Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

<p>Abstract</p> <p>Background</p> <p>Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria <it>Rhizobium etli </it>is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among <it>Rhizobium etli</it>.</p> <p>Results</p> <p>We identified high levels of DNA polymorphism in <it>R. etli</it>, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.</p> <p>Conclusion</p> <p>Our data suggest that <it>R. etli </it>is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.</p

Genetic differentiation in the Agave deserti (Agavaceae) complex of the Sonoran desert

The Agave deserti complex, comprising A. deserti, A. cerulata and A. subsimplex, represents a group of species and subspecies with a near allopatric distribution and clear differences in morphology. Genetic differentiation and taxonomic status with respect to spatial distribution of 14 populations of the complex were analyzed in an effort to understand the evolution and speciation process within the genus. Allelic frequencies, levels of genetic variation, expected heterozygosity (H S ), proportion of polymorphic loci (P), and genetic differentiation (y and Nei&apos;s genetic distance) were estimated using 41 putative RAPD loci. All three species show high levels of genetic variation (H S ¼ 0.12-0.29, P ¼ 63.4-95.1), and low genetic differentiation between populations and species (y populations ¼ 0.1470.02 (SE); G st ¼ 0.1170.02). Accordingly, gene flow among populations was estimated as high by three different methods (N m ¼ 2.91-6.14). Nei&apos;s genetic distances between the three species were low compared to the values obtained from other Agavaceae, and there was no clear correlation with taxonomic divisions. In a UPGMA analysis, A. subsimplex and A. cerulata formed exclusive monospecific clusters, whereas the A. deserti populations appear in more than one cluster together with other species. The results were consistent with a pattern of genetic isolation by distance

Diseño de encapsulados de Lactobacillus casei y su efecto en el peso de ratones Balb/c.

Los probióticos son reconocidos como microorganismos vivos que cuando se integran a la microbiota presentan efectos benéficos sobre el individuo que los consume. El objetivo del estudio consiste en diseñar cápsulas conteniendo Lactobacillus casei con capacidad de liberación a pH7, comparar la ganancia de peso de los ratones Balb/c alimentados con alimento comercial y capsulas de L. casei. El estudio experimental se llevó acabó con 30 ratones cepa Balb/c desde el destete hasta los 55 días de nacidos, el estudio radica en la distribución de dos grupos de estudio, 1) Grupo: 15 ratones alimentados con cápsulas conteniendo un concentrado L. casei, 2) Grupo: 15 ratones alimentados con alimento comercial. Se observó que el grupo con mayor promedio de ganancia de peso fue el grupo que recibió alimento comercial + cápsulas de L. casei, el cual presentó un peso de 23.86g y el peso del control fue de 18.33 g. Otro parámetro evaluado fue la determinación de las UFC/ ml, el cual se observó con un valor de 39x106 para el grupo alimentado con alimento comercial + cápsulas con L. casei, en tanto que el grupo alimentado solo con alimento comercial presentó un valor de 98 x105 UFC

Evaluation of the Impact of Genetically Modified Cotton After 20 Years of Cultivation in Mexico

For more than 20 years cotton has been the most widely sown genetically modified (GM) crop in Mexico. Its cultivation has fulfilled all requirements and has gone through the different regulatory stages. During the last 20 years, both research-institutions and biotech-companies have generated scientific and technical information regarding GM cotton cultivation in Mexico. In this work, we collected data in order to analyze the environmental and agronomic effects of the use of GM cotton in Mexico. In 1996, the introduction of Bt cotton made it possible to reactivate this crop, which in previous years was greatly reduced due to pest problems, production costs and environmental concerns. Bt cotton is a widely accepted tool for cotton producers and has proven to be efficient for the control of lepidopteran pests. The economic benefits of its use are variable, and depend on factors such as the international cotton-prices and other costs associated with its inputs. So far, the management strategies used to prevent development of insect resistance to GM cotton has been successful, and there are no reports of insect resistance development to Bt cotton in Mexico. In addition, no effects have been observed on non-target organisms. For herbicide tolerant cotton, the prevention of herbicide resistance has also been successful since unlike other countries, the onset of resistance weeds is still slow, apparently due to cultural practices and rotation of different herbicides. Environmental benefits have been achieved with a reduction in chemical insecticide applications and the subsequent decrease in primary pest populations, so that the inclusion of other technologies—e.g., use of non-Bt cotton- can be explored. Nevertheless, control measures need to be implemented during transport of the bolls and fiber to prevent dispersal of volunteer plants and subsequent gene flow to wild relatives distributed outside the GM cotton growing areas. It is still necessary to implement national research programs, so that biotechnology and plant breeding advances can be used in the development of cotton varieties adapted to the Mexican particular environmental conditions and to control insect pests of regional importance

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS

Diversidad filogenética y conservación: ejemplos a diferentes escalas y una propuesta a nivel poblacional para Agave victoriae-reginae en el desierto de Chihuahua, México

En este artículo presentamos una revisión de ideas y ejemplos en torno a distintas perspectivas de la diversidad filogenética. Los estudios de diversidad orientados a la conservación que utilizan exclusivamente la especie como unidad de análisis podrían beneficiarse de la incorporación de las propuestas de la diversidad filogenética, los análisis jerárquicos de la diversidad y de los análisis de complementariedad. Se revisan los índices de diversidad filogenética de Vane-Wright et al. (1991), May (1990) y Faith (1992), cuyos fundamentos son similares, y se ejemplifica su uso. Estos métodos de valoración diferencial de los taxa basados en la diversidad filogenética se pueden aplicar con base en datos de diferente calidad y a diferentes niveles taxonómicos y espaciales. Pueden ser utilizados para elegir: áreas de conservación con alto contenido de diversidad filogenética; de especies u otros taxa supraespecíficos que ameriten esfuerzos particulares de conservación, y para la elección de poblaciones dentro de una especie para orientar esfuerzos de conservación in situ y ex situ. El concepto de complementariedad implica encontrar el conjunto mínimo de áreas que contengan el mayor porcentaje de la diversidad filogenética total de un determinado taxón. Se recomienda aplicar este concepto con cuidado, ya que cada especie generalmente esta formada por varias poblaciones con diferentes historias de vida, adaptación local, etc., por lo que no sólo la riqueza filogenética es importante. Se revisa la partición jerárquica del índice de diversidad jerárquica propuesta por Pielou (1969) y se muestra su aplicación en la caracterización de la diversidad de tres bosques de Norteamérica. Finalmente, se desarrolla de manera explícita un análisis de diversidad filogenética para las diez poblaciones conocidas de Agave victoriae-reginae, una especie endémica y amenazada del desierto chihuahuense mexicano. Haciendo uso de una genealogía de poblaciones (dendrograma) derivada de distancias genéticas, y empleando datos demográficos y de diversidad genética, se identificaron las poblaciones prioritarias para la conservación