scholarly journals Identification of Transposable Elements in Conifer and Their Potential Application in Breeding

2020 ◽  
Vol 16 ◽  
pp. 117693432093026 ◽  
Author(s):  
Junhui Wang ◽  
Nan Lu ◽  
Fei Yi ◽  
Yao Xiao
Keyword(s):  
Gene Regulation ◽  
Picea Abies ◽  
Transposable Elements ◽  
Pinus Taeda ◽  
High Throughput ◽  
Genetic Study ◽  
High Throughput Sequencing ◽  
Genetics Research ◽  
Potential Applications ◽  
Functional Biology

Transposable elements (TEs) are known to play a role in genome evolution, gene regulation, and epigenetics, representing potential tools for genetics research in and breeding of conifers. Recently, thanks to the development of high-throughput sequencing, more conifer genomes have been reported. Using bioinformatics tools, the TEs of 3 important conifers ( Picea abies, Picea glauce, and Pinus taeda) were identified in our previous study, which provided a foundation for accelerating the use of TEs in conifer breeding and genetic study. Here, we review recent studies on the functional biology of TEs and discuss the potential applications for TEs in conifers.

scholarly journals Argonaute High-Throughput Sequencing of RNAs Isolated by Cross-Linking Immunoprecipitation Reveals a Snapshot of miRNA Gene Regulation in the Mammalian Retina

Biochemistry ◽  
2014 ◽  
Vol 53 (37) ◽  
pp. 5831-5833 ◽  
Author(s):  
Thomas R. Sundermeier ◽  
Hui Jin ◽  
Matthew L. Kleinjan ◽  
Debarshi Mustafi ◽  
Donny D. Licatalosi ◽  
...  
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Mirna Gene ◽  
Cross Linking ◽  
Mammalian Retina

scholarly journals Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci)

2019 ◽  
Author(s):  
Fraser John Combe ◽  
Evelyn Taylor cox ◽  
Graeme fox ◽  
Tommy Sandri ◽  
Bradley Cain ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Analysis ◽  
Illumina Miseq ◽  
Model Organisms ◽  
Conservation Genomics ◽  
Adaptive Genetic Variation ◽  
Genetics Research ◽  
Isolation And Characterization ◽  
Neutral Markers

High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The conservation genetics paradigm is that basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle & Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for non-model organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci, hereafter bongo), which has a clear and timely conservation imperative but lacks any described neutral markers.

scholarly journals On the optimal trimming of high-throughput mRNA sequence data

2013 ◽  
Author(s):  
Matthew D. MacManes
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Deep Understanding ◽  
Sequencing Technologies ◽  
Software Packages ◽  
Sequencing Quality ◽  
Functional Biology ◽  
Genome Level ◽  
Optimal Strength

AbstractThe widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score <2 or <5, is optimal for most studies across a wide variety of metrics.

scholarly journals Characterization of genomic regulation profiles in human mitral valve whole tissue to annotate genetic risk loci for mitral valve prolapse

2020 ◽  
Author(s):  
Sergiy Kyryachenko ◽  
Adrien Georges ◽  
Mengyao Yu ◽  
Takiy E. Berrandou ◽  
Patrick Bruneval ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Mitral Valve ◽  
High Throughput ◽  
Mitral Valve Prolapse ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Valve Disease ◽  
Open Chromatin ◽  
Mitral Valves ◽  
Causal Variants

Rationale: Mitral valve prolapse (MVP) is a common valve disease that leads to mitral insufficiency, heart failure and sudden death. The identification of risk loci provided insight into its genetic architecture, although the causal variants and target genes need to be fully characterized. Objective: To establish the chromatin accessibility profiles and gene regulation specificities of human mitral valve and identify functional variants and target genes at MVP loci. Methods and Results: We mapped the open chromatin accessible regions in nuclei from 11 human mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq). Compared to the heart tissue and cardiac fibroblasts, we found that mitral valve-specific ATAC-Seq peaks were enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. The most enriched motif in mitral valve-specific open chromatin peaks was for the nuclear factor of activated T cells (NFATC) family of transcription factors, involved in valve endocardial and interstitial cells formation. We also found that MVP-associated variants (p < 10-5) observed in the current MVP GWAS were significantly enriched (p<0.05) in mitral valve open chromatin peaks. Integration of the ATAC-Seq data with GWAS loci, extensive functional annotation, and gene reporter assay revealed plausible causal variants at two risk loci: rs6723013 at the IGFBP5/TNS1 locus and rs2641440 at the SMG6/SRR locus. Circular chromosome conformation capture followed by high-throughput sequencing provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on Chr2. Conclusions: Here we describe unprecedented genome-wide open chromatin profiles from human mitral valves that indicates specific gene regulation profiles, compared to the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms relevant to mitral valve disease.

scholarly journals STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data

2017 ◽  
Vol 3 (2) ◽  
Author(s):  
Cindy G. Santander ◽  
Philippe Gambron ◽  
Emanuele Marchi ◽  
Timokratis Karamitros ◽  
Aris Katzourakis ◽  
...  
Keyword(s):  
Transposable Elements ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
High Throughput Sequencing Data
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