Effects of intragenomic polymorphism in the SSU rRNA gene on estimating marine microeukaryotic diversity: A test for ciliates using single‐cell high‐throughput DNA sequencing

2019 ◽  
Vol 17 (10) ◽  
pp. 533-543 ◽  
Author(s):  
Feng Zhao ◽  
Sabine Filker ◽  
Kuidong Xu ◽  
Ju Li ◽  
Tong Zhou ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
High Throughput ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
High Throughput Dna Sequencing

scholarly journals phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Harald R. Gruber-Vodicka ◽  
Brandon K. B. Seah ◽  
Elmar Pruesse
Keyword(s):  
High Throughput ◽  
Small Subunit ◽  
General Purpose ◽  
Reference Database ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Domains Of Life ◽  
Environmental Microbes

ABSTRACT The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.

scholarly journals Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

2017 ◽  
Vol 83 (13) ◽  
Author(s):  
Andrés Núñez ◽  
Guillermo Amo de Paz ◽  
Zuzana Ferencova ◽  
Alberto Rastrojo ◽  
Raúl Guantes ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Urban Areas ◽  
Genetic Identification ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Spore Trap ◽  
Biological Particles ◽  
High Throughput Dna Sequencing ◽  
Biological Entities

ABSTRACT Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled >87% of the total relative abundance for bacterial diversity collected in each sampler, >89% for fungi, and >97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas. IMPORTANCE Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air.

scholarly journals Correction to: Ciliate Diversity From Aquatic Environments in the Brazilian Atlantic Forest as Revealed by High-Throughput DNA Sequencing

2021 ◽  
Author(s):  
Noemi M. Fernandes ◽  
Pedro H. Campello-Nunes ◽  
Thiago S. Paiva ◽  
Carlos A. G. Soares ◽  
Inácio D. Silva-Neto
Keyword(s):  
Dna Sequencing ◽  
Atlantic Forest ◽  
High Throughput ◽  
Aquatic Environments ◽  
Brazilian Atlantic Forest ◽  
High Throughput Dna Sequencing

scholarly journals Chemiluminiscence sensor for high-throughput DNA sequencing

2009 ◽  
Vol 1 (1) ◽  
pp. 1091-1094
Author(s):  
A R A Rahman ◽  
Shihui Foo ◽  
Sanket Goel
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
High Throughput Dna Sequencing

scholarly journals Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 16 ◽  
Author(s):  
Michael P Mullen ◽  
Christopher J Creevey ◽  
Donagh P Berry ◽  
Matt S McCabe ◽  
David A Magee ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Allele Frequency ◽  
High Throughput ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Polymorphism Discovery ◽  
Pooled Dna ◽  
High Throughput Dna Sequencing

Application of high-throughput DNA sequencing to score population-specific variants for rare disorders

2019 ◽  
Vol 305 ◽  
pp. S25
Author(s):  
M.C. Ergoren ◽  
E. Manara ◽  
S. Paolacci ◽  
S.G. Temel ◽  
G. Mocan ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Rare Disorders ◽  
High Throughput Dna Sequencing

TWO THEILERIA CERVI SSU RRNA GENE SEQUENCE TYPES FOUND IN ISOLATES FROM WHITE-TAILED DEER AND ELK IN NORTH AMERICA

1999 ◽  
Vol 35 (3) ◽  
pp. 458-465 ◽  
Author(s):  
Joon-seok Chae ◽  
Suryakant D. Waghela ◽  
Thomas M. Craig ◽  
Alan A. Kocan ◽  
Gerald G. Wagner ◽  
...  
Keyword(s):  
North America ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Rrna Gene Sequence ◽  
Ssu Rrna Gene ◽  
Ssu Rrna Gene Sequence ◽  
Sequence Types
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