Building a reference transcriptome for the hexaploid hard fescue turfgrass ( Festuca brevipila ) using a combination of pacbio iso‐seq and illumina sequencing

Abstract Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species. Results: Here, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and seed head tissues. We obtained 59,510 full-length transcripts, of which 38,595 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. To test the polyploid origin of F. brevipila, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the allopolyploid origin of F. brevipila. Conclusions: Overall, the F. brevipila Pacbio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders for gene discovery in this important turfgrass species.

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Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

npj Science of Food ◽

10.1038/s41538-021-00087-2 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Aoife J. McHugh ◽

Min Yap ◽

Fiona Crispie ◽

Conor Feehily ◽

Colin Hill ◽

...

Keyword(s):

Environmental Monitoring ◽

Illumina Sequencing ◽

Food Chain ◽

Control Measures ◽

Initial Assessment ◽

Limiting Factor ◽

Accurate Identification ◽

Processing Facility ◽

High Concentrations ◽

Sequencing Platforms

AbstractEfficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.

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Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus

Data in Brief ◽

10.1016/j.dib.2021.106852 ◽

2021 ◽

Vol 35 ◽

pp. 106852

Author(s):

Felix D. Guerrero ◽

Noushin Ghaffari ◽

Kylie G. Bendele ◽

Richard P. Metz ◽

C. Michael Dickens ◽

...

Keyword(s):

Illumina Sequencing ◽

Rhipicephalus Microplus ◽

Pacific Biosciences ◽

Genome Data ◽

Cattle Ticks ◽

Rhipicephalus Annulatus

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Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples

Brazilian Journal of Microbiology ◽

10.1016/j.bjm.2018.03.002 ◽

2018 ◽

Vol 49 ◽

pp. 1-8 ◽

Cited By ~ 3

Author(s):

Mariam Hassan ◽

Tamer Essam ◽

Salwa Megahed

Keyword(s):

Dna Extraction ◽

Illumina Sequencing ◽

Water Samples ◽

Environmental Water ◽

Environmental Water Samples ◽

Metagenomic Dna ◽

Cost Efficient

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A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition

Fungal Ecology ◽

10.1016/j.funeco.2015.12.009 ◽

2016 ◽

Vol 20 ◽

pp. 175-185 ◽

Cited By ~ 32

Author(s):

A.B. Siddique ◽

M. Unterseher

Keyword(s):

Community Composition ◽

Illumina Sequencing ◽

Cost Effective ◽

Fungal Communities ◽

Efficient Strategy

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Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

Current Microbiology ◽

10.1007/s00284-014-0609-5 ◽

2014 ◽

Vol 69 (4) ◽

pp. 457-466 ◽

Cited By ~ 21

Author(s):

Valeria Lentini ◽

Concetta Gugliandolo ◽

Boyke Bunk ◽

Jörg Overmann ◽

Teresa L. Maugeri

Keyword(s):

Illumina Sequencing ◽

Prokaryotic Community ◽

Sequencing Technology ◽

Shallow Marine

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Illumina Sequencing Reveals Conserved and Novel MicroRNAs of Dendrobium nobile Protocorm Involved in Synthesizing Dendrobine, a Potential Nanodrug

Journal of Biomedical Nanotechnology ◽

10.1166/jbn.2021.3036 ◽

2021 ◽

Vol 17 (3) ◽

pp. 416-425

Author(s):

Xu Qian ◽

Jieying Zhu ◽

Qingjun Yuan ◽

Qi Jia ◽

Hui Jin ◽

...

Keyword(s):

Signal Transduction ◽

Illumina Sequencing ◽

Plant Hormone ◽

Signal Transduction Pathway ◽

Perennial Herb ◽

Transduction Pathway ◽

Biological Regulation ◽

Dendrobium Nobile ◽

Short Period ◽

Post Transcriptional Regulation

Emergency of nanoparticulate drug delivery systems has improved the target, bioavailability, and curative effect of traditional Chinese medicine (TCM). However, the application of nano-preparation has been limited owing to the low content of active ingredients in part TCM. MicroRNAs (miRNAs) regulate plant growth, development, and response to environmental stresses at post-transcriptional regulation level by cleavage or translational inhibition. The molecular functions of miRNAs playing a role in synthesizing active comportments at medicinal plants have been widely researched. Dendrobium nobile is a perennial herb in the orchidaceae family. D. nobile protocorm can produce plant-specific metabolites at a short period. Therefore, it is a good substitute for producing metabolites. To understand the functions of miRNAs in D. nobile protocorm, Illumina sequencing of D. nobile protocorm (Dnp), D. officinale protocorm (Dcp), and D. nobile leaf (Dnl) were carried out. A total of 439, 412, and 432 miRNAs were identified from Dnp, Dcp, and Dnl, respectively. Some specific miRNAs were identified among them. Through combing GO and KEGG function annotation, miRNAs mainly involved metabolic pathways, plant hormone signal transduction, biological regulation, and protein binding. Acetyl-CoA acetyltransferase (AACT), mevalonate kinase (MK), 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), and 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (HDS), synthesizing basic precursor isoprene pyrophosphate (IPP) in terpenoid backbone biosynthesis pathway, were predicted as potential targets of 6 different miRNAs. Twenty-six miRNAs participated in auxin, cytokinin, abscisic acid, jasmonic acid, and salicylic acid signal transduction pathway. This report provided valuable candidate genes in Dnp involved in terpenoid biosynthesis and plant hormone signal transduction pathway. At the same time, it can help accelerate the use of dendrobine into nano preparation.

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Adaptation of gltA and ssrA assays for diversity profiling by Illumina sequencing to identify Bartonella henselae, B. clarridgeiae and B. koehlerae

Journal of Medical Microbiology ◽

10.1099/jmm.0.001400 ◽

2021 ◽

Vol 70 (7) ◽

Author(s):

Rosemonde Isabella Power ◽

Nichola Elisa Davies Calvani ◽

Yaarit Nachum-Biala ◽

Harold Salant ◽

Shimon Harrus ◽

...

Keyword(s):

Illumina Sequencing ◽

Type Species ◽

Bacterial Infections ◽

Sanger Sequencing ◽

Bartonella Henselae ◽

Diagnostic Methods ◽

Mixed Infections ◽

Accurate Identification ◽

Content Type ◽

Link Type

Introduction. Bartonellosis is an emerging zoonotic disease caused by bacteria of the genus Bartonella . Mixed Bartonella infections are a well-documented phenomenon in mammals and their ectoparasites. The accurate identification of Bartonella species in single and mixed infections is valuable, as different Bartonella species have varying impacts on infected hosts. Gap Statement. Current diagnostic methods are inadequate at identifying the Bartonella species present in mixed infections. Aim. The aim of this study was to adopt a Next Generation Sequencing (NGS) approach using Illumina sequencing technology to identify Bartonella species and demonstrate that this approach can resolve mixed Bartonella infections. Methodology. We used Illumina PCR amplicon NGS to target the ssrA and gltA genes of Bartonella in fleas collected from cats, dogs and a hedgehog in Israel. We included artificially mixed Bartonella samples to demonstrate the ability for NGS to resolve mixed infections and we compared NGS to traditional Sanger sequencing. Results. In total, we identified 74 Ctenocephalides felis, two Ctenocephalides canis, two Pulex irritans and three Archaeopsylla e. erinacei fleas. Real-time PCR of a subset of 48 fleas revealed that twelve were positive for Bartonella , all of which were cat fleas. Sanger sequencing of the ssrA and gltA genes confirmed the presence of Bartonella henselae , Bartonella clarridgeiae and Bartonella koehlerae . Illumina NGS of ssrA and gltA amplicons further confirmed the Bartonella species identity in all 12 flea samples and unambiguously resolved the artificially mixed Bartonella samples. Conclusion. The adaptation and multiplexing of existing PCR assays for diversity profiling via NGS is a feasible approach that is superior to traditional Sanger sequencing for Bartonella speciation and resolving mixed Bartonella infections. The adaptation of other PCR primers for Illumina NGS will be useful in future studies where mixed bacterial infections may be present.

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