排序方式: 共有7条查询结果,搜索用时 15 毫秒
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L.E. Palma-Cano H.A. Piñon-Castillo S.H. Tarango-Rivero A. Carbon J. Salas-Leiva L.N. Muñoz-Castellanos C. Cravo-Laureau R. Duran E. Orrantia-Borunda 《Letters in applied microbiology》2021,72(5):556-569
We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities. 相似文献
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Jose P. Llongueras Saraswathy Nair Dayana Salas-Leiva Andrea E. Schwarzbach 《Molecular biotechnology》2013,53(3):249-256
A comparative performance evaluation of DNA extraction methods from anti-diabetic botanical supplements using various commercial kits was conducted, to determine which produces the best quality DNA suitable for PCR amplification, sequencing and species identification. All plant materials involved were of suboptimal quality showing various levels of degradation and therefore representing real conditions for testing herbal supplements. Eight different DNA extraction methods were used to isolate genomic DNA from 13 medicinal plant products. Two methods for evaluation, DNA concentration measurements that included absorbance ratios as well as PCR amplifiability, were used to determine quantity and quality of extracted DNA. We found that neither DNA concentrations nor commonly used UV absorbance ratio measurements at A 260/A 280 between 1.7 and 1.9 are suitable for globally predicting PCR success in these plant samples, and that PCR amplifiablity itself was the best indicator of extracted product quality. However, our results suggest that A 260/A 280 ratios below about 1.3 and above 2.3 indicated a DNA quality too poor to amplify. Therefore, A 260/A 280 measurements are not useful to identify samples that likely will amplify but can be used to exclude samples that likely will not amplify reducing the cost for unnecessarily subjecting samples to PCR. The two Nucleospin® plant II kit extraction methods produced the most pure and amplifiable genomic DNA extracts. Our results suggest that there are clear, discernable differences between extraction methods for low quality plant samples in terms of producing contamination-free, high-quality genomic DNA to be used for further analysis. 相似文献
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Salas-Leiva Joan Mazón-Suástegui José Manuel Teles Andressa Tovar-Ramírez Dariel 《Molecular biology reports》2020,47(12):9627-9636
Molecular Biology Reports - Seriola rivoliana intestinal microbiota (IM) was characterised under aquaculture conditions through 16S rRNA amplicon sequencing. Specimens of 30 days after... 相似文献
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Dayana Elizabeth Salas-Leiva Víctor Manuel Mayor-Durn Nelson Toro-Perea 《Aquatic Botany》2009,91(3):187-193
This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (FRT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (FST = 0.10 for the Caribbean coast and FST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast. 相似文献
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Dayana E. Salas-Leiva Alan W. Meerow Michael Calonje M. Patrick Griffith Javier Francisco-Ortega Kyoko Nakamura Dennis W. Stevenson Carl E. Lewis Sandra Namoff 《Annals of botany》2013,112(7):1263-1278
Background and aims
Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree–species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera.Methods
DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree–species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted.Key Results
Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia–Lepidozamia–Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia.Conclusions
A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae. 相似文献6.
Sebastian G Gornik Victor Flores Franziska Reinhardt Lieselotte Erber Dayana E Salas-Leiva Olga Douvropoulou Imen Lassadi Elin Einarsson Mario Mrl Anna Git Peter F Stadler Arnab Pain Ross F Waller 《Molecular biology and evolution》2022,39(10)
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression. 相似文献
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Dayana Elizabeth Salas-Leiva Víctor Manuel Mayor-Durán Nelson Toro-Perea 《Hydrobiologia》2009,620(1):17-24
The species Avicennia germinans in natural and reforested areas was analyzed to obtain information about its genetic diversity in a highly disturbed mangrove
ecosystem and to generate a useful tool for determining the donor and receptor populations of propagules. Tissue of 149 individuals
was collected in the protected areas of the Tayrona National Natural Park (Tayrona-NNP) and the Salamanca Island Parkway (Salamanca-IP).
A total of 38 alleles were found in seven microsatellite loci, leading to the detection of high levels of heterozygosity in
the two protected areas. The impact of the highway on the Salamanca-IP-south population was shown when the inbreeding coefficient
from younger individuals was compared with older ones; inbreeding increased 4.2 times. The inbreeding coefficient in the reforested
area was 2.2 times higher than that in the Salamanca-IP-south zone. Thus, for future reforestations in this area, the collecting
of propagules should come from two sectors—one to the north of the highway including Tayrona-NNP and the other to the south.
Finally, we consider that the viability of the reforested population in the short and medium term would be improved if good
reforestation practices are implemented for A. germinans.
Handling editor: C. Sturmbauer 相似文献
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