scholarly journals High-throughput sequencing techniques to flax genetics and breeding

2020 ◽  
Author(s):  
Alena Olegovna Akhmetshina ◽  
Ksenia Vladimirovna Strygina ◽  
Elena Konstantinovna Khlestkina ◽  
Elisaveta Alexandrovna Porokhovinova ◽  
Nina Borisovna Brutch
Keyword(s):  
Stress Responses ◽  
High Throughput Sequencing ◽  
Molecular Genetic ◽  
Stress Factors ◽  
Fundamental Interest ◽  
Genetic Mechanisms ◽  
High Marker Density ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Selection Of

Flax (Lnum usitatssimum L.) is an important oil and fiber crop. Using modern methods for flax breeding allows accelerating the introduction of some desired genes into the genotypes of future varieties. Today, an important condition for their creation is the development of research, that is based on next-generation sequencing (NGS). This review summarizes the results obtained using NGS sequencing in flax research. To date, a linkage map with a high marker density has been obtained for L. usitatssimum, which is already being used for a more efficient search for quantitative traits loci. Comparative studies of transcriptomes and miRNomes of flax under stress and in control conditions elucidated molecular-genetic mechanisms of abiotic and biotic stress responses. The very accurate model for genomic selection of flax resistant to pasmo was constructed. Based on NGS-sequencing also some details of the genus Linum evolution were clarified. The knowledge systematized in the review can be useful for researchers working in flax breeding and whereas fundamental interest for understanding the phylogenetic relationships within the genus Linum, the ontogenesis, and the mechanisms of the response of flax plants to various stress factors.

scholarly journals Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods

2020 ◽  
Vol 9 (7) ◽  
pp. 2036
Author(s):  
Jaroslaw Bilinski ◽  
Mikolaj Dziurzynski ◽  
Pawel Grzesiowski ◽  
Edyta Podsiadly ◽  
Anna Stelmaszczyk-Emmel ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Fecal Microbiota ◽  
Dead Cell ◽  
Series Of Experiments ◽  
Multi Method Approach ◽  
The Stability ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Selection Of

Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find “super-donor” indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of “good” donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and Anaeroplasma found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.

scholarly journals Prioritization of potato genes involved in the formation of agronomically valuable traits using the SOLANUM TUBEROSUM knowledge base

2019 ◽  
Vol 23 (3) ◽  
pp. 312-319
Author(s):  
P. S. Demenkov ◽  
O. V. Saik ◽  
T. V. Ivanisenko ◽  
N. A. Kolchanov ◽  
A. V. Kochetov ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Knowledge Base ◽  
Candidate Genes ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Biological Data ◽  
Targeted Mutagenesis ◽  
Pubmed Database ◽  
Genetic Mechanisms ◽  
Selection Of

The development of highly efficient technologies in genomics, transcriptomics, proteomics and metabolomics, as well as new technologies in agriculture has led to an “information explosion” in plant biology and crop production, including potato production. Only a small part of the information reaches formalized databases (for example, Uniprot, NCBI Gene, BioGRID, IntAct, etc.). One of the main sources of reliable biological data is the scientific literature. The well-known PubMed database contains more than 18 thousand abstracts of articles on potato. The effective use of knowledge presented in such a number of non-formalized documents in natural language requires the use of modern intellectual methods of analysis. However, in the literature, there is no evidence of a widespread use of intelligent methods for automatically extracting knowledge from scientific publications on cultures such as potatoes. Earlier we developed the SOLANUM TUBEROSUM knowledge base (http://www-bionet.sysbio.cytogen. ru/and/plant/). Integrated into the knowledge base information about the molecular genetic mechanisms underlying the selection of significant traits helps to accelerate the identification of candidate genes for the breeding characteristics of potatoes and the development of diagnostic markers for breeding. The article searches for new potential participants of the molecular genetic mechanisms of resistance to adverse factors in plants. Prioritizing candidate genes has shown that the PHYA, GF14, CNIH1, RCI1A, ABI5, CPK1, RGS1, NHL3, GRF8, and CYP21-4 genes are the most promising for further testing of their relationships with resistance to adverse factors. As a result of the analysis, it was shown that the molecular genetic relationships responsible for the formation of significant agricultural traits are complex and include many direct and indirect interactions. The construction of associative gene networks and their analysis using the SOLANUM TUBEROSUM knowledge base is the basis for searching for target genes for targeted mutagenesis and marker-oriented selection of potato varieties with valuable agricultural characteristics.

scholarly journals NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases

2021 ◽  
Author(s):  
I. Perea-Romero ◽  
F. Blanco-Kelly ◽  
I. Sanchez-Navarro ◽  
I. Lorda-Sanchez ◽  
S. Tahsin-Swafiri ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Diagnostic Yield ◽  
A Priori ◽  
Retinal Diseases ◽  
Human Phenotype ◽  
Whole Exome ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Clinical Category ◽  
Selection Of

AbstractSyndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.

scholarly journals Association of miR-1251-5p/miR-6892-5p Expression With Clinicopathological Factors in Premenopausal Endometrial Cancer

2021 ◽  
Author(s):  
Jing Zhang ◽  
Bin Li ◽  
Yang Liu ◽  
Fei Wang ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Target Genes ◽  
Tumor Grading ◽  
Node Metastasis ◽  
Predict Mirna Target ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing ◽  
Menarche Age ◽  
Selection Of

Abstract Background This study is aim to profile the differentially expressed microRNAs (DEMs) of premenopausal endometrial cancer (EC), identify their target genes and understand their roles in carcinogenesis. Methods Next-generation sequencing (NGS) was performed on 3 premenopausal EC and 3 premenopausal normal endometrial tissues. Selection of candidate miRNAs and subsequent validation were performed by qRT-PCR on 20 premenopausal EC, 30 premenopausal normal endometrial and 40 postmenopausal EC samples. The relationship between DEMs and clinical characteristics was analyzed. Moreover, bioinformatic software programs and databases were applied to predict miRNA target genes, molecular functions, and signaling pathways. Results 136 upregulated and 131 downregulated DEMs were identified. The expression of miR-1251-5p was highly upregulated in premenopausal EC samples compared with premenopausal normal endometrial samples and significantly downregulated compared with postmenopausal EC samples. The expression of miR-6892-5p was highly upregulated in premenopausal EC samples compared with premenopausal normal endometrial samples and postmenopausal EC samples. In the premenopausal EC group, miR-1251-5p expression was closely correlated with menarche age, number of pregnancies, tumor grading, myometrial infiltration and lymph node metastasis; miR-6892-5p expression was closely correlated with BMI, hypertension, tumor grading, and metastasis. Conclusions miR-1251-5p and miR-6892-5p may play important roles in tumorigenesis progression of premenopausal EC.

scholarly journals Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

2020 ◽  
Vol 9 (1) ◽  
pp. 132 ◽  
Author(s):  
Rute Pereira ◽  
Jorge Oliveira ◽  
Mário Sousa
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Genetics ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Process Data ◽  
Next Generation Sequencing Analysis ◽  
Generate Process ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Selection Of

Clinical genetics has an important role in the healthcare system to provide a definitive diagnosis for many rare syndromes. It also can have an influence over genetics prevention, disease prognosis and assisting the selection of the best options of care/treatment for patients. Next-generation sequencing (NGS) has transformed clinical genetics making possible to analyze hundreds of genes at an unprecedented speed and at a lower price when comparing to conventional Sanger sequencing. Despite the growing literature concerning NGS in a clinical setting, this review aims to fill the gap that exists among (bio)informaticians, molecular geneticists and clinicians, by presenting a general overview of the NGS technology and workflow. First, we will review the current NGS platforms, focusing on the two main platforms Illumina and Ion Torrent, and discussing the major strong points and weaknesses intrinsic to each platform. Next, the NGS analytical bioinformatic pipelines are dissected, giving some emphasis to the algorithms commonly used to generate process data and to analyze sequence variants. Finally, the main challenges around NGS bioinformatics are placed in perspective for future developments. Even with the huge achievements made in NGS technology and bioinformatics, further improvements in bioinformatic algorithms are still required to deal with complex and genetically heterogeneous disorders.

scholarly journals Sequencing your genome: your future is here, but are you sure you want to know it?

2014 ◽  
Vol 96 ◽  
Author(s):  
NIR PILLAR ◽  
OFER ISAKOV ◽  
NOAM SHOMRON
Keyword(s):  
Next Generation Sequencing ◽  
Research Laboratory ◽  
High Throughput Sequencing ◽  
Genomic Research ◽  
Sequencing Technology ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
The Past ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS; also known as deep sequencing or ultra-high throughput sequencing) has probably been the most important tool for genomic research over the past few years. NGS has led to numerous discoveries and scientific breakthroughs in the genetic field. The sequencing technology that has entered the research laboratory in the past decade is now being introduced into the clinical diagnostic laboratory. Consequently, NGS results are becoming available in the medical arena as abundance of clinically relevant variants, conferring predisposition to disease, are being discovered at a growing rate (Stanley, 2014).

scholarly journals Isolation and Abiotic Stress Resistance Analyses of a Catalase Gene fromIpomoea batatas(L.) Lam

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Bin Yong ◽  
Xiaoyan Wang ◽  
Pan Xu ◽  
Haiyan Zheng ◽  
Xueting Fei ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Stress Responses ◽  
Reading Frame ◽  
Calmodulin Binding ◽  
C Terminus ◽  
Young Leaves ◽  
Quantitative Analyses ◽  
Encoding Gene ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

As an indicator of the antioxidant capability of plants, catalase can detoxify reactive oxygen species (ROS) generated by environmental stresses. Sweet potato is one of the top six most important crops in the world. However, its catalases remain largely unknown. In this study, a catalase encoding gene,IbCAT2(accession number: KY615708), was identified and cloned from sweet potato cv. Xushu 18. It contained a 1479 nucleotides’ open reading frame (ORF). S-R-L, Q-K-L, and a putative calmodulin binding domain were located at the C-terminus of IbCAT2, which suggests that IbCAT2 could be a peroxisomal catalase. Next-generation sequencing (NGS) based quantitative analyses showed thatIbCAT2was mainly expressed in young leaves and expanding tuberous roots under normal conditions. When exposed to 10% PEG6000 or 200 mmol/L NaCl solutions,IbCAT2was upregulated rapidly in the first 11 days and then downregulated, although different tissues showed different degree of change. Overexpression ofIbCAT2conferred salt and drought tolerance inEscherichia coliandSaccharomyces cerevisiae. The positive response ofIbCAT2to abiotic stresses suggested thatIbCAT2might play an important role in stress responses.

scholarly journals Analysis of Copy Number Variations in Solid Tumors Using a Next Generation Sequencing Custom Panel

2021 ◽  
Vol 2 (2) ◽  
pp. 123-134
Author(s):  
Marta Vives-Usano ◽  
Beatriz García Pelaez ◽  
Ruth Román Lladó ◽  
Mónica Garzón Ibañez ◽  
Erika Aldeguer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Copy Number Variations ◽  
Next Generation ◽  
Ffpe Samples ◽  
Custom Panel ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Approach Time ◽  
Selection Of

Somatic copy number variations (CNV; i.e., amplifications and deletions) have been implicated in the origin and development of multiple cancers and some of these aberrations are designated targets for therapies. Although FISH is still considered the gold standard for CNV detection, the increasing number of potentially druggable amplifications to be assessed makes a gene-by-gene approach time- and tissue-consuming. Here we investigated the potential of next generation sequencing (NGS) custom panels to simultaneously determine CNVs across FFPE solid tumor samples. DNA was purified from cell lines and FFPE samples and analyzed by NGS sequencing using a 20-gene custom panel in the GeneReader Platform®. CNVs were identified using an in-house algorithm based on the UMI read coverage. Retrospective validation of in-house algorithm to identify CNVs showed 97.1% concordance rate with the NGS custom panel. The prospective analysis was performed in a cohort of 243 FFPE samples from patients arriving at our hospital, which included 74 NSCLC tumors, 148 CRC tumors, and 21 other tumors. Of them, 33% presented CNVs by NGS and in 14 cases (5.9%) the CNV was the only alteration detected. We have identified CNV alterations in about one-third of our cohort, including FGFR1, CDK6, CDK4, EGFR, MET, ERBB2, BRAF, or KRAS. Our work highlights the need to include CNV testing as a part of routine NGS analysis in order to uncover clinically relevant gene amplifications that can guide the selection of therapies.

scholarly journals High-Throughput Sequencing of Virus-infected Cucurbita pepo Samples Revealed The Presence of Zucchini Shoestring Virus in Zimbabwe

2019 ◽  
Author(s):  
Charles Karavina ◽  
Jacques Davy Ibaba ◽  
Augustine Gubba
Keyword(s):  
South African ◽  
Cucurbita Pepo ◽  
High Throughput Sequencing ◽  
Gc Content ◽  
Large Open Reading Frame ◽  
Polya Tail ◽  
Reading Frame ◽  
Growing Seasons ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Objectives: Plant-infecting viruses remain a serious challenge towards achieving food security worldwide. Cucurbits, in Zimbabwe, like in the other parts of the world, are used in various ways. A small-scaled cucurbit virus survey was conducted in Zimbabwe during the 2014 and 2015 growing seasons. Cucurbit leaf samples displaying virus-like symptoms were collected and stored until analysis. The samples were then subjected to next-generation sequencing (NGS). The data generated from NGS were analysed using genomics technologies. Zucchini shoestring virus (ZSSV), a cucurbit-infecting potyvirus previously described in South Africa was one of the viruses identified. The genomes of three ZSSV isolates from Zimbabwe are described in this note. Results: The three ZSSV isolates had the same genome size of 10297 bp excluding the polyA tail with a 43% GC content. The large open reading frame (ORF) was found at positions 69 to 10106 on the genome and encodes a 3345 amino acids long polyprotein which had the same cleavage site sequences as those described on the South African isolates except for the P1-pro site. The smaller ORF, also called the pretty interesting Potyviridae ORF, was located at positions 3611 to 3793 on the genomes for all three ZSSV isolates.

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