scholarly journals Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2418 ◽  
Author(s):  
Laura Taillebois ◽  
Christine Dudgeon ◽  
Safia Maher ◽  
David A. Crook ◽  
Thor M. Saunders ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Reef Fish ◽  
Illumina Miseq ◽  
Design Criteria ◽  
Stock Identification ◽  
Northern Australia ◽  
Reef Fish Species ◽  
Generation Sequencing

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapperLutjanus johnii, blackspotted croakerProtonibea diacanthusand grass emperorLethrinus laticaudisusing a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

scholarly journals Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Mike J. Wilkinson ◽  
Claudia Szabo ◽  
Caroline S. Ford ◽  
Yuval Yarom ◽  
Adam E. Croxford ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Dna Barcodes ◽  
Next Generation ◽  
Generation Sequencing

Targeted next-generation sequencing as a diagnostic tool in gastrointestinal system cancer/polyposis patients

2020 ◽  
Vol 106 (6) ◽  
pp. 510-517
Author(s):  
Sinem Yalcintepe ◽  
Hakan Gurkan ◽  
Selma Demir ◽  
Hilmi Tozkir ◽  
Huseyin Ahmet Tezel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Cancer ◽  
Illumina Miseq ◽  
Cancer Predisposition ◽  
Next Generation ◽  
Personalized Care ◽  
Screening Programs ◽  
Predisposition Genes ◽  
Generation Sequencing ◽  
Dependent Probe

Background: Recent advances in next-generation sequencing (NGS) technology have enabled multigene testing and changed the diagnostic approach to hereditary gastrointestinal cancer/polyposis syndromes. The aim of this study was to analyze different cancer predisposition genes in hereditary/sporadic gastrointestinal cancer/polyposis. Methods: Cancer predisposition genes were analyzed with an Illumina MiSeq NGS system in 80 patients with gastrointestinal cancer/polyposis who were examined between the years 2016 and 2019. Deletion/duplication analysis of MLH1, MSH2, and EPCAM genes was performed by using the multiplex ligation-dependent probe amplification method. Results: Germline testing of hereditary cancer-related genes was performed in 80 patients with gastrointestinal cancer/polyposis. A total of 30 variants in 30 cases (37.5%) were assessed as pathogenic/likely pathogenic. A total of 19 heterozygous variants were assessed as variants of uncertain clinical significance in 17 cases (21.25%) and 18 (22.5%) novel variations (9 pathogenic/likely pathogenic, 9 variants of uncertain significance) were determined. In 4 (5%) cases, multiplex ligation-dependent probe amplification detected deletions in MLH1, MSH2, and EPCAM genes. Conclusion: The accumulation of analyses with multigene testing will increase the available data for cancer predisposition genes in hereditary gastrointestinal cancer/polyposis. Educational campaigns for prevention, efficient screening programs, and more personalized care based on the profile of individual patients are necessary.

scholarly journals Next-Generation Sequencing reveals relationship between the larval microbiome and food substrate in the polyphagous Queensland fruit fly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rajib Majumder ◽  
Brodie Sutcliffe ◽  
Phillip W. Taylor ◽  
Toni A. Chapman
Keyword(s):  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Fruit Fly ◽  
Egg Laying ◽  
Food Sources ◽  
Natural Food ◽  
Next Generation ◽  
North East ◽  
Host Fruit ◽  
Generation Sequencing

Abstract Insects typically host substantial microbial communities (the ‘microbiome’) that can serve as a vital source of nutrients and also acts as a modulator of immune function. While recent studies have shown that diet is an important influence on the gut microbiome, very little is known about the dynamics underpinning microbial acquisition from natural food sources. Here, we addressed this gap by comparing the microbiome of larvae of the polyphagous fruit fly Bactrocera tryoni (‘Queensland fruit fly’) that were collected from five different fruit types (sapodilla [from two different localities], hog plum, pomegranate, green apple, and quince) from North-east to South-east Australia. Using Next-Generation Sequencing on the Illumina MiSeq platform, we addressed two questions: (1) what bacterial communities are available to B. tryoni larvae from different host fruit; and (2) how does the microbiome vary between B. tryoni larvae and its host fruit? The abundant bacterial taxa were similar for B. tryoni larvae from different fruit despite significant differences in the overall microbial community compositions. Our study suggests that the bacterial community structure of B. tryoni larvae is related less to the host fruit (diet) microbiome and more to vertical transfer of the microbiome during egg laying. Our findings also suggest that geographic location may play a quite limited role in structuring of larval microbiomes. This is the first study to use Next-Generation Sequencing to analyze the microbiome of B. tryoni larvae together with the host fruit, an approach that has enabled greatly increased resolution of relationships between the insect’s microbiome and that of the surrounding host tissues.

scholarly journals Next-Generation Sequencing of a Single Domain Antibody Repertoire Reveals Quality of Phage Display Selected Candidates

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0149393 ◽  
Author(s):  
Kendrick B. Turner ◽  
Jennifer Naciri ◽  
Jinny L. Liu ◽  
George P. Anderson ◽  
Ellen R. Goldman ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Phage Display ◽  
Single Domain ◽  
Antibody Repertoire ◽  
Next Generation ◽  
Single Domain Antibody ◽  
Domain Antibody ◽  
Generation Sequencing

scholarly journals Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11842
Author(s):  
Yen-Yi Liu ◽  
Bo-Han Chen ◽  
Chih-Chieh Chen ◽  
Chien-Shun Chiou
Keyword(s):  
Next Generation Sequencing ◽  
Core Genome ◽  
Read Depth ◽  
Sequence Type ◽  
Performance Ratio ◽  
Next Generation ◽  
Food Borne ◽  
The Cost ◽  
Generation Sequencing

With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.

scholarly journals Pengembangan Metode In-House HLA-Typing Gen HLA Kelas I (HLA A, HLA B, dan HLA C) Menggunakan Next Generation Sequencing Illumina MiSeq

2015 ◽  
Vol 47 (3) ◽  
pp. 152-159
Author(s):  
Rika Yuliwulandari ◽  
Kinasih Prayuni ◽  
Kenconoviyati ◽  
R. W. Susilowati ◽  
Abdul Salam M. Sofro
Keyword(s):  
Next Generation Sequencing ◽  
Illumina Miseq ◽  
Hla Typing ◽  
Next Generation ◽  
Generation Sequencing
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