Phytoplankton diversity and ecology through the lens of high throughput sequencing technologies

AbstractThe use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

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Detection of novel allelic variations in soybean mutant population using Tilling by Sequencing

10.1101/711440 ◽

2019 ◽

Author(s):

Reneth Millas ◽

Mary Espina ◽

CM Sabbir Ahmed ◽

Angelina Bernardini ◽

Ekundayo Adeleke ◽

...

Keyword(s):

Fatty Acid ◽

High Throughput ◽

Reverse Genetics ◽

High Throughput Sequencing ◽

Fatty Acid Biosynthesis ◽

Induced Mutations ◽

Mutant Population ◽

Sequencing Technologies ◽

Allelic Variations ◽

Tilling By Sequencing

ABSTRACTOne of the most important tools in genetic improvement is mutagenesis, which is a useful tool to induce genetic and phenotypic variation for trait improvement and discovery of novel genes. JTN-5203 (MG V) mutant population was generated using an induced ethyl methane sulfonate (EMS) mutagenesis and was used for detection of induced mutations in FAD2-1A and FAD2-1B genes using reverse genetics approach. Optimum concentration of EMS was used to treat 15,000 bulk JTN-5203 seeds producing 1,820 M2 population. DNA was extracted, normalized, and pooled from these individuals. Specific primers were designed from FAD2-1A and FAD2-1B genes that are involved in the fatty acid biosynthesis pathway for further analysis using next-generation sequencing. High throughput mutation discovery through TILLING-by-Sequencing approach was used to detect novel allelic variations in this population. Several mutations and allelic variations with high impacts were detected for FAD2-1A and FAD2-1B. This includes GC to AT transition mutations in FAD2-1A (20%) and FAD2-1B (69%). Mutation density for this population is estimated to be about 1/136kb. Through mutagenesis and high-throughput sequencing technologies, novel alleles underlying the mutations observed in mutants with reduced polyunsaturated fatty acids will be identified, and these mutants can be further used in breeding soybean lines with improved fatty acid profile, thereby developing heart-healthy-soybeans.

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Adenosine-to-inosine RNA editing may be implicated in human pathogenesis

Bulletin of Russian State Medical University ◽

10.24075/brsmu.2019.028 ◽

2019 ◽

pp. 22-25

Author(s):

AA Kliuchnikova ◽

SA Moshkovskii

Keyword(s):

Immune Responses ◽

Rna Editing ◽

High Throughput ◽

High Throughput Sequencing ◽

Common Mechanism ◽

Adenosine Deaminases ◽

Human Transcriptome ◽

Sequencing Technologies

Adenosine-to-inosine (A-to-I) RNA editing is a common mechanism of post-transcriptional modification in many metazoans including vertebrates; the process is catalyzed by adenosine deaminases acting on RNA (ADARs). Using high-throughput sequencing technologies resulted in finding thousands of RNA editing sites throughout the human transcriptome however, their functions are still poorly understood. The aim of this brief review is to draw attention of clinicians and biomedical researchers to ADAR-mediated RNA editing phenomenon and its possible implication in development of neuropathologies, antiviral immune responses and cancer.

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Overview of High Throughput Sequencing Technologies to Elucidate Molecular Pathways in Cardiovascular Diseases

Circulation Research ◽

10.1161/circresaha.113.300939 ◽

2013 ◽

Vol 112 (12) ◽

pp. 1613-1623 ◽

Cited By ~ 49

Author(s):

Jared M. Churko ◽

Gary L. Mantalas ◽

Michael P. Snyder ◽

Joseph C. Wu

Keyword(s):

Cardiovascular Diseases ◽

High Throughput ◽

High Throughput Sequencing ◽

Molecular Pathways ◽

Sequencing Technologies

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Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers

Bioinformatics ◽

10.1093/bioinformatics/btaa915 ◽

2020 ◽

Author(s):

Yuansheng Liu ◽

Xiaocai Zhang ◽

Quan Zou ◽

Xiangxiang Zeng

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

De Novo ◽

Supplementary Information ◽

Supplementary Data ◽

Complementary Strand ◽

Short Reads ◽

Sequencing Technologies ◽

Computational Resources

Abstract Summary Removing duplicate and near-duplicate reads, generated by high-throughput sequencing technologies, is able to reduce computational resources in downstream applications. Here we develop minirmd, a de novo tool to remove duplicate reads via multiple rounds of clustering using different length of minimizer. Experiments demonstrate that minirmd removes more near-duplicate reads than existing clustering approaches and is faster than existing multi-core tools. To the best of our knowledge, minirmd is the first tool to remove near-duplicates on reverse-complementary strand. Availability and implementation https://github.com/yuansliu/minirmd. Supplementary information Supplementary data are available at Bioinformatics online.

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