Search results for "Sequencing"
showing 10 items of 1087 documents
Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations.
2017
Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population str…
Editorial: Exploring Plant Rhizosphere, Phyllosphere and Endosphere Microbial Communities to Improve the Management of Polluted Sites
2021
International audience
How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)
2022
Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coa…
Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha
2019
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a close…
De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)
2021
Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was gene…
Cytological and molecular characterization of three gametoclones of Citrus clementina
2013
Abstract Background Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). Results Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a sing…
The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild
2013
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al.
Nested core collections maximizing genetic diversity in Arabidopsis thaliana.
2004
Summary The successful exploitation of natural genetic diversity requires a basic knowledge of the extent of the variation present in a species. To study natural variation in Arabidopsis thaliana, we defined nested core collections maximizing the diversity present among a worldwide set of 265 accessions. The core collections were generated based on DNA sequence data from a limited number of fragments evenly distributed in the genome and were shown to successfully capture the molecular diversity in other loci as well as the morphological diversity. The core collections are available to the scientific community and thus provide an important resource for the study of genetic variation and its …
Achievement of partial nitrification under different carbon-to-nitrogen ratio and ammonia loading rate for the co-treatment of landfill leachate with…
2019
Abstract Partial nitrification (PN) is a technically and economically effective solution for the treatment of wastewater featuring low C/N ratio, allowing to achieve approximately 25% energy saving and 40% carbon source for denitrification. This study investigated the effect of different carbon to nitrogen ratio (C/N) and ammonia loading rate (ALR) on PN performances in a sequencing batch reactor (SBR) treating landfill leachate with municipal wastewater. The aim was to find an optimum range for C/N and ALR to maximize PN performances. Results demonstrated that a proper balancing between ALR and C/N is crucial to achieve high PN efficiency. The results highlighted the existence of an optimu…
Bioplastic recovery from wastewater: A new protocol for polyhydroxyalkanoates (PHA) extraction from mixed microbial cultures
2019
Abstract A new protocol for polyhydroxyalkanoates (PHA) extraction from mixed microbial cultures (MMCs) is proposed. PHA-accumulating capacity of the MMC was selected in a sequencing batch reactor (SBR) fed with a synthetic effluent emulating a fermented oil mill wastewater (OMW). The highest recovery yield and purity (74 ± 8% and 100 ± 5%, respectively) was obtained when using NH4-Laurate for which operating conditions of the extraction process such as temperature, concentration and contact time were optimized. Best conditions for PHA extraction from MMC turned to be: i) a pre-treatment with NaClO at 85 °C with 1 h of contact time, followed by ii) a treatment with lauric acid in a ratio ac…