scholarly journals The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

2022 ◽  
Vol 12 ◽  
Author(s):  
David Navarro-Payá ◽  
Antonio Santiago ◽  
Luis Orduña ◽  
Chen Zhang ◽  
Alessandra Amato ◽  
...  
Keyword(s):  
Gene Function ◽  
Gene Selection ◽  
Crop Improvement ◽  
Model Organisms ◽  
Supporting Evidence ◽  
Specific Expression ◽  
Public And Private ◽  
Diverse Range ◽  
Submission Form ◽  
Cumulative Knowledge

Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species’ pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications.

scholarly journals Brassinosteroid Signaling Pathways Interplaying with Diverse Signaling Cues for Crop Enhancement

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 556
Author(s):  
Hyeona Hwang ◽  
Hojin Ryu ◽  
Hyunwoo Cho
Keyword(s):  
Plant Growth ◽  
Signaling Pathways ◽  
Stress Responses ◽  
Environmental Changes ◽  
Crop Yields ◽  
Crop Improvement ◽  
Fine Tuning ◽  
Model Organisms ◽  
Diverse Range ◽  
Recent Advances

The signaling pathways of brassinosteroids (BRs), a unique plant steroid hormone, are critically involved in a diverse range of plant growth and developmental processes as well as many important agronomic traits. Recent advances in the understanding of BR biosynthetic and signaling pathways in model organisms and crops have increased the feasibility of modulating BR responses in crop plants to enhance adaptation to various vulnerable environmental changes. In particular, the identification and functional analysis of BR signaling components in rice (Oryza sativa) present the possibility of their utilization to improve many agricultural traits involved in crop yields. In this review, we summarize recent advances and progress in the understanding of the BR signaling pathway and its interactions with diverse internal and external signaling cues. We also discuss how these physiological modulations of BR and the abundant signaling crosstalk can be applied to enhance rice productivity through the manipulation of plant architecture and fine-tuning of stress responses. Finally, we discuss how the complex regulation of BR signaling pathways could favor application in the molecular design of plant growth and development, precise breeding strategies, and cultivation methods for rice crop improvement.

scholarly journals Human Genes Escaping X-inactivation Revealed by Single Cell Expression Data

2018 ◽  
Author(s):  
Kerem Wainer Katsir ◽  
Michal Linial
Keyword(s):  
Single Cell ◽  
X Chromosome ◽  
Noncoding Rna ◽  
Phenotypic Variability ◽  
Cell Types ◽  
X Inactivation ◽  
Specific Expression ◽  
X Chromosomes ◽  
Human Genes ◽  
Cumulative Knowledge

AbstractBackgroundIn mammals, sex chromosomes pose an inherent imbalance of gene expression between sexes. In each female somatic cell, random inactivation of one of the X-chromosomes restores this balance. While most genes from the inactivated X-chromosome are silenced, 15-25% are known to escape X-inactivation (termed escapees). The expression levels of these genes are attributed to sex-dependent phenotypic variability.ResultsWe used single-cell RNA-Seq to detect escapees in somatic cells. As only one X-chromosome is inactivated in each cell, the origin of expression from the active or inactive chromosome can be determined from the variation of sequenced RNAs. We analyzed primary, healthy fibroblasts (n=104), and clonal lymphoblasts with sequenced parental genomes (n=25) by measuring the degree of allelic-specific expression (ASE) from heterozygous sites. We identified 24 and 49 candidate escapees, at varying degree of confidence, from the fibroblast and lymphoblast transcriptomes, respectively. We critically test the validity of escapee annotations by comparing our findings with a large collection of independent studies. We find that most genes (66%) from the unified set were previously reported as escapees. Furthermore, out of the overlooked escapees, 11 are long noncoding RNA (lncRNAs).ConclusionsX-chromosome inactivation and escaping from it are robust, permanent phenomena that are best studies at a single-cell resolution. The cumulative information from individual cells increases the potential of identifying escapees. Moreover, despite the use of a limited number of cells, clonal cells (i.e., same X-chromosomes are coordinately inhibited) with genomic phasing are valuable for detecting escapees at high confidence. Generalizing the method to uncharacterized genomic loci resulted in lncRNAs escapees which account for 20% of the listed candidates. By confirming genes as escapees and propose others as candidates from two different cell types, we contribute to the cumulative knowledge and reliability of human escapees.

scholarly journals A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

2021 ◽  
Author(s):  
Richard J White ◽  
Eirinn Mackay ◽  
Stephen W Wilson ◽  
Elisabeth M Busch-Nentwich
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed Gene ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Specific Gene ◽  
Wild Type ◽  
Specific Expression ◽  
Genomic Location ◽  
Allele Specific

In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation. Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation. Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.

scholarly journals A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Michelle Spoto ◽  
Changhui Guan ◽  
Elizabeth Fleming ◽  
Julia Oh
Keyword(s):  
Gene Function ◽  
Large Scale ◽  
Essential Gene ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Model Organisms ◽  
Design Parameters ◽  
Bacterial Genomes ◽  
Wide Range ◽  
User Friendly

ABSTRACT The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species. IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.

scholarly journals Tamoxifen-inducible cardiac-specific Cre transgenic mouse using VIPR2 intron

2020 ◽  
Vol 36 (1) ◽  
Author(s):  
Hyun Jung Chin ◽  
So-young Lee ◽  
Daekee Lee
Keyword(s):  
Transgenic Mice ◽  
Transgenic Mouse ◽  
Gene Function ◽  
Regulatory Region ◽  
Genetically Engineered ◽  
Specific Gene ◽  
Specific Expression ◽  
Genetically Engineered Mouse Models ◽  
Reporter Mice ◽  
Vasoactive Intestinal Peptide Receptor

Abstract Genetically engineered mouse models through gene deletion are useful tools for analyzing gene function. To delete a gene in a certain tissue temporally, tissue-specific and tamoxifen-inducible Cre transgenic mice are generally used. Here, we generated transgenic mouse with cardiac-specific expression of Cre recombinase fused to a mutant estrogen ligand-binding domain (ERT2) on both N-terminal and C-terminal under the regulatory region of human vasoactive intestinal peptide receptor 2 (VIPR2) intron and Hsp68 promoter (VIPR2-ERT2CreERT2). In VIPR2-ERT2CreERT2 transgenic mice, mRNA for Cre gene was highly expressed in the heart. To further reveal heart-specific Cre expression, VIPR2-ERT2CreERT2 mice mated with ROSA26-lacZ reporter mice were examined by X-gal staining. Results of X-gal staining revealed that Cre-dependent recombination occurred only in the heart after treatment with tamoxifen. Taken together, these results demonstrate that VIPR2-ERT2CreERT2 transgenic mouse is a useful model to unveil a specific gene function in the heart.

scholarly journals De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Yannick Cogne ◽  
Davide Degli-Esposti ◽  
Olivier Pible ◽  
Duarte Gouveia ◽  
Adeline François ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Molecular Diversity ◽  
De Novo ◽  
Model Organisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Gammarus Fossarum ◽  
Male Individual ◽  
Taxonomic Groups ◽  
Whole Transcriptome

Abstract Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species.

scholarly journals The tissue specific regulation of miR22 expression in the lung and brain by ribosomal protein L29

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mohammad Ishaque Ali ◽  
Linrui Li ◽  
Lexing Li ◽  
Lun Yao ◽  
Jie Liu ◽  
...  
Keyword(s):  
Inhibitory Effect ◽  
Poly I:C ◽  
Mouse Lung ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Negative Effects ◽  
Specific Expression ◽  
Diverse Range ◽  
Cell Specificity ◽  
Specific Regulation

Abstract Endogenous miR22 is associated with a diverse range of biological processes through post-translational modification of gene expression and its deregulation results in various diseases including cancer. Its expression is usually tissue or cell-specific, however, the reasons behind this tissue or cell specificity are not clearly outlined till-date. Therefore, our keen interest was to investigate the mechanisms of tissue or cell-specific expression of miR22. In the current study, miR22 expression showed a tissues-specific difference in the poly(I:C) induced inflammatory mouse lung and brain tissues. The cell-specific different expression of miR22 was also observed in inflammatory glial cells and endothelial cells. The pattern of RPL29 expression was also similar to miR22 in these tissues and cells under the same treatment. Interestingly, the knockdown of RPL29 exerted an inhibitory effect on miR22 and its known transcription factors including Fos-B and c-Fos. Fos-B and c-Fos were also differentially expressed in the two cell lines transfected with poly(I:C). The knockdown of c-Fos also exerted its negative effects on miR22 expression in both cells. These findings suggest that RPL29 might have regulatory roles on tissue or cell-specific expression of miR22 through the transcription activities of c-Fos and also possibly through Fos-B.

Considering RNAi experimental design in parasitic helminths

Parasitology ◽  
2012 ◽  
Vol 139 (5) ◽  
pp. 589-604 ◽  
Author(s):  
JOHNATHAN J. DALZELL ◽  
NEIL D. WARNOCK ◽  
PAUL MCVEIGH ◽  
NIKKI J. MARKS ◽  
ANGELA MOUSLEY ◽  
...  
Keyword(s):  
Rna Interference ◽  
Experimental Design ◽  
Gene Function ◽  
Experimental Validation ◽  
Parasite Species ◽  
Model Organisms ◽  
Helminth Parasites ◽  
Parasitic Helminth ◽  
Parasitic Helminths ◽  
Parasite Biology

SUMMARYAlmost a decade has passed since the first report of RNA interference (RNAi) in a parasitic helminth. Whilst much progress has been made with RNAi informing gene function studies in disparate nematode and flatworm parasites, substantial and seemingly prohibitive difficulties have been encountered in some species, hindering progress. An appraisal of current practices, trends and ideals of RNAi experimental design in parasitic helminths is both timely and necessary for a number of reasons: firstly, the increasing availability of parasitic helminth genome/transcriptome resources means there is a growing need for gene function tools such as RNAi; secondly, fundamental differences and unique challenges exist for parasite species which do not apply to model organisms; thirdly, the inherent variation in experimental design, and reported difficulties with reproducibility undermine confidence. Ideally, RNAi studies of gene function should adopt standardised experimental design to aid reproducibility, interpretation and comparative analyses. Although the huge variations in parasite biology and experimental endpoints make RNAi experimental design standardization difficult or impractical, we must strive to validate RNAi experimentation in helminth parasites. To aid this process we identify multiple approaches to RNAi experimental validation and highlight those which we deem to be critical for gene function studies in helminth parasites.

scholarly journals Understanding meiosis and the implications for crop improvement

2009 ◽  
Vol 36 (7) ◽  
pp. 575 ◽  
Author(s):  
Jason A. Able ◽  
Wayne Crismani ◽  
Scott A. Boden
Keyword(s):  
Bread Wheat ◽  
Crop Improvement ◽  
Triticum Aestivum L ◽  
Model Organisms ◽  
Yeast Saccharomyces Cerevisiae ◽  
Breeding Lines ◽  
Plant Kingdom ◽  
The Past ◽  
Cereal Breeding ◽  
Beneficial Traits

Over the past 50 years, the understanding of meiosis has aged like a fine bottle of wine: the complexity is developing but the wine itself is still young. While emphasis in the plant kingdom has been placed on the model diploids Arabidopsis (Arabidopsis thaliana L.) and rice (Orzya sativa L.), our research has mainly focussed on the polyploid, bread wheat (Triticum aestivum L.). Bread wheat is an important food source for nearly two-thirds of the world’s population. While creating new varieties can be achieved using existing or advanced breeding lines, we would also like to introduce beneficial traits from wild related species. However, expanding the use of non-adapted and wild germplasm in cereal breeding programs will depend on the ability to manipulate the cellular process of meiosis. Three important and tightly-regulated events that occur during early meiosis are chromosome pairing, synapsis and recombination. Which key genes control these events in meiosis (and how they do so) remains to be completely answered, particularly in crops such as wheat. Although the majority of published findings are from model organisms including yeast (Saccharomyces cerevisiae) and the nematode Caenorhabditis elegans, information from the plant kingdom has continued to grow in the past decade at a steady rate. It is with this new knowledge that we ask how meiosis will contribute to the future of cereal breeding. Indeed, how has it already shaped cereal breeding as we know it today?

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