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Background Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility. Scope World-wide interest in how green plants have evolved under different conditions – whether in small, isolated populations, or globally – suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany , consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids. Conclusion Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy – generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses. [ABSTRACT FROM AUTHOR]

Meriz goat is a native goat breed found along the northern boundary of the Iraqi Kurdistan region near the center of species diversity and domestication. This economically important breed is distinguished by its production of fine hair, high persistence, and ability to thrive in harsh environmental conditions. Although the phenotype and productive traits of the Meriz goat have been described, the complete mitochondrial genome, maternal lineage, and genetic diversity of the breed have yet to be identified. Therefore, the whole genome sequencing data and bioinformatics analysis were used to assemble the complete mitochondrial genome, generate a maternal phylogeny, and identify some mitogenomic diversity features of Meriz goats from the Iraqi Kurdistan region. The complete mitochondrial genome of the two individuals was assembled with lengths of 16641 and 16639 bp, respectively (MH165338 and MH165339). The mitogenome comprises13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes and one non-coding control region. In addition, our data revealed that the mitogenome copy number is greater in female goats than in males. Integration into a phylogenetic tree with other goat breeds showed that Meriz goats belong to the most predominant maternal haplogroup A (HPGA). Furthermore, nucleotide diversity and mitogenomic analysis indicated that Meriz goats have a high level of mitogenomic similarity to Chinese Cashmere goats and Turkish Angora goats within the same maternal lineage. The molecular data reported here provide useful insights into the evolutionary relationships and mitogenomic diversity of domestic and wild goats from the center of diversity of animal species in the Middle East. [ABSTRACT FROM AUTHOR]

The study of plant evolution and development in a phylogenetic context has accelerated research advances in both areas over the last decade. The addition of a robust phylogeny for plant taxa based on DNA as well as morphology has given a strong context for this research. Genetics and genomics, including sequencing of many genes, and a better understanding of non-genetic, responsive changes, by plants have increased knowledge of how the different body forms of plants have arisen. Here, I overview the papers in this Special Issue of Annals of Botany on Morphological Adaptation, bringing together a range of papers that link phylogeny and morphology. These lead to models of development and functional adaptation across a range of plant systems, with implications for ecology and ecosystems, as well as development and evolution. [ABSTRACT FROM AUTHOR]

The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350-fold range from 63 to 149 000 Mb, divided into n = 2 to n = approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well-conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production. [ABSTRACT FROM AUTHOR]

Background/Aims: Transposable elements (TEs) are dynamic components of eukaryotic genomes. We aimed to characterize TEs to help elucidate their impact on the genomic architecture, diversity and evolution of chromosomes in the D. buzzatii cluster of species (repleta group). Methods: A full TE element of D. buzzatii, named PERI, was identified in a BAC clone available in GenBank. PERI was further analysed using bioinformatics tools, PCR and in-situ hybridization to metaphase chromosomes and DNA fibers. Results: PERI shares several structures in common with DINE-1, an abundant TE found widespread along the Drosophila genus. The central region of PERI is very dynamic but revealed a disrupted pattern of nucleotide variability among its internal tandem repeats. The minimal sequence variation in D. serido suggests recent amplification. PERI accumulates near or at heterochromatic regions of all 6 pairs of chromosomes, especially on the sex chromosomes, with some clustering. Conclusions: PERI is an abundant type of DINE-1 transposon but with characteristic sequence signatures and probably restricted to the buzzatii complex. The conservation of different central domains and association with genes suggests selective constraints. Although at or near heterochromatin, the distribution of PERI does not overlap with satDNAs, probably a consequence of functional or molecular constraints. Copyright © 2010 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

We present the isolation and characterization of 10 microsatellite loci for striped marlin, Tetrapturus audax. Thirty individuals from each of four locations revealed that all loci were polymorphic with two to 31 alleles per locus. Observed levels of heterozygosity ranged from 0.3000 to 0.9667. Significant deviations from Hardy–Weinberg equilibrium were detected in two loci, TA105 in Hawaii and New Zealand and TA155 in Hawaii, and null alleles may be present in loci TA105 and TA155 in those locations, and in locus TA193 in Mexico. No significant linkage disequilibrium was detected in any pairwise-locus comparison. [ABSTRACT FROM AUTHOR]

Resistance genes (R genes) in plants are abundant and may represent more than 1% of all the genes. Their diversity is critical to the recognition and response to attack from diverse pathogens. Like many other crops, banana and plantain face attacks from potentially devastating fungal and bacterial diseases, increased by a combination of worldwide spread of pathogens, exploitation of a small number of varieties, new pathogen mutations, and the lack of effective, benign and cheap chemical control. The challenge for plant breeders is to identify and exploit genetic resistances to diseases, which is particularly difficult in banana and plantain where the valuable cultivars are sterile, parthenocarpic and mostly triploid so conventional genetic analysis and breeding is impossible. In this paper, we review the nature of R genes and the key motifs, particularly in the Nucleotide Binding Sites (NBS), Leucine Rich Repeat (LRR) gene class. We present data about identity, nature and evolutionary diversity of the NBS domains of Musa R genes in diploid wild species with the Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), M. textilis (T), M. velutina and M. ornata genomes, and from various cultivated hybrid and triploid accessions, using PCR primers to isolate the domains from genomic DNA. Of 135 new sequences, 75% of the sequenced clones had uninterrupted open reading frames (ORFs), and phylogenetic UPGMA tree construction showed four clusters, one from Musa ornata, one largely from the B and T genomes, one from A and M. velutina, and the largest with A, B, T and S genomes. Only genes of the coiled-coil (non-TIR) class were found, typical of the grasses and presumably monocotyledons. The analysis of R genes in cultivated banana and plantain, and their wild relatives, has implications for identification and selection of resistance genes within the genus which may be useful for plant selection and breeding and also for defining relationships and genome evolution patterns within the genus using the multi-copy and variable resistance genes. Copyright © 2008 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Crosses between populations of Tigriopus californicus result in backcross and F2 hybrid breakdown for a variety of fitness related measures. The magnitude of this hybrid breakdown is correlated with evolutionary divergence. We assessed the chromosomal basis of viability differences in nonrecombinant backcross hybrids using markers mapped to individual chromosomes. To assess effects of evolutionary divergence we crossed one population to three different populations: two distantly related (∼18% mitochondrial COI sequence divergence) and one closely related (∼1% mitochondrial COI sequence divergence). We found that all three interpopulation crosses resulted in significant deviations from expected Mendelian ratios at a majority of the loci studied. In all but one case, deviations were due to a deficit of parental homozygotes. This pattern implies that populations of T. californicus carry a significant genetic load, and that a combination of beneficial dominance and deleterious homozygote–heterozygote interactions significantly affects hybrid viability. Pairwise tests of linkage disequilibrium detected relatively few significant interactions. For the two divergent crosses, effects of individual chromosomes were highly concordant. These two crosses also showed higher heterozygote excess in females than males across the vast majority of chromosomes. [ABSTRACT FROM AUTHOR]

Human myeloid leukemia cell lines are induced to terminal differentiation into monocyte lineage by 1,25-dihydroxyvitamin D3 (1,25D3) or its analogs (deltanoids). However, translation of these findings to the clinic is limited by calcemic effects of deltanoids. Strategies to overcome this problem include combination of deltanoids with other compounds to induce differentiation at lower, noncalcemic, deltanoid concentrations. We previously showed that either carnosic acid, an antioxidant, or SB202190, a p38 MAPK inhibitor, increase the potency of 1,25D3 in the HL60 cell line. Here, we report that simultaneous addition of both these agents further increases differentiation potency of deltanoids in this cell line and in freshly obtained leukemic cells ex vivo. Activity of MAPK pathways showed that increased differentiation was associated with enhanced activity of JNK pathway in all responding cell subtypes. Our studies suggest that patients with CML or AML subtypes M2 and M4, but not M1, M3 or M4eo, are particularly suitable for this combination therapy. We conclude that the established cell line HL60 presents a good model for some, but not all, subtypes of myeloid leukemia, and that the JNK pathway plays an important role in monocytic differentiation of human leukemic cells ex vivo, as well as in vitro.Leukemia (2005) 19, 1812–1817. doi:10.1038/sj.leu.2403916; published online 18 August 2005 [ABSTRACT FROM AUTHOR]

Explores the relationship between retroelements and similarities with virus sequences. Presence of integrated sequences of the family of plant pararetroviruses; Assessment of conserved domains and amino acid residues; Order of the genes in the elements.

We show that cryogenically cooled, photon counting superconducting tunnel junctions (STJs) can be used to simultaneously record the optical spectra from multiple biological fluorochromes. Measurements with a single-pixel tantalum STJ with a wavelength resolving power R=λ/Δλ of about 10 confirm the expected sensitivity advantage with respect to the photomultiplier-based detectors commonly used to record signals from microarrays and other fluorescent biological systems. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Eleven microsatellite loci were isolated and characterized for the intertidal copepod Tigriopus californicus. Primers reliably amplify alleles in inbred lines derived from two divergent populations previously shown to have genetic distances of 18% for the mitochondrial cytochrome oxidase I gene. The 11 loci provided markers for eight of the species’ 12 chromosomes. [ABSTRACT FROM AUTHOR]

The article discusses the implication for centromere specification, activity, and evolution in the cetromeric and nucleosomes of DNA. It mentions the revelation of DNA classes including retrotransposons, transposons, and genes that are under the kinetochore, and microtubule attachment sites due to the advancement of sequencing technology. It notes that the correct chromosome segregation is the combination of the exquisite control of centromere function, and the highest stability of the process.

A preface to "Annals of Botany," is presented.

The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (HPGA) and European (HPGB) haplogroups, as well as the rarer Anatolian haplogroup HPGC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs. [ABSTRACT FROM AUTHOR]

A preface for the Highlight section of "Annals of Botany" is presented.

Background and Aims Tandemly repeated DNA and transposable elements represent most of the DNA in higher plant genomes. High-throughput sequencing allows a survey of the DNA in a genome, but whole-genome assembly can miss a substantial fraction of highly repeated sequence motifs. Chrysanthemum nankingense (2 n  = 2 x  = 18; genome size = 3.07 Gb; Asteraceae), a diploid reference for the many auto- and allopolyploids in the genus, was considered as an ancestral species and serves as an ornamental plant and high-value food. We aimed to characterize the major repetitive DNA motifs, understand their structure and identify key features that are shaped by genome and sequence evolution. Methods Graph-based clustering with RepeatExplorer was used to identify and classify repetitive motifs in 2.14 millions of 250-bp paired-end Illumina reads from total genomic DNA of C. nankingense. Independently, the frequency of all canonical motifs k -bases long was counted in the raw read data and abundant k -mers (16, 21, 32, 64 and 128) were extracted and assembled to generate longer contigs for repetitive motif identification. For comparison, long terminal repeat retrotransposons were checked in the published C. nankingense reference genome. Fluorescent in situ hybridization was performed to show the chromosomal distribution of the main types of repetitive motifs. Key Results Apart from rDNA (0.86 % of the total genome), a few microsatellites (0.16 %), and telomeric sequences, no highly abundant tandem repeats were identified. There were many transposable elements: 40 % of the genome had sequences with recognizable domains related to transposable elements. Long terminal repeat retrotransposons showed widespread distribution over chromosomes, although different sequence families had characteristic features such as abundance at or exclusion from centromeric or subtelomeric regions. Another group of very abundant repetitive motifs, including those most identified as low-complexity sequences (9.07 %) in the genome, showed no similarity to known sequence motifs or tandemly repeated elements. Conclusions The Chrysanthemum genome has an unusual structure with a very low proportion of tandemly repeated sequences (~1.02 %) in the genome, and a high proportion of low-complexity sequences, most likely degenerated remains of transposable elements. Identifying the presence, nature and genomic organization of major genome fractions enables inference of the evolutionary history of sequences, including degeneration and loss, critical to understanding biodiversity and diversification processes in the genomes of diploid and polyploid Chrysanthemum , Asteraceae and plants more widely. [ABSTRACT FROM AUTHOR]

Background and Aims Diploid and polyploid Urochloa (including Brachiaria , Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the ' brizantha ' and ' humidicola ' agamic complexes and U. maxima. Key Results Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha , U. decumbens and U. ruziziensis , and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands. [ABSTRACT FROM AUTHOR]

Background Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction. Methods We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations. Results We observed three highly differentiated subpopulations in U. brizantha , which were unrelated to ploidy: one intermixed with U. decumbens , and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola , unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima. Conclusions Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens , which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha , U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual–apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas. [ABSTRACT FROM AUTHOR]

Background and Aims The C4 Urochloa species (syn. Brachiaria) and Megathyrsus maximus (syn. Panicum maximum) are used as pasture for cattle across vast areas in tropical agriculture systems in Africa and South America. A key target for variety improvement is forage quality: enhanced digestibility could decrease the amount of land required per unit production, and enhanced lipid content could decrease methane emissions from cattle. For these traits, loss-of-function (LOF) alleles in known gene targets are predicted to improve them, making a reverse genetics approach of allele mining feasible. We therefore set out to look for such alleles in diverse accessions of Urochloa species and Megathyrsus maximus from the genebank collection held at the CIAT. Methods We studied allelic diversity of 20 target genes (11 for digestibility, nine for lipid content) in 104 accessions selected to represent genetic diversity and ploidy levels of U. brizantha , U. decumbens , U. humidicola , U. ruziziensis and M. maximum. We used RNA sequencing and then bait capture DNA sequencing to improve gene models in a U. ruziziensis reference genome to assign polymorphisms with high confidence. Key Results We found 953 non-synonymous polymorphisms across all genes and accessions; within these, we identified seven putative LOF alleles with high confidence, including those in the non-redundant SDP1 and BAHD01 genes present in diploid and tetraploid accessions. These LOF alleles could respectively confer increased lipid content and digestibility if incorporated into a breeding programme. Conclusions We demonstrated a novel, effective approach to allele discovery in diverse accessions using a draft reference genome from a single species. We used this to find gene variants in a collection of tropical grasses that could help reduce the environmental impact of cattle production. [ABSTRACT FROM AUTHOR]

The F1 AABBRHch hybrids studied here were produced by crosses between the Portuguese triticale cultivar ‘Douro’ (AABBRR) and the tritordeum line HT9 (AABBHchHch). Fluorescent in situ hybridization performed with genomic DNA probes genomic in situ hybridization (GISH) from rye and Hordeum chilense allowed the unequivocal parental genomes discrimination in all hybrids. Among 55 plants, one presented a spontaneous wheat–rye translocation which was successfully detected after GISH. Recombinant chromosomes identification was made after reprobe with pTa71 and pSc119.2. Nine rDNA loci were detected by pTa71 and pSc119.2 identified the chromosome arms involved in the translocation, after comparing the observed hybridization patterns with those described by several authors. We identified the spontaneous wheat–rye translocation as being the 7BS/7RL. Many wheat–rye translocations have been found (e.g. 1BL.1RS and 1AL.1RS), but as far as we know, this is the first time that this translocation is reported. We considered it helpful for wheat breeding programmes as it could provide the transference of interesting agronomic characteristics from rye (e.g. leaf rust resistance) to wheat. [ABSTRACT FROM AUTHOR]

Background and Aims: The diploid goat grass Aegilops tauschii (2n = 2x = 14) is native to the Middle East and is the D-genome donor to hexaploid bread wheat. The aim of this study was to measure the diversity of different subspecies and varieties of wild Ae. tauschii collected across the major areas where it grows in Iran and to examine patterns of diversity related to the taxa and geography. [ABSTRACT FROM PUBLISHER]

The DNA hypomethylation effect of 5-azacytine (5-AC; a cytosine analog) is widely known. This agent has been used for rRNA gene expression studies of Triticeae amphiploids and hybrids regarding rye rRNA genes suppression caused by the wheat nucleolar dominance phenomenon. However, this situation is reverted by 5-AC treatment which activates rye rRNA gene expression as it has been intensively observed in triticale. For nucleo|ar dominance studies, we produced F1 multigeneric hybrids (AABBRHCh; 2n=6x=42) from crosses between the triticale cultivar 'Corgo' (AABBRR; 2u=6x=42) and the tritordeum cultivars HT9 and HT31 (AABBHchHch; 2n=6x=42). The hybrid seeds were germinated in a low concentration of 5-AC (treatment) and in distilled water (nontreated control plants). Silver nitrate staining performed in one 5-AC-treated F1 hybrid revealed a reduced number of interphase cells with seven nucleoli, metaphases with eight Ag-NORs, and neocentromeres in the long arm of three wheat chromosomes. Nontreated hybrids presented six Ag-NORs per mitotic metaphase cell and a maximum of six nucleoli per interphase because of the 1R Ag-NOR suppression. No neocentromere was found in the control F1 hybrid plants. Both treated and nontreated seedlings were subsequently evaluated by fluorescent in situ hybridization performed with genomic and repetitive DNA probes to identify Hch and rye genomes, to confirm Ag-NORs location, and to detect inactive rDNA loci. DAPI counterstaining was also helpful for the detection of neocentromeres in the lung arm of three wheat chromosomes. This study allowed us to suggest that 5-AC treatment specifically induced wheat neocentromeres in the F1 multigeneric triticale x tritordeum hybrids. [ABSTRACT FROM AUTHOR]

Through the processes of natural selection and genetic drift, allopatric populations diverge genetically and may ultimately become reproductively incompatible. In cases of prezygotic reproductive isolation, candidate systems for speciation genes logically include genes involved in mate or gamete recognition. However, where only postzygotic isolation exists, candidate speciation genes could include any genes that affect hybrid performance. We hypothesize that because mitochondrial genes frequently evolve more rapidly than the nuclear genes with which they interact, interpopulation hybridization might be particularly disruptive to mitochondrial function. Understanding the potential impact of intergenomic (nuclear and mitochondrial) coadaptation on the evolution of allopatric populations of the intertidal copepod Tigriopus californicus has required a broadly integrative research program; here we present the results of experiments spanning the spectrum of biological organization in order to demonstrate the consequences of molecular evolution on physiological performance and organismal fitness. We suggest that disruption of mitochondrial function, known to result in a diverse set of human diseases, may frequently underlie reduced fitness in interpopulation and interspecies hybrids in animals. [ABSTRACT FROM AUTHOR]

Three families of pararetrovirus-like sequences were isolated from the genome of potato using PCR of a characteristic fragment extending from the end of the transactivator domain. The potato pararetrovirus-like sequences are abundant in the nuclear genome of potato as demonstrated by their hybridisation to high-molecular weight DNA in Southern transfers and by fluorescence in situ hybridisation. Sequencing of cloned PCR products demonstrated that the potato pararetrovirus-like sequences were similar to other pararetroviral sequences and also to some expressed sequences from tobacco and tomato, notably from callus and Agrobacterium-infected tissue. It is possible that the potato pararetroviral sequences defend against viral genes via silencing mechanisms, although, as in Petunia or banana, their transcription and recombination may cause infection under stress conditions. Copyright © 2005 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Crosses between populations of the copepod Tigriopus californicus typically result in outbreeding depression. In this study, replicate hybrid populations were initiated with first generation backcross hybrids between two genetically distinct populations from California: Royal Palms (RP) and San Diego (SD). Reciprocal F1 were backcrossed to SD, resulting in expected starting frequencies of 25% RP/75% SD nuclear genes on either a pure RP cytoplasmic or a pure SD cytoplasmic background. After 1 year of hybridization (up to 15 generations), seven microsatellite loci were scored in two replicates on each cytoplasmic background. Frequencies of the rarer RP alleles increased significantly in all four replicates, regardless of cytoplasmic source, producing a mean hybridity of 0.97 (maximum = 1), instead of the expected 0.50. Explicit tests for heterozygote excess across loci and replicates showed significant deviations. Only the two physically linked markers showed linkage disequilibrium in all replicates. Subsequent fitness assays in parental populations and early generation hybrids revealed lower fitness in RP than SD, and significant F2 breakdown. Computer simulations showed that selection must be invoked to explain the shift in allele frequencies. Together, these results suggest that hybrid inferiority in early generations gave way to hybrid superiority in later generations. [ABSTRACT FROM AUTHOR]

The old Portuguese wheat landrace aggregate known as 'Barbela' shows good productivity under the low-fertility conditions often associated with acid soils. The use of genomic rye DNA, in combination with 45S rDNA and the repetitive sequences dpTa1 and pSc119.2 as probes, in two sequential in situ hybridization steps enabled the identification of all chromosomes in the 'Barbela' wheat lines and the detection of the introgression of rye-origin chromatin onto wheat chromosome arm 2DL in two of the lines. Amplification of microsatellite loci using published primer pairs showed that the distal segment of wheat chromosome 2DL, which was involved in the rye translocation, was deleted. The identification and characterization of small recombinant chromosome segments in wheat–rye lines may allow their use in plant breeding programmes. Their presence in farmer-maintained material demonstrates the importance of maintaining, characterizing, and collecting landrace material before valuable genetic combinations are lost as uniform commercial crops are introduced.Key words: biodiversity, in situ hybridization, microsatellites, plant breeding, recombination, alien chromosomes, marker selection.La vieille variété de pays amalgamée d'origine portugaise connue sous le nom de 'Barbela' montre une bonne productivité en conditions de faible fertilité, lesquelles sont souvent rencontrées dans des sols acides. L'emploi comme sondes de l'ADN génomique du seigle en combinaison avec l'ADNr 45S et les séquences répétitives dpTa1 ainsi que pSc119.2, lors d'hybridations in situ séquentielles, a permis d'identifier tous les chromosomes au sein des lignées du blé 'Barbela' et la détection d'une introgression de chromatine provenant du seigle au sein du bras chromosomique 2DL chez deux des lignées. L'amplification de microsatellites à l'aide d'amorces déjà caractérisées a montré que le segment distal du chromosome 2DL, celui impliqué dans la translocation avec le seigle, a été délété. L'identification et la caractérisation de courts segments chromosomiques recombinants dans des lignées blé–seigle pourraient ouvrir la voie à leur utilisation dans des programmes de sélection. Leur présence au sein de lignées retenues par les agriculteurs démontre l'importance du maintien, de la caractérisation et de la collection de variétés de pays avant que ne soient perdues des combinaisons génétiques de valeur avec l'introduction de cultures commerciales uniformes.Mots clés : biodiversité, hybridation in situ, microsatellite, amélioration génétique, recombinaison, chromosomes étrangers, sélection de marqueurs[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

The evolution of chromosomes in species in the family Bovidae includes fusion and fission of chromosome arms (giving different numbers of acrocentric and metacentric chromosomes with a relatively conserved total number of arms) and evolution in both DNA sequence and copy number of the pericentromeric α-satellite I repetitive DNA sequence. Here, a probe representing the sheep α-satellite I sequence was isolated and hybridized to genomic DNA digests and metaphase chromosomes from various Bovidae species. The probe was highly homologous to the centromeric sequence in all species in the tribe Caprini, including sheep (Ovis aries ), goat (Capra hircus ) and the aoudad or Barbary sheep (Amnotragus lervia ), but showed no detectable hybridization to the α-satellite I sequence present in the tribe Bovini and at most very weak to species in the tribes Hippotragini, Alcelaphini or Aepycerotini. The sex chromosomes of sheep, goat and aoudad did not contain detectable α-satellite I sequence; in sheep, one of the three metacentric autosomal chromosomes does not carry the sequence, while in aoudad, it is essentially absent in three large autosomal pairs as well as the large metacentric chromosome pair. The satellite probes can be used as robust chromosome and karyotype markers of evolution among tribes and increase the resolution of the evolutionary tree at the base of the Artiodactyla. Copyright © 2001 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Despite the many questions regarding satellite DNA sequences and their cellular roles, the evolutionary history of eukaryotic genomes seems to have been largely influenced by this dynamic and multifaceted genomic component. The bovine genome is highly rich in diverse satDNA sequences that differ in monomer sequence and length, complexity, chromosomal location and abundance, as well as in their sequences' evolutionary mechanisms. In the evolution of the Bovidae family, the genomes' repetitive fraction played a central role in karyotype reorganisation, and in the last few decades several studies have demonstrated and reinforced an association between centromeric satDNAs and the process of chromosome evolution in remodelling genomes of Bovidae species. Here, we review different aspects of the molecular nature and genome behaviour of all the satDNA families identified in the bovine genome, including their organisation, abundance, chromosome localisation, variation in sequence, and evolutionary history in the Bovidae family and in particular in the Bovinae subfamily, taking an integrative perspective. "Evolution and satDNA" can be addressed through two complementary views: the satDNA sequence evolution per se, and genome evolution promoted by the satDNA dynamism. SatDNA both provides phylogenetic information and is a critical genomic component that enables sequence and chromosome evolution – features arising from its presence, absence or alteration. [ABSTRACT FROM AUTHOR]

Background Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. Scope Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. Conclusion Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop. [ABSTRACT FROM AUTHOR]

Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a prosurvival gene expression program that alters cellular metabolism and neutralizes oxidative stress. In a recent genotype-phenotype study, we classified 40% of KEAP1 mutations as ANCHOR mutants. By immunoprecipitation, these mutants bind more NRF2 than wild-type KEAP1 and ubiquitylate NRF2, but they are incapable of promoting NRF2 degradation. BioID-based protein interaction studies confirmed increased abundance of NRF2 within the KEAP1 ANCHOR mutant complexes, with no other statistically significant changes to the complexes. Discrete molecular dynamic simulation modeling and limited proteolysis suggest that the ANCHOR mutations stabilize residues in KEAP1 that contact NRF2. The modeling supports an intramolecular salt bridge between the R470C ANCHOR mutation and E493; mutation of the E493 residue confirmed the model, resulting in the ANCHOR phenotype. In live cells, the KEAP1 R320Q and R470C ANCHOR mutants colocalize with NRF2, p62/SQSTM1, and polyubiquitin in structured spherical droplets that rapidly fuse and dissolve. Transmission electron microscopy coupled with confocal fluorescent imaging revealed membraneless phase-separated biomolecular condensates. We present a model wherein ANCHOR mutations form p62-dependent biomolecular condensates that may represent a transitional state between impaired proteasomal degradation and autophagy. [ABSTRACT FROM AUTHOR]

Background Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. Approaches Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. Conclusions The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution. [ABSTRACT FROM AUTHOR]

*Background and Aims: Saffron (Crocus sativus) is a sterile triploid (2N = 3x = 24) cultivated species, of un known origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus series Crocus. Using DNA markers, this study aimed to examine the diversity and relationships within and between species of Crocus series Crocus. *Methods: Eleven inter-retroelement amplified polymorphism (IRAP) primers were used in 63 different combina tions with 35 single-plant accessions of C. sativus and related Crocus species in order to determine genetic variabil ity and to conduct phylogenetic analysis. *Key Results: A total of 4521 distinct polymorphic bands from 100 bp to approx. 4 kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values var ied from approx. 0-37 to approx. 0-05 (mean 0-17 ± 0-1) and the major allele frequency had a mean of 0-87. High levels of polymorphism were identified between accessions of the six species of Crocus series Crocus related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained in the region from Kashmir through Iran to Spain. *Conclusions In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal ge netic variation, and it is concluded that the triploid hybrid species has most probably arisen only once. The data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saf fron with improved characteristics, and show the need for conservation and collection of wild Crocus. [ABSTRACT FROM AUTHOR]

Background and Aims The genus Nicotiana includes diploid and tetraploid species, with complementary ecological, agronomic and commercial characteristics. The species are of economic value for tobacco, as ornamentals, and for secondary plant-product biosynthesis. They show substantial differences in disease resistance because of their range of secondary products. In the last decade, sexual hybridization and transgenic technologies have tended to eclipse protoplast fusion for gene transfer. Somatic hybridization was exploited in the present investigation to generate a new hybrid combination involving two sexually incompatible tetraploid species. The somatic hybrid plants were characterized using molecular, molecular cytogenetic and phenotypic approaches. Methods Mesophyll protoplasts of the wild fungus-resistant species N. debneyi (2n = 4x = 48) were electrofused with those of the ornamental interspecific sexual hybrid N. × sanderae (2n = 2x = 18). From 1570 protoplast-derived cell colonies selected manually in five experiments, 580 tissues were sub-cultured to shoot regeneration medium. Regenerated plants were transferred to the glasshouse and screened for their morphology, chromosomal composition and disease resistance. Key Results Eighty-nine regenerated plants flowered; five were confirmed as somatic hybrids by their intermediate morphology compared with parental plants, cytological constitution and DNA-marker analysis. Somatic hybrid plants had chromosome complements of 60 or 62. Chromosomes were identified to parental genomes by genomic in situ hybridization and included all 18 chromosomes from N. × sanderae, and 42 or 44 chromosomes from N. debneyi. Four or six chromosomes of one ancestral genome of N. debneyi were eliminated during culture of electrofusion-treated protoplasts and plant regeneration. Both chloroplasts and mitochondria of the somatic hybrid plants were probably derived from N. debneyi. All somatic hybrid plants were fertile. In contrast to parental plants of N. × sanderae, the seed progeny of somatic hybrid plants were resistant to infection by Peronospora tabacina, a trait introgressed from the wild parent, N. debneyi. Conclusions Sexual incompatibility between N. × sanderae and N. debneyi was circumvented by somatic hybridization involving protoplast fusion. Asymmetrical nuclear hybridity was seen in the hybrids with loss of chromosomes, although importantly, somatic hybrids were fertile and stable. Expression of fungal resistance makes these somatic hybrids extremely valuable germplasm in future breeding programmes in ornamental tobacco. [ABSTRACT FROM AUTHOR]

Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM × DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.Heredity (2009) 102, 453–464; doi:10.1038/hdy.2009.9; published online 4 March 2009 [ABSTRACT FROM AUTHOR]

The morphological, yield, cytological and molecular characteristics of bread wheat x tritordeum F1 hybrids (2n = 6x = 42; AABBDHch) and their parents were analysed. Morphologically, these hybrids resembled the wheat parent. They were slightly bigger than both parents, had more spikelets per spike, and tillered more profusely. The hybrids are self-fertile but a reduction of average values of yield parameters was observed. For the cytological approach we used a double-target fluorescence in situ hybridization performed with total genomic DNA from Hordeum chilense L. and the ribosomal sequence pTa71. This technique allowed us to confirm the hybrid nature and to analyse chromosome pairing in this material. Our results showed that the expected complete homologous pairing (14 bivalents plus 14 univalents) was only observed in 9.59% of the pollen mother cells (PMCs) analysed. Some PMCs presented autosyndetic pairing of Hch and A, B or D chromosomes. The average number of univalents was higher in the wheat genome (6.8) than in the Hch genome (5.4). The maximum number of univalents per PMC was 20. We only observed wheat multivalents (one per PMC) but the frequency of trivalents (0.08) was higher than that of quadrivalents (0.058). We amplified 50 RAPD bands polymorphic between the F1 hybrid and one of its parents, and 31 ISSR polymorphic bands. Both sets of markers proved to be reliable for DNA fingerprinting. The complementary use of morphological and yield analysis, molecular cytogenetic techniques and molecular markers allowed a more accurate evaluation and characterization of the hybrids analysed here. [ABSTRACT FROM AUTHOR]

Repetitive DNA in the mammalian genome is a valuable record and marker for evolution, providing information about the order and driving forces related to evolutionary events. The evolutionarily young 1.709 satellite IV DNA family is present near the centromeres of many chromosomes in the Bovidae. Here, we isolated 1.709 satellite DNA sequences from five Bovidae species belonging to Bovini: Bos taurus (BTA, cattle), Bos indicus (BIN, zebu), Bubalus bubalis (BBU, water buffalo) and Tragelaphini tribes: Taurotragus oryx (TOR, eland) and Tragelaphus euryceros (TEU, bongo). Its presence in both tribes shows the sequence predates the evolutionary separation of the two tribes (more than 10 million years ago), and primary sequence shows increasing divergence with evolutionary distance. Genome organization (Southern hybridization) and physical distribution (in situ hybridization) revealed differences in the molecular organization of these satellite DNA sequences. The data suggest that the sequences on the sex chromosomes and the autosomes evolve as relatively independent groups, with the repetitive sequences suggesting that Bovini autosomes and the Tragelaphini sex chromosomes represent the more primitive chromosome forms. Copyright © 2006 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

From a recombinant DNA-library fromCrocus vernus, two closely related clones of highly repetitive DNA, pCvKB7 and pCvKB8, were sequenced and their genomic distribution and organization were investigated by Southern and in situ hybridization. The lengths of the clones were 181 and 178 bp respectively; the sequences were approximately 85% identical, and thus belonged to a sequence family, named the pCvKB8-family. No homologous sequences were found in the databases (BLAST made may 2004). The presence of pCvKB8 in 52Crocusspecies and six species from other genera were analyzed by Southern hybridization. The sequence family was essentiallyCrocus-specific. However, the distribution of hybridization signal across the genus showed poor agreement with the taxonomic structure of theCrocusgenus, suggesting that the subdivision does not follow the phylogeny of this sequence family. The chromosomal distribution on threeCrocusspecies was essentially identical: tandem organization close to all telomeres and most centromeres, with a few additional intercalary sites. [ABSTRACT FROM AUTHOR]

Ensete ventricosum (Musaceae, enset) is an Ethiopian food security crop. To realize the potential of enset for rural livelihoods, further knowledge of enset diversity, genetics and genomics is required to support breeding programs and conservation. This study was conducted to explore the enset genome to develop molecular markers, genomics resources, and characterize enset landraces while giving insight into the organization of the genome. We identified 233 microsatellites (simple sequence repeats, SSRs) per Mbp in the enset genome, representing 0.28% of the genome. Mono- and di-nucleotide repeats motifs were found in a higher proportion than other classes of SSR-motifs. In total, 154,586 non-redundant enset microsatellite markers (EMM) were identified and 40 selected for primer development. Marker validation by PCR and low-cost agarose gel electrophoresis revealed that 92.5% were polymorphic, showing a high PIC (Polymorphism Information Content; 0.87) and expected heterozygosity (He = 0.79–0.82). In silico analysis of genomes of closely related species showed 46.86% of the markers were transferable among enset species and 1.90% were transferable to Musa. The SSRs are robust (with basic PCR methods and agarose gel electrophoresis), informative, and applicable in measuring enset diversity, genotyping, selection and potentially breeding. Enset SSRs are available in a web-based database at https://enset-project.org/EnMom@base.html (or https://enset.aau.edu.et/index.html, downloadable from Figshare). [ABSTRACT FROM AUTHOR]

Sequence data and genomic in situ hybridization identify the New World diploid Panicum capillare as an ancestral genome of the Old World tetraploid cereal broomcorn millet, P. miliaceum.Panicum miliaceum (broomcorn millet) is a tetraploid cereal, which was among the first domesticated crops, but is now a minor crop despite its high water use efficiency. The ancestors of this species have not been determined; we aimed to identify likely candidates within the genus, where phylogenies are poorly resolved. Nuclear and chloroplast DNA sequences from P. miliaceum and a range of diploid and tetraploid relatives were used to develop phylogenies of the diploid and tetraploid species. Chromosomal in situ hybridization with genomic DNA as a probe was used to characterize the genomes in the tetraploid P. miliaceum and a tetraploid accession of P. repens. In situ hybridization showed that half the chromosomes of P. miliaceum hybridized more strongly with labelled genomic DNA from P. capillare, and half with labelled DNA from P. repens. Genomic DNA probes differentiated two sets of 18 chromosomes in the tetraploid P. repens. Our phylogenetic data support the allotetraploid origin of P. miliaceum, with the maternal ancestor being P. capillare (or a close relative) and the other genome being shared with P. repens. Our P. repens accession was also an allotetraploid with two dissimilar but closely related genomes, the maternal genome being similar to P. sumatrense. Further collection of Panicum species, particularly from the Old World, is required. It is important to identify why the water-efficient P. miliaceum is now of minimal importance in agriculture, and it may be valuable to exploit the diversity in this species and its ancestors. [ABSTRACT FROM AUTHOR]