Consulta: subjectFacets:"High-throughput sequencing"
Registros recuperados: 6
Data/hora: 09/06/2024 13:52:31

Benthic protists: the under-charted majority
Provedor de dados: 5
Autores: Forster, Dominik; Dunthorn, Micah; Mahe, Frederic; Dolan, John R.; Audic, Stephane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-michel; Decelle, Johan; Edvardsen, Bente; Egge, Elianne; Eikrem, Wenche; Gobet, Angelique; Kooistra, Wiebe H. C. F.; Logares, Ramiro; Massana, Ramon; Montresor, Marina; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Romac, Sarah; Shalchian-tabrizi, Kamran; Simon, Nathalie; Richards, Thomas A.; Santini, Sebastien; Sarno, Diana; Siano, Raffaele; Vaulot, Daniel; Wincker, Patrick; Zingone, Adriana; De Vargas, Colomban; Stoeck, Thorsten.
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbour greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and...
Tipo: Text
Palavras-chave: Benthic microbial communities; Coastal environments; Protist diversity; High-throughput sequencing.
Ano: 2016
URL: https://archimer.ifremer.fr/doc/00341/45233/44658.pdf

Metabarcoding on planktonic larval stages: an efficient approach for detecting and investigating life cycle dynamics of benthic aliens
Provedor de dados: 5
Autores: Couton, Marjorie; Comtet, Thierry; Le Cam, Sabrina; Corre, Erwan; Viard, Frédérique.
High-throughput sequencing (HTS) technologies offer new promise to support surveillance programs targeting marine non-indigenous species (NIS). Metabarcoding might surpass traditional monitoring methods, for example through its ability to detect rare species, a key feature in early detection of NIS. Another interest of this approach is the identification of organisms difficult to identify based on morphology only (e.g., early developmental stages), making it relevant in the context of management programs. Because many marine benthic NIS have a biphasic benthopelagic life cycle, targeting their pelagic larval stages in zooplankton may allow early detection and assessment of their establishment and potential spread. We illustrate this approach with an...
Tipo: Text
Palavras-chave: Zooplankton; Time-series; Non-indigenous species; Estuary; High-throughput sequencing; Surveillance; Monitoring.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00599/71127/69442.pdf

Monitoring of four DNA extraction methods upstream of high-throughput sequencing of Anisakidae nematodes
Provedor de dados: 5
Autores: Seesao, Y.; Audebert, C.; Verrez-bagnis, Veronique; Merlin, S.; Jerome, Marc; Viscogliosi, E.; Dei-cas, E.; Aliouat-denis, C. M.; Gay, Melanie.
Different methods were evaluated to extract DNA from pooled nematodes belonging to Anisakis, Contracaecum, Pseudoterranova and Hysterothylacium genera isolated from edible fish. Pooled DNA extraction is the first and compulsory step to allow the identification of a large number of samples through high-throughput DNA sequencing with drastic time and cost reductions.
Tipo: Text
Palavras-chave: Anisakidae; High-throughput sequencing; Nematode; Pooled DNA extraction; Marine fish; COX2.
Ano: 2014
URL: https://archimer.ifremer.fr/doc/00189/30020/28607.pdf

Long-range PCR and high-throughput sequencing of Ostreid herpesvirus 1 indicate high genetic diversity and complex evolution process
Provedor de dados: 5
Autores: Bai, Chang-ming; Morga, Benjamin; Rosani, Umberto; Shi, Jie; Li, Chen; Xin, Lu-sheng; Wang, Chong-ming.
Ostreid herpesvirus 1 (OsHV-1) is an important pathogen associated with mass mortalities of cultivated marine mollusks worldwide. Since no cell line allows OsHV-1 replication in vitro, it is difficult to isolate enough high-purity viral DNA for High-Throughput Sequencing (HTS). We developed an efficient approach for the enrichment of OsHV-1 DNA for HTS with long-range PCR. Twenty-three primer pairs were designed to cover 99.3% of the reference genome, and their performances were examined on ten OsHV-1 infected samples. Amplicon mixtures from six successfully amplified samples were sequenced with Illumina platform, and one of them (ZK0118) was also sequenced with the PacBio platform. PacBio reads were assembled into 2 scaffolds compared to 9−68 scaffolds...
Tipo: Text
Palavras-chave: Long-range PCR; OsHV-1; High-throughput sequencing; Evolution; Diversity.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00464/57566/64184.pdf

The Effect of Hydrated Sodium Calcium Aluminosilicate on Fatty Liver and the Composition of the Intestinal Microbiota in Overfed Landes Geese
Provedor de dados: 89
Autores: Tang,J; Fang,Q; Lu,M; Shao,R; Shen,J; Lu,L; Niu,D.
ABSTRACT Goose fatty liver is a delicious food product and the overfeeding will cause the abnormal physiology of the geese. The objective of this study was to investigate the effect of supplementation with hydrated sodium calcium aluminosilicate (HSCAS) on the fatty liver, ileal and cecal microbiota of Landes geese during overfeeding. Sixty 70-day-old Landes geese (body weight= 3.0 ± 0.05 kg) were randomly divided into three groups, two of which were overfed with whole corn supplemented with or without HSCAS for 20 days when the fatty liver reaches to the maximum size and the negative control group was ad libitum access to the corn basal diet. The intestinal contents of the ileum and cecum from three geese per group were used for high-throughput...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Landes geese; Microbial diversity; Overfeeding; Hydrated sodium calcium aluminosilicate; High-throughput sequencing.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2018000200393

Detection and sequencing of Potato virus Y (PVY) and Potato leafroll virus (PLRV) in a volunteer plant of Solanum tuberosum L. cv. Diacol-Capiro
Provedor de dados: 109
Autores: Cárdenas,Héctor Medina; Sánchez,Pablo Gutiérrez; Montoya,Mauricio Marín.
Abstract Viral diseases are among the most limiting factors in the production of potato in Colombia and the rest of the world. The best strategy to control plant viruses consists on the use of certified seed tubers, control of arthropod vectors and the use of adequate crop management practices that reduce mechanical transmission and the presence of viral reservoirs like weeds and volunteer plants. However, the successful implementation of these practices relies on the availability of highly sensitive techniques that allow for the asymptomatic detection of viruses. In this work, we tested the performance of Next-generation sequencing (NGS) and real time RT-PCR (RT-qPCR) on a single volunteer potato plant (cv. Diacol-Capiro) growing naturally in a seed-tuber...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Polerovirus; Potyvirus; RT-qPCR; High-throughput sequencing; Solanaceae.
Ano: 2017
URL: http://www.scielo.org.co/scielo.php?script=sci_arttext&pid=S0120-28122017000400625