scholarly journals Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

2018 ◽  
Vol 46 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Pietro GRAMAZIO ◽  
Jaime PROHENS ◽  
Mariola PLAZAS ◽  
Giulio MANGINO ◽  
Francisco J. HERRAIZ ◽  
...  
Keyword(s):  
Solanum Melongena ◽  
Relevant Information ◽  
Wild Relatives ◽  
Biological Processes ◽  
Vegetable Crops ◽  
Genomic Tools ◽  
Wide Range ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Dramatic advances in genomics during the last decades have led to a revolution in the field of vegetable crops breeding. Some vegetables, like tomato, have served as model crops in the application of genomic tools to plant breeding but other important crops, like eggplant (Solanum melongena), lagged behind. The advent of next generation sequencing (NGS) technologies and the continuous decrease of the sequencing costs have allowed to develop genomic tools with a greatly benefit for no-model plants such as eggplant. In this review we present the currently available genomic resources in eggplant and discuss their interest for breeding. The first draft of eggplant genome sequence and the new upcoming improved assembly, as well as, the transcriptomes and RNA-based studies represent important genomic tools. The transcriptomes of cultivated eggplant and several wild relatives of eggplant are also available and have provided relevant information for the development of markers and understanding biological processes in eggplant. In addition, a historical overview of the eggplant genetic mapping studies, performed with different types of markers and experimental populations, provides a picture of the increase over time of the precision and resolution in the identification of candidate genes and QTLs for a wide range of stresses, and morpho-agronomic and domestication traits. Finally, we discuss how the development of new genetic and genomic tools in eggplant can pave the way for increasing the efficiency of eggplant breeding for developing improved varieties able to cope with the old and new challenges in horticultural production.

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

scholarly journals Angolan vegetable crops have unique genotypes of potential value for future breeding programmes

2016 ◽  
Vol Volume 112 (Number 3/4) ◽  
Author(s):  
José P. Domingos ◽  
Ana M. Fita ◽  
María B. Picó ◽  
Alicia Sifres ◽  
Isabel H. Daniel ◽  
...  
Keyword(s):  
Strong Dependence ◽  
The Other ◽  
Vegetable Crops ◽  
Cucurbita Maxima ◽  
Capsicum Chinense ◽  
Local Markets ◽  
Potential Value ◽  
Wide Range ◽  
Different Types ◽  
Breeding Programmes

Abstract A survey was carried out in Angola with the aim of collecting vegetable crops. Collecting expeditions were conducted in Kwanza-Sul, Benguela, Huíla and Namibe Provinces and a total of 80 accessions belonging to 22 species was collected from farmers and local markets. Species belonging to the Solanaceae (37 accessions) and Cucurbitaceae (36 accessions) families were the most frequently found with pepper and eggplant being the predominant solanaceous crops collected. Peppers were sold in local markets as a mixture of different types, even different species: Capsicum chinense, C. baccatum, C. frutescens and C. pubescens. Most of the eggplant accessions collected belonged to Solanum aethiopicum L. Gilo Group, the so-called ‘scarlet eggplant’. Cucurbita genus was better represented than the other cucurbit crops. A high morphological variation was present in the Cucurbita maxima and C. moschata accessions. A set of 22 Cucurbita accessions from Angola, along with 32 Cucurbita controls from a wide range of origins, was cultivated in Valencia, Spain and characterised based on morphology and molecularity using a set of 15 microsatellite markers. A strong dependence on latitude was found in most of the accessions and as a result, many accessions did not set fruit. The molecular analysis showed high molecular variability and uniqueness in the collected accessions, as shown by their segregation from the set of global controls. In summary, the material collected is quite valuable because of its uniqueness and the potential of the breeding characteristics it possesses.

scholarly journals Reversing resistance: different routes and common themes across pathogens

2017 ◽  
Vol 284 (1863) ◽  
pp. 20171619 ◽  
Author(s):  
Richard C. Allen ◽  
Jan Engelstädter ◽  
Sebastian Bonhoeffer ◽  
Bruce A. McDonald ◽  
Alex R. Hall
Keyword(s):  
Fitness Cost ◽  
Biological Processes ◽  
Short Supply ◽  
Compensatory Evolution ◽  
Wide Range ◽  
Different Types ◽  
Cost Of Resistance

Resistance spreads rapidly in pathogen or pest populations exposed to biocides, such as fungicides and antibiotics, and in many cases new biocides are in short supply. How can resistance be reversed in order to prolong the effectiveness of available treatments? Some key parameters affecting reversion of resistance are well known, such as the fitness cost of resistance. However, the population biological processes that actually cause resistance to persist or decline remain poorly characterized, and consequently our ability to manage reversion of resistance is limited. Where do susceptible genotypes that replace resistant lineages come from? What is the epidemiological scale of reversion? What information do we need to predict the mechanisms or likelihood of reversion? Here, we define some of the population biological processes that can drive reversion, using examples from a wide range of taxa and biocides. These processes differ primarily in the origin of revertant genotypes, but also in their sensitivity to factors such as coselection and compensatory evolution that can alter the rate of reversion, and the likelihood that resistance will re-emerge upon re-exposure to biocides. We therefore argue that discriminating among different types of reversion allows for better prediction of where resistance is most likely to persist.

scholarly journals Next-generation sequencing in neuropathological diagnosis of infections of the nervous system

2016 ◽  
Author(s):  
Steven L. Salzberg ◽  
Florian Breitwieser ◽  
Anupama Kumar ◽  
Haiping Hao ◽  
Peter Burger ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Nervous System ◽  
Next Generation Sequencing ◽  
Large Scale ◽  
Infectious Agent ◽  
Next Generation ◽  
Dna And Rna ◽  
Wide Range ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Objective: To determine the feasibility of next-generation sequencing (NGS) microbiome approaches in the diagnosis of infectious disorders in brain or spinal cord biopsies in patients with suspected central nervous system (CNS) infections. Methods: In a prospective-pilot study, we applied NGS in combination with a new computational analysis pipeline to detect the presence of pathogenic microbes in brain or spinal cord biopsies from ten patients with neurological problems indicating possible infection but for whom conventional clinical and microbiology studies yielded negative or inconclusive results. Results: Direct DNA and RNA sequencing of brain tissue biopsies generated 8.3 million to 29.1 million sequence reads per sample, which successfully identified with high confidence the infectious agent in three patients, identified possible pathogens in two more, and helped to understand neuropathological processes in three others, demonstrating the power of large-scale unbiased sequencing as a novel diagnostic tool. Validation techniques confirmed the pathogens identified by NGS in each of the three positive cases. Clinical outcomes were consistent with the findings yielded by NGS on the presence or absence of an infectious pathogenic process in eight of ten cases, and were non-contributory in the remaining two. Conclusions: NGS-guided metagenomic studies of brain, spinal cord or meningeal biopsies offer the possibility for dramatic improvements in our ability to detect (or rule out) a wide range of CNS pathogens, with potential benefits in speed, sensitivity, and cost. NGS-based microbiome approaches present a major new opportunity to investigate the potential role of infectious pathogens in the pathogenesis of neuroinflammatory disorders.

Mutational landscape of AKT1/2/3 in Chinese patients with solid tumors.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15566-e15566
Author(s):  
Hui Kong ◽  
Weijia Fang ◽  
Haibo Mou ◽  
Feng Xiao Chen ◽  
Lingxiang Liu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Chinese Patients ◽  
Great Promise ◽  
Central Component ◽  
Next Generation ◽  
Gene Panel Testing ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

e15566 Background: As a central component of PI3K/AKT pathway, AKT serves as an attractive target of anti-cancer strategy with various AKT inhibitors, which show great promise in phase I/II clinical trials. This study aimed to investigate AKT1/2/3 status in different types of cancers by using next generation sequencing (NGS). Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor samples were collected from 10,010 Chinese patients with solid tumors and subjected to next-generation sequencing (NGS)-based 450 gene panel testing carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Genomic alterations, tumor mutational burden (TMB) values, and microsatellite instability (MSI) status were assessed with a mean coverage of 1000X, including single base substitutions, short and long insertion/deletions, copy number variations, gene fusions, and rearrangements. Genomic data and immune checkpoint inhibitors (ICIs) treatment outcome of a cohort of 1610 patients with solid tumors were derived from cBioPortal (MSKCC, Nat Genet. 2019). Results: AKT1/2/3 were found to be mutually exclusive with each other and accounted for 3.4% in this cohort. The frequencies of AKT1/2/3 variations were 1.1%, 1.6%, and 0.8%, respectively. The most common co-altered genes associated with AKT1/2/3 variations were TP53 (69.4%), PIK3CA (19.3%), KRAS (19%), CCNE1 (18.4%), CDKN2A (16.6%), and 11q13 (6.5%). AKT1/2/3 variations were significantly associated with higher TMB, and independent of MSI status. Outcome data from the MSKCC cohort showed that patients with AKT1/2/3 variations had a remarkable clinical benefit to ICIs treatment compared to patients with wild-type AKT1/2/3 in overall survival (OS) (NA vs 18 months, p = 0.009). Furthermore, AKT1/2/3 variations were independent risk factors of OS (HR: 0.55, 95%CI: 0.34-0.87, p = 0.012). Conclusions: The prevalence of AKT1/2/3 somatic alterations across different types of solid tumors in China was 3.4%. AKT1/2/3 variations were associated with an increased TMB and favorable response to ICIs, suggesting that A KT1/2/3 variations may be biomarkers for guiding anti-AKT agents and ICI treatment.

scholarly journals Prevalence of pharmacogenomic variants in 100 pharmacogenes among Southeast Asian populations under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Chakkaphan Runcharoen ◽  
Koya Fukunaga ◽  
Insee Sensorn ◽  
Nareenart Iemwimangsa ◽  
Sommon Klumsathian ◽  
...  
Keyword(s):  
Drug Efficacy ◽  
Cost Effective ◽  
Southeast Asian ◽  
Research Network ◽  
Serious Adverse Events ◽  
Asian Populations ◽  
Effective Technology ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractPharmacogenomics can enhance the outcome of treatment by adopting pharmacogenomic testing to maximize drug efficacy and lower the risk of serious adverse events. Next-generation sequencing (NGS) is a cost-effective technology for genotyping several pharmacogenomic loci at once, thereby increasing publicly available data. A panel of 100 pharmacogenes among Southeast Asian (SEA) populations was resequenced using the NGS platform under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm). Here, we present the frequencies of pharmacogenomic variants and the comparison of these pharmacogenomic variants among different SEA populations and other populations used as controls. We investigated the different types of pharmacogenomic variants, especially those that may have a functional impact. Our results provide substantial genetic variations at 100 pharmacogenomic loci among SEA populations that may contribute to interpopulation variability in drug response phenotypes. Correspondingly, this study provides basic information for further pharmacogenomic investigations in SEA populations.

scholarly journals Proteogenomics and its applications in biology and precision medicine

2021 ◽  
Vol 19 (1) ◽  
pp. 1-14
Author(s):  
Phan Van Chi ◽  
Le Thi Bich Thao
Keyword(s):  
Mass Spectrometry ◽  
Precision Medicine ◽  
Open Reading Frames ◽  
Biological Processes ◽  
New Genes ◽  
Fundamental Research ◽  
Diagnostic Research ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Reading Frames

In this review, we briefly discuss proteogenomics, the integration of proteomics with genomics and transcriptomics, whereby the underlying technologies are next-generation sequencing (NGS) and mass spectrometry (MS) with processing the resulting data, an emerging field that promises to accelerate fundamental research related to transcription and translation, as well as its applicability. By combining genomic and proteomic information, scientists are achieving new results due to a more complete and unified understanding of complex molecular biological processes. Part of this review introduces some of the results of using proteogenomics in solving problems such as annotation, gene/genome re-annotation, including editing of open reading frames (ORFs), or improving a process to detect new genes in a number of different organisms, including humans. In particular, the paper also discusses the potential of proteogenomics through research achievements on human genome/proteome in precision medicine, especially in projects on phylogenetic and diagnostic research. and cancer treatment. The challenges and future of proteogenomics are also discussed and documented.

scholarly journals Association Mapping for Improving Fiber Quality in Upland Cottons

2021 ◽  
Author(s):  
Khezir Hayat ◽  
Adem Bardak ◽  
Mehboob-ur-Rahman ◽  
Hafiz Muhammad Imran ◽  
Furqan Ahmad ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Association Mapping ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Fiber Quality ◽  
Crop Species ◽  
Genomic Tools ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Mapping Populations

Improved fiber yield is considered a constant goal of upland cotton (Gossypium hirsutum) breeding worldwide, but the understanding of the genetic basis controlling yield-related traits remains limited. Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL) by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and power. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information with the development of high-throughput genotyping, phenotyping will be a major challenge for genetic mapping studies. We believe that high-quality phenotyping and appropriate experimental design coupled with new statistical models will accelerate progress in dissecting the genetic architecture of complex traits.

scholarly journals Insight into the hidden bacterial diversity of Lake Balaton, Hungary

2020 ◽  
Vol 71 (4) ◽  
pp. 383-391 ◽  
Author(s):  
E. Tóth ◽  
M. Toumi ◽  
R. Farkas ◽  
K. Takáts ◽  
Cs. Somodi ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Cell Counting ◽  
Lake Balaton ◽  
Extended Spectrum Beta Lactamase ◽  
Littoral Region ◽  
Different Types ◽  
Organotrophic Bacteria ◽  
Next Generation Sequencing Ngs ◽  
Insight Into ◽  
Generation Sequencing

AbstractIn the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum beta-lactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.

scholarly journals DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6596 ◽  
Author(s):  
Alison J. Moran ◽  
Sean W.J. Prosser ◽  
Jonathan A. Moran
Keyword(s):  
Alimentary Tract ◽  
Selasphorus Rufus ◽  
Non Invasive ◽  
Single Pellet ◽  
Wide Range ◽  
Dna Metabarcoding ◽  
Rufous Hummingbird ◽  
Almost All ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.

Sign in / Sign up

Export Citation Format

Share Document