ABSTRACT
Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation. Here, we report a first draft of the 44.2 Mbp genome assembly of an environmental strain of the fungus Scedosporium apiospermum. The assembly consisted of 178 high-quality DNA scaffolds with 1.93% of sequence repeats identified. A total of 11,195 protein-coding genes were predicted including a diverse group of gene families involved in hydrocarbon degradation pathways like dioxygenases and cytochrome P450. The metabolic pathways identified in the genome can potentially degrade hydrocarbons like chloroalkane/alkene, chorocyclohexane, and chlorobenzene, benzoate, aminobenzoate, fluorobenzoate, toluene, caprolactam, geraniol, naphthalene, styrene, atrazine, dioxin, xylene, ethylbenzene, and polycyclic aromatic hydrocarbons. The comparison analysis between this strain and the previous sequenced clinical strain showed important differences in terms of annotated genes involved in the hydrocarbon degradation process.
ABSTRACT
The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites.
Subject(s)
Phylogeny , Plants/genetics , Rhizaria/genetics , Animals , Eukaryota , Plants/parasitology , Rhizaria/pathogenicity , Sequence AlignmentABSTRACT
El 16s rDNA es utilizado para la identificación bacteriana dada su tasa de variación entre especies. Algunas de las regiones variables de la subunidad ribosomal son más informativas que otras por lo cual en este estudio se evalúa el potencial de identificación aportado por cada región y combinaciones entre ellas. Se extrajeron las regiones variables V1 a la V8 del 16s rDNA de diferentes cepas y especies de Lactobacillus y se analizaron mediante los paquetes de STAP (ss-RNA Taxonomy Assigning Pipeline) y RDP (Ribosomal Database Project) multiclassifier. Adicionalmente se evaluaron árboles filogenéticos de máxima verosimilitud. Nuestros resultados muestran que la mayoría de regiones variables logran dar una correcta clasificación hasta género, sin embargo no son suficientes para clasificar hasta especie usando STAP. La región que presenta el mayor número de amplímeros es V5V6, sin embargo es la que presenta la mayor cantidad de falsos negativos. La que presenta el mayor número de verdaderos positivos es V1V3 (especie) para STAP y V5V8(género) para RDP. Las filogenias evaluadas mostraron que la topología de referencia se puede obtener con diferentes combinaciones de regiones variables e.g., V1V3 y V1V8. El estudio experimental de las cepas contenidas en un tampón comercial mostró que el amplicón V1V8 y el V1V3 dan una misma clasificación correcta. Proponemos la región V1V3 como la región mínima para clasificación correcta de Lactobacillus spp.. En conclusión, la región mínima para clasificar especies del género Lactobacillus es la V1V3, la cual es útil para estudios metagenómicos de muestras de probióticos.
16s rDNA is used for bacterial identification because its variation rate between species allows differentiation. The gene for this ribosomal subunit has 9 variable regions and some of them give more information than others. We were interested in evaluating the potential for species identification of each region and their combinations. We extracted the V1 to V8 regions of 16s rDNA from different strains and species of Lactobacillus and analyzed them using STAP (ss-RNA Taxonomy Assigning Pipeline) and RDP (Ribosomal Database Project) multiclassifier packages. Phylogenetic trees obtained by maximum likelihood analyses were compared. Classification results show that many regions give the correct genus classification using RDP and STAP, however they are not enough to classify up to the level of species. V5V6 region presents the highest quantity of informative fragments but also present the highest rate of false negatives. V1V3 region presents the highest rate of true positives (species) using STAP and the region V5V8 in RDP (genus).The phylogenetic result shows that the reference topology could be obtained using different combination of regions as V1V3 and V1V8.The experimental validation was done using commercial strains from a probiotic tampon. Sequencing analysis show that the V1V3 region gives the same information and result as the complete 16s rDNA; the three isolated strains correspond to the strains indicated in the product. We conclude that the V1V3 region is the minimum required region to classify Lactobacillus spp. in the correct way and this region is useful in metagenomics to analyze probiotics samples.
