Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1150734 | ENA |
REPOSITORIES: ENA
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Project description:microRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. Here, we perform a comprehensive analysis of miRNAs in the zoonotic parasite E. canadensis G7, one of the causative agents of the neglected disease cystic echinococcosis. Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. As a result, we found transcriptional evidence of 37 miRNAs thus expanding the miRNA repertoire of E. canadensis G7. Differential expression analysis showed significant regulated miRNAs between life cycle stages of E. canadensis G7. We confirmed the remarkable loss of conserved miRNA families in E. canadensis, reflecting their low morphological complexity and high adaptation to parasitism. This study will provide valuable information for better understanding the complex biology of this parasite and could help to find new potential targets for therapy and/or diagnosis. Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. For each sample type, two libraries were constructed from two independent samples in order to have biological replicates.
2015-02-09 | E-GEOD-64705 | biostudies-arrayexpress
Project description:microRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. Here, we perform a comprehensive analysis of miRNAs in the zoonotic parasite E. canadensis G7, one of the causative agents of the neglected disease cystic echinococcosis. Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. As a result, we found transcriptional evidence of 37 miRNAs thus expanding the miRNA repertoire of E. canadensis G7. Differential expression analysis showed significant regulated miRNAs between life cycle stages of E. canadensis G7. We confirmed the remarkable loss of conserved miRNA families in E. canadensis, reflecting their low morphological complexity and high adaptation to parasitism. This study will provide valuable information for better understanding the complex biology of this parasite and could help to find new potential targets for therapy and/or diagnosis.
2015-02-09 | GSE64705 | GEO
Project description:Traditionally, the study of evolution has focused on heritable variation, because selection on non-heritable phenotypic variation was deemed non-important for its inability to cause evolutionary responses such as diversification of lineages. Recently however, it has been suggested that also environmentally induced phenotypic variation such as phenotypic plasticity can play an important role in adaptive responses resulting in diversification. The purpose of this study is to investigate the importance of phenotypic plasticity for the diversification of lineages, using life history, morphological traits, and genomic profiling during post embryonic development in plastic and non-plastic genotypes of the common frog Rana temporaria. Six animals each originating from four different islands were reared in either constant or reduced water conditions and hepatic mRNA levels of Gosner stage 37 animals evaluated by MAGEX DNA array analysis.
2014-03-18 | E-GEOD-42274 | biostudies-arrayexpress
Project description:The páramo ecosystem has the highest rate of diversification across plant lineages on earth, of which the genus Espeletia (Asteraceae) is a prime example. The current distribution and molecular phylogeny of Espeletia suggest the influence of Andean geography and past climatic fluctuations on the diversification of this genus. However, molecular markers have failed to reveal subtle biogeographical trends in Espeletia diversification, and metabolomic evidence for allopatric segregation in plants has never been reported. Here, we present for the first time a metabolomics approach based on liquid chromatography-mass spectrometry for revealing subtle biogeographical trends in Espeletia diversification. We demonstrate that Espeletia lineages can be distinguished by means of different metabolic fingerprints correlated to the country of origin on a global scale and to the páramo massif on a regional scale. Distinctive patterns in the accumulation of secondary metabolites according to the main diversification centers of Espeletia are also identified and a comprehensive phytochemical characterization is reported. These findings demonstrate that a variation in the metabolic fingerprints of Espeletia lineages followed the biogeography of this genus, suggesting that our untargeted metabolomics approach can be potentially used as a model to understand the biogeographic history of additional plant groups in the páramo ecosystem.
2018-11-20 | MTBLS445 | MetaboLights
Project description:Traditionally, the study of evolution has focused on heritable variation, because selection on non-heritable phenotypic variation was deemed non-important for its inability to cause evolutionary responses such as diversification of lineages. Recently however, it has been suggested that also environmentally induced phenotypic variation such as phenotypic plasticity can play an important role in adaptive responses resulting in diversification. The purpose of this study is to investigate the importance of phenotypic plasticity for the diversification of lineages, using life history, morphological traits, and genomic profiling during post embryonic development in plastic and non-plastic genotypes of the common frog Rana temporaria.
2014-03-18 | GSE42274 | GEO
Project description:The Danioninae subfamily of teleost fishes boasts up to four hundred distinct species that have evolved to display a stunning diversity of morphological forms. Here we use newly assembled genome sequences of four laboratory and wild zebrafish strains as well as eleven species of the Danio and Danionella genera to explore their phylogenetic history and the genetic basis of pigment pattern diversification. Phylogenomic analyses uncover extensive introgression and incomplete lineage sorting that have obscured phylogenetic relationships within Danio and corroborate an ancient hybrid origin of zebrafish. Whereas D. rerio inherited ancestral horizontal stripes, relatives repeatedly evolved spots and vertical bars. Interspecific complementation tests reveal functional divergence of the adhesion molecule gene igsf11 and the gap junction gene gja5b between the striped zebrafish and Danio species with divergent patterns. Comparative genomic and transcriptomic analyses suggest that protein and regulatory evolution have accompanied pigment pattern diversification. Our analyses elucidate complex genetic changes underlying the phylogenetic history and morphological diversification in the Danio genus. Resolved phylogenetic relationships, available genome assemblies, transcriptomes, and genetic tractability establish Danio fish species as excellent models for biomedical research in vertebrates.
2026-02-11 | GSE319137 | GEO
Project description:The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations at least 100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa, instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history .220 samples were analysed with the Illumina HumanOmni2.5-Quad BeadChip and are described herein.
2012-09-22 | E-MTAB-1259 | biostudies-arrayexpress
Project description:Phylogeny and diversification history of the genus Philodendron (Araceae)
| PRJEB25709 | ENA
Project description:First brain methylome and transcriptomic data of two simple eusocial insects: Polistes canadensis paper wasp and Dinoponera quadriceps dinosaur ant
2015-09-30 | GSE59525 | GEO
Project description:Although the majority of previous work on campylobacteriosis has centered on the species Campylobacter jejuni, Campylobacter coli, the sister group to C. jejuni, is also a significant problem, but remains a much less studied organism. The purpose of this study was to develop and apply an expanded 16 locus MLST genotyping scheme to a large collection of C. coli isolates sampled from a wide range of host species, and to complete microarray comparative genomic hybridizations for these same strains, in order to: (1) determine whether host specific clones, genotypes, or clonal complexes are evident and (2) evaluate whether there are particular genes comprising the dispensable portion of the C. coli genome that are more commonly associated with certain host species. Genotyping and ClonalFrame analyses of the expanded MLST data suggest that (1) host preferred groups have tended to evolve in the diversification of C. coli, (2) this has happened repeatedly, at different times, throughout the evolutionary history of the species, and (3) recombination has played varying roles in the diversification of the different groups. Concomitant with the information on evolutionary history derived from the MLST data, the microarray data suggests that a combination of common ancestry in some cases and lateral gene transfer in others are behind a tendency for sets of genes to be common to isolates derived from particular hosts. Keywords: comparative genomic hybridization
2010-02-02 | GSE16787 | GEO