Search results for "barcoding"

Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.

2020

Genetic diseases are driven by aberrations of the human genome. Identification of such aberrations including structural variations (SVs) is key to our understanding. Conventional short-reads whole genome sequencing (cWGS) can identify SVs to base-pair resolution, but utilizes only short-range information and suffers from high false discovery rate (FDR). Linked-reads sequencing (10XWGS) utilizes long-range information by linkage of short-reads originating from the same large DNA molecule. This can mitigate alignment-based artefacts especially in repetitive regions and should enable better prediction of SVs. However, an unbiased evaluation of this technology is not available. In this study, w…

Composition and Genetic Diversity of Mosquitoes (Diptera: Culicidae) on Islands and Mainland Shores of Kenya's Lakes Victoria and Baringo.

2016

The Lake Baringo and Lake Victoria regions of Kenya are associated with high seroprevalence of mosquito-transmitted arboviruses. However, molecular identification of potential mosquito vector species, including morphologically identified ones, remains scarce. To estimate the diversity, abundance, and distribution of mosquito vectors on the mainland shores and adjacent inhabited islands in these regions, we collected and morphologically identified adult and immature mosquitoes and obtained the corresponding sequence variation at cytochrome c oxidase 1 (COI) and internal transcribed spacer region 2 (ITS2) gene regions. A total of 63 species (including five subspecies) were collected from both…

A practical method for barcoding and size-trimming PCR templates for amplicon sequencing

2016

Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5′ end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.

Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches

2018

Mercury (Hg) is a highly toxic element for living organisms and is known to bioaccumulate and biomagnify. Here, we analyze the response of benthic foraminifera communities cultured in mesocosm and exposed to different concentrations of Hg. Standard morphological analyses and environmental DNA metabarcoding show evidence that Hg pollution has detrimental effects on benthic foraminifera. The molecular analysis provides a more complete view of foraminiferal communities including the soft-walled single-chambered monothalamiids and small-sized hard-shelled rotaliids and textulariids than the morphological one. Among these taxa that are typically overlooked in morphological studies we found poten…

Active and secreted IgA-coated bacterial fractions from the human gut reveal an under-represented microbiota core

2013

AbstractHost-associated microbiota varies in distribution depending on the body area inhabited. Gut microbes are known to interact with the human immune system, maintaining gut homoeostasis. Thus, we studied whether secreted-IgA (S-IgA) coat specific microbial taxa without inducing strong immune responses. To do so, we fractionated gut microbiota by flow cytometry. We found that active and S-IgA-coated bacterial fractions were characterized by a higher diversity than those observed in raw faecal suspensions. A long-tail effect was observed in family distribution, revealing that rare bacteria represent up to 20% of total diversity. While Firmicutes was the most abundant phylum, the majority …

Tassonomia integrata per lo studio della biodiversità vegetale

2010

Diversi marcatori plastidiali sono stati testati su varie specie della flora vascolare spontanea al fine di valutarne il potere discriminante come DNA barcoding, da integrare nell'identificazione tassonomica con i dati morfologici, cariologici, fenologici e biogeografici.

Insects and fungi: ecological interactions and functional biodiversity

Barcoding of parasitoid wasps (Braconidae and Chalcidoidea) associated with wild and cultivated olives in the Western Cape of South Africa 1

2019

Wild and cultivated olives harbor and share a diversity of insects, some of which are considered agricultural pests, such as the olive fruit fly. The assemblage of olive-associated parasitoids and seed wasps is rich and specialized in sub-Saharan Africa, with native species possibly coevolving with their hosts. Although historical entomological surveys reported on the diversity of olive wasp species in the Western Cape Province of South Africa, no comprehensive study has been performed in the region in the molecular era. In this study, a dual approach combining morphological and DNA-based methods was used for the identification of adult specimens reared from olive fruits. Four species of Br…

On the occurrence of the invasive Atlantic blue crab Callinectes sapidus Rathbun 1896 (Decapoda: Brachyura: Portunidae) in Sicilian inland waters

2022

The Atlantic blue crab Callinectes sapidus Rathbun, 1896 is included among the worst invasive alien species in the Mediterranean Sea. Here, we report the finding of the species in two Sicilian rivers, the Irminio and the Imera Meridionale, where it was collected up to 6 km from the river mouths. Although several records of the species are already available from Italy, this is the first evidence of the occurrence of this invasive crab so far from the coastline in the whole country. In the light of the well-known impact of the Atlantic blue crab on the invaded water bodies, the monitoring of the species and appropriate mitigation strategies should be implemented in order to protect the threat…

The Impact of Environmental Conditions on Efficiency of Host Plant DNA Barcoding for Polyphagous Beetles.

2015

Recently, several papers were published dealing with host plant identification for selected species of insects, including beetles. These studies took advantage of the DNA barcoding approach and generally showed that it is possible to identify diet composition from plant DNA present in insect guts. However, none of these studies considered how the impact of environmental conditions affected the likelihood of insect feeding and, therefore, the presence of host plant DNA that could be amplified and sequenced. In the present study, individuals of the polyphagous weevil Centricnemus leucogrammus (Germar, 1824) (Curculionidae: Entiminae) were used to test the hypothesis that harsh environmental c…