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1.
M. E. Manetti M. Rossi M. Nakabashi M. A. Grandbastien Marie Anne Van Sluys 《Molecular genetics and genomics : MGG》2009,281(3):261-271
Eukaryotic genome expansion/retraction caused by LTR-retrotransposon activity is dependent on the expression of full length
copies to trigger efficient transposition and recombination-driven events. The Tnt1 family of retrotransposons has served
as a model to evaluate the diversity among closely related elements within Solanaceae species and found that members of the
family vary mainly in their U3 region of the long terminal repeats (LTRs). Recovery of a full length genomic copy of Retrosol
was performed through a PCR-based approach from wild potato, Solanum oplocense. Further characterization focusing on both LTR sequences of the amplified copy allowed estimating an approximate insertion
time at 2 million years ago thus supporting the occurrence of transposition cycles after genus divergence. Copy number of
Tnt1-like elements in Solanum species were determined through genomic quantitative PCR whereby results sustain that Retrosol in Solanum species is a low copy number retrotransposon (1–4 copies) while Retrolyc1 has an intermediate copy number (38 copies) in
S. peruvianum. Comparative analysis of retrotransposon content revealed no correlation between genome size or ploidy level and Retrosol
copy number. The tetraploid cultivated potato with a cellular genome size of 1,715 Mbp harbours similar copy number per monoploid
genome than other diploid Solanum species (613–884 Mbp). Conversely, S. peruvianum genome (1,125 Mbp) has a higher copy number. These results point towards a lineage specific dynamic flux regarding the history
of amplification/activity of Tnt1-like elements in the genome of Solanum species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
2.
Short‐term hybridisation activates Tnt1 and Tto1 Copia retrotransposons in wild tuber‐bearing Solanum species 下载免费PDF全文
Interspecific hybridisation in tuber‐bearing species of Solanum is a common phenomenon and represents an important source of variability, crucial for adaptation and speciation of potato species. In this regard, the effects of interspecific hybridisation on retrotransposon families present in the genomes, and their consequent effects on generation of genetic variability in wild tuber‐bearing Solanum species, are poorly characterised. The aim of this study was to analyse the activity of retrotransposons in inter‐ and intraspecific hybrids between S. kurtzianum and S. microdontum, obtained by controlled crosses, and the effects on morphological, genetic and epigenetic variability. For genetic and epigenetic analysis, S‐SAP (sequence‐specific amplification polymorphism) and TMD (transposon methylation display) techniques were used, respectively, with specific primers for Tnt1 and Tto1 retrotransposon families (Order LTR, Superfamily Copia). The results indicate that at morphological level, interspecific hybrid genotypes differ from their parental species, whereas derived intraspecific hybrids do not. In both cases, we observed significant reductions in pollen grain viability, and a negative correlation with Tnt1 mobility. Both retrotransposons, Tto1 and Tnt1, were mobilised in the genotypes analysed, with mobility ranging from 0 to 7.8%. Furthermore, at the epigenetic level, demethylation was detected in the vicinity of Tnt1 and Tto1 in the hybrids compared with the parental genotypes. These patterns were positively correlated with the activity of the retrotransposons. The results suggest a possible mechanism through which hybridisation events generate genetic variability in tuber‐bearing species of Solanum through retrotranposon activation. 相似文献
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5.
《Bioscience, biotechnology, and biochemistry》2013,77(12):2398-2400
A previous study generated lettuce (Lactuca sativa) mutant lines tagged by retrotransposon Tnt1 from tobacco (Nicotiana tabacum) and identified a homozygous mutant, Tnt6a, that exhibited severe dwarf phenotype. Here we show that Tnt1 is inserted into the intron of gibberellin biosynthetic gene LsGA3ox1 in Tnt6a mutants. Expression analysis suggests that LsGA3ox1 is nearly knocked out in the Tnt6a mutants. 相似文献
6.
Determination of vertebral heart score in three species of Spider monkey (Ateles fusciceps,A. hybridus and A. paniscus) 下载免费PDF全文
Background
The vertebral heart score (VHS) is a method of evaluation of cardiac size well documented in domestic mammals and in other primate species, and the aim of this study was to determine the VHS in three species of Spider monkey.Methods
In this retrospective study, right lateral radiographs of thirty clinically well animals were reviewed and VHS determined. The species included were Ateles fusciceps (n=17), Ateles hybridus (n=8) and Ateles paniscus (n=5).Results
The VHS was found to vary between species and was 9.73±0.81 for A. fusciceps, 10.53±0.37 for A. hybridus and 10.45±0.27 for A. paniscus.Conclusions
The observed values appear consistent with values determined for other primate species. There was statistically significant variation noted between species, and so VHS should be considered species‐specific in this genus. The values determined may be of benefit in objectively evaluating cardiac size in the species investigated. 相似文献7.
Anelia Iantcheva Mireille Chabaud Viviane Cosson Marielle Barascud Bernadette Schutz Catherine Primard-Brisset Patricia Durand David G. Barker Mariana Vlahova Pascal Ratet 《Plant cell reports》2009,28(10):1563-1572
Insertion mutant collections are powerful tools for genetic studies in plants. Although large-scale insertional mutagenesis
using T-DNA is not feasible in legumes, the Tnt1 tobacco retrotransposon can be used as a very efficient mutagen in the Medicago truncatula R108 genotype. In this article, we show that Tnt1 can also be exploited to create insertional mutants via transformation and/or regeneration in the reference cultivar Jemalong.
Tnt1 insertional mutagenesis in Jemalong following Agrobacterium tumefaciens-mediated transformation was found to be very efficient, with an average of greater than 15 insertions/line. In contrast,
regeneration using low-copy transgenic starter lines resulted in a highly variable rate of new Tnt1 insertions. With the goal of increasing the number of additional Tnt1 insertions during regeneration of starter lines, we have compared the insertion frequencies for a number of different regeneration
protocols. In addition, we have been able to show that sucrose-mediated osmotic shock preceding regeneration significantly
increases the transposition frequency. Under optimal conditions, 95% of the regenerated Jemalong plants possess new insertions. 相似文献
8.
Reversing expansion of Calamagrostis epigejos in a grassland biodiversity hotspot: Hemiparasitic Rhinanthus major does a better job than increased mowing intensity 下载免费PDF全文
Questions
Can hemiparasitic Rhinanthus major originating from a local population suppress the competitive clonal grass Calamagrostis epigejos and reverse its expansion in species‐rich semi‐natural grasslands? Does sowing seeds of R. major facilitate restoration of target meadow vegetation? Is R. major more beneficial for biodiversity restoration/conservation than increased mowing intensity, a conventional measure to suppress C. epigejos?Location
?ertoryje National Nature Reserve, Bílé Karpaty (White Carpathians) Protected Landscape Area, Czech Republic.Methods
We conducted a before‐after‐control‐impact experiment in meadow patches heavily infested by C. epigejos: eight blocks, each containing four plots with four treatment combinations: (1) traditional management, i.e. mowing once in summer, (2) mowing in summer and autumn (3) mowing in summer and seed sowing of R. major, (4) mowing in summer and autumn and seed sowing of R. major. Above‐ground biomass of C. epigejos and vegetation composition of each of the plots were monitored every year from 2013 to 2016. To assess the effects of treatments, we analysed biomass production of C. epigejos, herb layer cover and vegetation composition.Results
Both sowing R. major and an additional autumn meadow cut significantly suppressed C. epigejos. Their effects were additive and of comparable size. Both treatments also had significant but markedly different effects on community composition. Rhinanthus major facilitated directional community composition change towards the regional Brachypodio‐Molinetum meadows. In contrast, increased mowing intensity significantly decreased frequency of threatened species, which however may have also been influenced by R. major.Conclusions
Sowing of autochthonous R. major seeds was demonstrated as an efficient tool to suppress C. epigejos and facilitate community restoration. It can be combined with an additional meadow cut to further accelerate decline of the grass. The additional cut should however be used as a short‐term practice (1–2 years) only to minimize potential negative effects of its long‐term application on some threatened plant species. The effects of R. major are comparable to those of Rhinanthus alectorolophus reported previously. As a species occurring naturally in species‐rich dry grasslands, R. major has a broader and longer‐term application potential than R. alectorolophus in ecological restoration and conservation of these communities. 相似文献9.
10.
N. Nayan A.S.M. Sonnenberg W.H. Hendriks J.W. Cone 《Journal of applied microbiology》2018,125(2):468-479
Aim
In this study, the biological variation for improvement of the nutritive value of wheat straw by 12 Ceriporiopsis subvermispora, 10 Pleurotus eryngii and 10 Lentinula edodes strains was assessed. Screening of the best performing strains within each species was made based on the in vitro degradability of fungal‐treated wheat straw.Methods and Results
Wheat straw was inoculated with each strain for 7 weeks of solid state fermentation. Weekly samples were evaluated for in vitro gas production (IVGP) in buffered rumen fluid for 72 h. Out of the 32 fungal strains studied, 17 strains showed a significantly higher (P < 0·05) IVGP compared to the control after 7 weeks (227·7 ml g?1 OM). The three best Ceriporiopsis subvermispora strains showed a mean IVGP of 297·0 ml g?1 OM, while the three best P. eryngii and L. edodes strains showed a mean IVGP of 257·8 and 291·5 ml g?1 OM, respectively.Conclusion
Ceriporiopsis subvermispora strains show an overall high potential to improve the ruminal degradability of wheat straw, followed by L. edodes and P. eryngii strains.Significance and Impact of the Study
Large variation exists within and among different fungal species in the valorization of wheat straw, which offers opportunities to improve the fungal genotype by breeding. 相似文献11.
The evolutionary analysis of the Tnt1 retrotransposon in Nicotiana species reveals the high variability of its regulatory sequences 总被引:2,自引:0,他引:2
We studied the evolution of the tobacco Tnt1 retrotransposon by analyzing
Tnt1 partial sequences containing both coding domains and U3 regulatory
sequences obtained from a number of Nicotiana species. We detected three
different subfamilies of Tnt1 elements, Tnt1A, Tnt1B, and Tnt1C, that
differ completely in their U3 regions but share conserved flanking coding
and LTR regions. U3 divergence between the three subfamilies is found in
the region that contains the regulatory sequences that control the
expression of the well-characterized Tnt1-94 element. This suggests that
expression of the three Tnt1 subfamilies might be differently regulated.
The three Tnt1 subfamilies were present in the Nicotiana genome at the time
of species divergence, but have evolved independently since then in the
different genomes. Each Tnt1 subfamily seems to have conserved its ability
to transpose in a limited and different number of Nicotiana species. Our
results illustrate the high variability of Tnt1 regulatory sequences. We
propose that this high sequence variability could allow these elements to
evolve regulatory mechanisms in order to optimize their coexistence with
their host genome.
相似文献
12.
L.I.I. Ouoba C. Kando C. Parkouda H. Sawadogo‐Lingani B. Diawara J.P. Sutherland 《Journal of applied microbiology》2012,113(6):1428-1441
Aim
To investigate physicochemical characteristics and especially genotypic diversity of the main culturable micro‐organisms involved in fermentation of sap from Borassus akeassii, a newly identified palm tree from West Africa.Methods and Results
Physicochemical characterization was performed using conventional methods. Identification of micro‐organisms included phenotyping and sequencing of: 26S rRNA gene for yeasts, 16S rRNA and gyrB genes for lactic acid bacteria (LAB) and acetic acid bacteria (AAB). Interspecies and intraspecies genotypic diversities of the micro‐organisms were screened respectively by amplification of the ITS1‐5.8S rDNA‐ITS2/16S‐23S rDNA ITS regions and repetitive sequence‐based PCR (rep‐PCR). The physicochemical characteristics of samples were: pH: 3·48–4·12, titratable acidity: 1·67–3·50 mg KOH g?1, acetic acid: 0·16–0·37%, alcohol content: 0·30–2·73%, sugars (degrees Brix): 2·70–8·50. Yeast included mainly Saccharomyces cerevisiae and species of the genera Arthroascus, Issatchenkia, Candida, Trichosporon, Hanseniaspora, Kodamaea, Schizosaccharomyces, Trigonopsis and Galactomyces. Lactobacillus plantarum was the predominant LAB species. Three other species of Lactobacillus were also identified as well as isolates of Leuconostoc mesenteroides, Fructobacillus durionis and Streptococcus mitis. Acetic acid bacteria included nine species of the genus Acetobacter with Acetobacter indonesiensis as predominant species. In addition, isolates of Gluconobacter oxydans and Gluconacetobacter saccharivorans were also identified. Intraspecies diversity was observed for some species of micro‐organisms including four genotypes for Acet. indonesiensis, three for Candida tropicalis and Lactobacillus fermentum and two each for S. cerevisiae, Trichosporon asahii, Candida pararugosa and Acetobacter tropicalis.Conclusion
fermentation of palm sap from B. akeassii involved multi‐yeast‐LAB‐AAB cultures at genus, species and intraspecies level.Significance and Impact of the Study
First study describing microbiological and physicochemical characteristics of palm wine from B. akeassii. Genotypic diversity of palm wine LAB and AAB not reported before is demonstrated and this constitutes valuable information for better understanding of the fermentation which can be used to improve the product quality and develop added value by‐products. 相似文献13.
Brittany E. Harlow Michael D. Flythe Glen E. Aiken 《Journal of applied microbiology》2018,124(1):58-66
Aims
The objective was to determine the effect of the isoflavone biochanin A (BCA) on rumen cellulolytic bacteria and consequent fermentative activity.Methods and Results
When bovine microbial rumen cell suspensions (n = 3) were incubated (24 h, 39°C) with ground hay, cellulolytic bacteria proliferated, short‐chain fatty acids were produced and pH declined. BCA (30 μg ml?1) had no effect on the number of cellulolytic bacteria or pH, but increased acetate, propionate and total SCFA production. Addition of BCA improved total digestibility when cell suspensions (n = 3) were incubated (48 h, 39°C) with ground hay, Avicel, or filter paper. Fibrobacter succinogenes S85, Ruminococcus flavefaciens 8 and Ruminococcus albus 8 were directly inhibited by BCA. Synergistic antimicrobial activity was observed with BCA and heat killed cultures of cellulolytic bacteria, but the effects were species dependent.Conclusions
These results indicate that BCA improves fibre degradation by influencing cellulolytic bacteria competition and guild composition.Significance and Impact of the Study
BCA could serve as a feed additive to improve cellulosis when cattle are consuming high‐fibre diets. Future research is needed to evaluate the effect of BCA on fibre degradation and utilization in vivo. 相似文献14.
Background
The copper (Cu) transporter (COPT/Ctr) gene family has an important role in the maintenance of Cu homeostasis in different species. The rice COPT-type gene family consists of seven members (COPT1 to COPT7). However, only two, COPT1 and COPT5, have been characterized for their functions in Cu transport. 相似文献15.
Inhibitory effects of Eucalyptus globulus on understorey plant growth and species richness are greater in non‐native regions 下载免费PDF全文
Pablo I. Becerra Jane A. Catford Inderjit Morgan Luce McLeod Krikor Andonian Erik T. Aschehoug Daniel Montesinos Ragan M. Callaway 《Global Ecology and Biogeography》2018,27(1):68-76
Aim
We studied the novel weapons hypothesis in the context of the broadly distributed tree species Eucalyptus globulus. We evaluated the hypothesis that this Australian species would produce stronger inhibitory effects on species from its non‐native range than on species from its native range.Location
We worked in four countries where this species is exotic (U.S.A., Chile, India, Portugal) and one country where it is native (Australia).Time period
2009–2012.Major taxa studied
Plants.Methods
We compared species composition, richness and height of plant communities in 20 paired plots underneath E. globulus individuals and open areas in two sites within its native range and each non‐native region. We also compared effects of litter leachates of E. globulus on root growth of seedlings in species from Australia, Chile, the U.S.A. and India.Results
In all sites and countries, the plant community under E. globulus canopies had lower species richness than did the plant community in open areas. However, the reduction was much greater in the non‐native ranges: species richness declined by an average of 51% in the eight non‐native sites versus 8% in the two native Australian sites. The root growth of 15 out of 21 species from the non‐native range were highly suppressed by E. globulus litter leachates, whereas the effect of litter leachate varied from facilitation to suppression for six species native to Australia. The mean reduction in root growth for Australian plants was significantly lower than for plants from the U.S.A., Chile and India.Main conclusions
Our results show biogeographical differences in the impact of an exotic species on understorey plant communities. Consistent with the novel weapons hypothesis, our findings suggest that different adaptations of species from the native and non‐native ranges to biochemical compounds produced by an exotic species may play a role in these biogeographical differences. 相似文献16.
Anna Schleimer Alain C. Frantz Lorraine Richart Jörg Mehnert Gono Semiadi Wirdateti Johanna Rode-Margono Michel Mittelbronn Stuart Young Frank Drygala 《Diversity & distributions》2023,29(6):713-726
Aim
The biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.Location
Malay Archipelago, with focus on Bawean and Java.Methods
We employed genome-wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times and to perform demographic model selection.Results
In contrast to the hypothesis of recent divergence during the last glacial maximum, S. blouchi was found to have diverged from S. verrucosus at least 166 k years ago following a founder event. The contemporary S. blouchi population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of S. blouchi, as was previously proposed based on morphometrics. The demographic history of S. verrucosus showed evidence of secondary contact with the sympatric banded pig (S. scrofa vittatus) that colonised Java 70 k years ago.Main Conclusions
While the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both S. verrucosus and S. blouchi. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation. 相似文献17.
Kseniya A Golovnina Elena Ya Kondratenko Alexander G Blinov Nikolay P Goncharov 《BMC plant biology》2010,10(1):168
Background
Variability of the VRN1 promoter region of the unique collection of spring polyploid and wild diploid wheat species together with diploid goatgrasses (donor of B and D genomes of polyploid wheats) were investigated. Accessions of wild diploid (T. boeoticum, T. urartu) and tetraploid (T. araraticum, T. timopheevii) species were studied for the first time. 相似文献18.
Stefan Kirsch Juanjo Pasantes Andreas Wolf Nadia Bogdanova Claudia Münch Petra Pennekamp Michael Krawczak Bernd Dworniczak Werner Schempp 《BMC evolutionary biology》2008,8(1):263
Background
The autosomal dominant polycystic kidney disease (ADPKD) is mostly caused by mutations in the PKD1 (polycystic kidney disease 1) gene located in 16p13.3. Moreover, there are six pseudogenes of PKD1 that are located proximal to the master gene in 16p13.1. In contrast, no pseudogene could be detected in the mouse genome, only a single copy gene on chromosome 17. The question arises how the human situation originated phylogenetically. To address this question we applied comparative FISH-mapping of a human PKD1 -containing genomic BAC clone and a PKD1 -cDNA clone to chromosomes of a variety of primate species and the dog as a non-primate outgroup species. 相似文献19.
Karina Reiter Christoph Plutzar Dietmar Moser Philipp Semenchuk Karl-Heinz Erb Franz Essl Andreas Gattringer Helmut Haberl Fridolin Krausmann Bernd Lenzner Johannes Wessely Sarah Matej Robin Pouteau Stefan Dullinger 《Global Ecology and Biogeography》2023,32(6):855-866
Aim
Land use is the most pervasive driver of biodiversity loss. Predicting its impact on species richness (SR) is often based on indicators of habitat loss. However, the degradation of habitats, especially through land-use intensification, also affects species. Here, we evaluate whether an integrative metric of land-use intensity, the human appropriation of net primary production, is correlated with the decline of SR in used landscapes across the globe.Location
Global.Time period
Present.Major taxa studied
Birds, mammals and amphibians.Methods
Based on species range maps (spatial resolution: 20 km × 20 km) and an area-of-habitat approach, we calibrated a “species–energy model” by correlating the SR of three groups of vertebrates with net primary production and biogeographical covariables in “wilderness” areas (i.e., those where available energy is assumed to be still at pristine levels). We used this model to project the difference between pristine SR and the SR corresponding to the energy remaining in used landscapes (i.e., SR loss expected owing to human energy extraction outside wilderness areas). We validated the projected species loss by comparison with the realized and impending loss reconstructed from habitat conversion and documented by national Red Lists.Results
Species–energy models largely explained landscape-scale variation of mapped SR in wilderness areas (adjusted R2-values: 0.79–0.93). Model-based projections of SR loss were lower, on average, than reconstructed and documented ones, but the spatial patterns were correlated significantly, with stronger correlation in mammals (Pearson's r = 0.68) than in amphibians (r = 0.60) and birds (r = 0.57).Main conclusions
Our results suggest that the human appropriation of net primary production is a useful indicator of heterotrophic species loss in used landscapes, hence we recommend its inclusion in models based on species–area relationships to improve predictions of land-use-driven biodiversity loss. 相似文献20.
F. Casasnovas E.N. Fantini J.M. Palazzini G. Giaj‐Merlera S.N. Chulze M.M. Reynoso A.M. Torres 《Journal of applied microbiology》2013,114(6):1782-1792