suggest that differing evolutionary forces can affect duplicate loci arising from allopolyploidization.

Asteraceae↗

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↗

Genes involved in biosynthesis and signalisation of ethylene in Brassica oleracea and Arabidopsis thaliana: identification and genome comparative mapping of specific gene homologues.

The study reported was aimed at the identification and determination of the chromosomal organisation of genes involved in the ethylene biosynthesis and signalling pathways in Brassica oleracea, on the basis of the Arabidopsis thaliana DNA probes and in silico genome analysis. Because of its polyploidal origin, the B. oleracea genome is characterised by extensive gene redundancy. Therefore, an important aspect of gene expression in B. oleracea response to environmental stimuli is to identify the specific gene copy involved. This aspect should also be taken into consideration while studying the genetic basis of biosynthesis and signal transduction in relation to basic phytohormones. Our present work concerns the identification of homologue genes involved in ethylene biosynthesis such as SAM, ACS and ACO, as well as those involved in the ethylene signalling pathway, mainly ETR1, CTR1, MKK4, MKK5, EIN2, EIN3, EREBP, ERF5 and ERF7 on the basis of the restriction fragment length polymorphism (RFLP) and PCR mapping. In the case of ACC synthases, (ACSs) the in silico analysis of gene variants in the genome of A. thaliana was followed by the identification of homologues to ACS2, ACS6 and ACS7 in the B. oleracea database. In total, 22 loci with sequence homology to the genes under analysis were included in the existing B. oleracea RFLP chromosomal map. Based on the stress responsiveness of most of the A. thaliana genes analysed in this study, we performed initial functional analysis of some gene homologues mapped. With the use of the RT-PCR approach the conservation of differential transcriptional induction of ACS homologues in the B. oleracea and A. thaliana was demonstrated during ozone stress.

Arabidopsis↗

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↗

[Biological effects in natural populations of small rodents in radiation contaminated areas. The frequency of bone marrow polyploid cells of bank voles in different years following Chernobyl accident].

On the basis of the metaphase analysis results, the peculiarities of dynamics of the genome mutation frequency (polyploid cells) were studied in bone marrow of bank voles inhabiting the areas with different radiocontamination level due to the Chernobyl accident (8-1526 kBq/m2 for 137Cs) in 1986-1991. Unexpectedly high frequencies of polypoid cells exceeding the pre-accidental level by a factor of 10(1)-10(3) were recorded in all populations studied. Relationship between the frequency of the parameter studied and the concentration of radionuclides incorporated in animal carcasses was proved. A statistically significant rise in the frequency of genome mutations with the time was revealed up to 1991, i.e. approximately to 12th post-accidental animal generation.

Animals↗

Gene amplification as a developmental strategy: isolation of two developmental amplicons in Drosophila.

Gene amplification is known to be critical for upregulating gene expression in a few cases, but the extent to which amplification is utilized in the development of diverse organisms remains unknown. By quantifying genomic DNA hybridization to microarrays to assay gene copy number, we identified two additional developmental amplicons in the follicle cells of the Drosophila ovary. Both amplicons contain genes which, following their amplification, are expressed in the follicle cells, and the expression of three of these genes becomes restricted to specialized follicle cells late in differentiation. Genetic analysis establishes that at least one of these genes, yellow-g, is critical for follicle cell function, because mutations in yellow-g disrupt eggshell integrity. Thus, during follicle cell differentiation the entire genome is overreplicated as the cells become polyploid, and subsequently specific genomic intervals are overreplicated to facilitate gene expression.

Animals↗