Modern Approaches for Transcriptome Analyses in Plants

Riaño‐Pachón, Diego Mauricio; Espitia-Navarro, Hector F.; Riascos, John J.; Margarido, Gabriel Rodrigues Alves

doi:10.1007/978-3-030-80352-0_2

Cited by 3 publications

(2 citation statements)

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“…Two complementary strategies have successfully been used to identify genes involved in fertility in fungi: reverse and forward genetics. Apart from reverse genetics approaches based on transcriptomic analyses (Garg and Jain, 2013; Riaño-Pachón et al, 2021; Strickler et al, 2012), reverse genetics requires that genes governing the trait of interest have been characterized in one or several model species, and therefore assumes that the genetic processes underlying the trait of interest are similar in the model and focal species. Combined with comparative genomics, such candidate genes approaches brought considerable insights in the understanding of sexual reproduction in Ascomycetes (Ellena et al, 2020; Passer et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Identification of genetic bases of male fertility inPyricularia oryzaeby Genome Wide Association Study (GWAS)

Lassagne,

Adreit,

Malagnac

et al. 2024

Preprint

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The reproductive system of an organism impacts the emergence and evolution of adaptive variants in response to selective constraints. The understanding of the sexual mode of reproduction in pathogens helps to understand their life history. In filamentous Ascomycete fungi, mating type system and the production of gametes are required to reproduce sexually. In the phytopathogenic AscomycetePyricularia oryzae, studies of the genetic determinants of sexual reproduction are still limited to the mating type system. This study focuses on identifying the genes involved in male fertility through the production of male gametes known as microconidia. We performed a GWAS analysis coupled with a local score approach on a wild recombinant population ofPyricularia oryzaephenotyped for microconidia production. We identified one genomic region significantly associated with the quantity of microconidia produced. This region contained nine candidate genes, some of them annotated with functions associated to sexual reproduction in model fungi such asNeurospora crassa,Podospora anserinaandSordaria macrospora. The most promising candidate gene contains a Jumonji domain. Proteins belonging to the Jumonji family are conserved among Eukaryotes and are known to be involved in chromatin regulation.

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Section: Introductionmentioning

confidence: 99%

Identification of genetic bases of male fertility inPyricularia oryzaeby Genome Wide Association Study (GWAS)

Lassagne,

Adreit,

Malagnac

et al. 2024

Preprint

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“…CRISPR/ Cas9 technology is an important breakthrough in genome editing in recent years because it is efficient, accurate and economical, and can realize the targeted editing of specific genes. Through the establishment of this model, we will simulate muscular dystrophy disease and deeply study the changes of transcriptome in its muscle tissue, so as to reveal the pathogenesis of muscular dystrophy [22][23][24][25] .…”

mentioning

confidence: 99%

Model Construction and Muscle Transcriptome Study of Zebrafish with Laminin-Alpha 2 Muscular Dystrophy

Zhou,

Huang,

Wang

2023

IJPS

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The purpose of this study was to simulate muscular dystrophy disease by constructing a laminin-alpha 2 zebrafish model, and to study the changes of muscle transcriptome using transcriptomic methods. Using clustered regularly interspaced short palindromic repeats associated protein 9 gene editing technology; the zebrafish laminin-alpha 2 gene was knocked out or mutated. First, the appropriate guide RNA sequence was designed, and then the guide RNA and clustered regularly interspaced short palindromic repeats associated protein 9 proteins were synthesized and injected into zebrafish embryos. The lamininalpha 2 model fish is screened and identified by detecting the mutation of DNA or messenger RNA in the progeny fish genome. The muscle phenotype identification results of zebrafish model 4 showed that the muscle phenotypes of normal and unable swimming individuals in laminin-alpha 2 knockout group were abnormal, while the muscle phenotypes of clustered regularly interspaced short palindromic repeats associated protein 9 control group were not. The muscular dystrophy characteristics of laminin-alpha 2 model fish were confirmed. Functional enrichment and pathway analysis of differentially expressed genes were performed to further reveal the biological processes and regulatory pathways associated with muscular dystrophy in laminin-alpha 2 model fish. Transcriptome sequencing analysis revealed the difference in transcriptome expression between the muscle tissue of laminin-alpha 2 zebrafish model and wild-type zebrafish. These differentially expressed genes are involved in biological processes such as muscle development, metabolism and signal transduction, providing important clues for further understanding of the pathogenesis of muscular dystrophy. Through functional enrichment and pathway analysis, the key signaling pathways and molecular mechanisms involved in the pathogenesis of muscular dystrophy were identified. These findings provide theoretical basis for the discovery of new therapeutic targets and formulation of corresponding therapeutic strategies, and provide new ideas and methods for the treatment of muscle diseases.

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Northern light reviews – Application of orthology and network biology to infer gene functions in non‐model plants

Vandepoele,

Thierens,

Van Bel

2024

Physiologia Plantarum

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Approximately 60% of the genes and gene products in the model species Arabidopsis thaliana have been functionally characterized. In non‐model plant species, the functional annotation of the gene space is largely based on homology, with the assumption that genes with shared common ancestry have conserved functions. However, the wide variety in possible morphological, physiological, and ecological differences between plant species gives rise to many species‐ and clade‐specific genes, for which this transfer of knowledge is not possible. Other complications, such as difficulties with genetic transformation, the absence of large‐scale mutagenesis methods, and long generation times, further lead to the slow characterization of genes in non‐model species. Here, we discuss different resources that integrate plant gene function information. Different approaches that support the functional annotation of gene products, based on orthology or network biology, are described. While sequence‐based tools to characterize the functional landscape in non‐model species are maturing and becoming more readily available, easy‐to‐use network‐based methods inferring plant gene functions are not as prevalent and have limited functionality.

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Modern Approaches for Transcriptome Analyses in Plants

Cited by 3 publications

References 273 publications

Identification of genetic bases of male fertility inPyricularia oryzaeby Genome Wide Association Study (GWAS)

Identification of genetic bases of male fertility inPyricularia oryzaeby Genome Wide Association Study (GWAS)

Model Construction and Muscle Transcriptome Study of Zebrafish with Laminin-Alpha 2 Muscular Dystrophy

Northern light reviews – Application of orthology and network biology to infer gene functions in non‐model plants

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