FIBexDB: a new online transcriptome platform to analyze development of plant cellulosic fibers

Mokshina, Natalia; Gorshkov, Oleg; Takasaki, Hironori; Onodera, Hitomi; Sakamoto, Shingo; Горшкова, Т. А.; Mitsuda, Nobutaka

doi:10.1111/nph.17405

Cited by 9 publications

(7 citation statements)

References 15 publications

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“…To analyze coexpressed genes, a gene page for each individual flax gene was used, and the data was downloaded as tab-delimited text. FIBexDB and the supplementary file of the related paper [12] contain a detailed sample description, a tutorial file, the NCBI Acc No. of the used RNA-SEQ projects, and references.…”

Section: Methodsmentioning

confidence: 99%

“…SAM-shoot apical meristem [15]; AR_Bet-apical region (unpublished), cPAR-parenchyma cells, iFIB-the intrusively growing phloem fibers [16,17]; tFIBa, tFIB_Gr, tFIB_Li, tFIB_Bi, tFIBb-the isolated phloem fibers with tertiary cell wall (different cultivars, [17][18][19]; sXYLa, sXYLb-xylem part of the stem enriched with secondary cell wall [17,18]. The detailed sample descriptions and references are presented in FIBexDB and the supplementary file of the related paper [12]. The genes downregulated in roots during the infection but which initially had a lower level of expression in the control root samples were expressed in stem tissues under normal conditions.…”

Section: Cluster 1: Lectin Genes Downregulated In Flax Root Tips In R...mentioning

confidence: 99%

“…In the current work, we consider flax lectins via the prism of their "classic" function (as defense proteins) and analyze the behavior of flax lectins in root tips during fungal infection. The transcriptomic data for different flax cultivars' root tips, which reflected the early response of flax plants to Fusarium oxysporum action [10], was integrated into the FIBexDB [11,12], and we were able to assess the response of stagespecific genes encoding proteins with lectin domains in the case of Fusarium wilt of flax plants and compare them to samples attributed to stem tissues of plants grown under normal conditions.…”

Section: Introductionmentioning

confidence: 99%

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Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Petrova

Mokshina

2022

Plants

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Plant proteins with lectin domains play an essential role in plant immunity modulation, but among a plurality of lectins recruited by plants, only a few members have been functionally characterized. For the analysis of flax lectin gene expression, we used FIBexDB, which includes an efficient algorithm for flax gene expression analysis combining gene clustering and coexpression network analysis. We analyzed the lectin gene expression in various flax tissues, including root tips infected with Fusarium oxysporum. Two pools of lectin genes were revealed: downregulated and upregulated during the infection. Lectins with suppressed gene expression are associated with protein biosynthesis (Calreticulin family), cell wall biosynthesis (galactose-binding lectin family) and cytoskeleton functioning (Malectin family). Among the upregulated lectin genes were those encoding lectins from the Hevein, Nictaba, and GNA families. The main participants from each group are discussed. A list of lectin genes, the expression of which can determine the resistance of flax, is proposed, for example, the genes encoding amaranthins. We demonstrate that FIBexDB is an efficient tool both for the visualization of data, and for searching for the general patterns of lectin genes that may play an essential role in normal plant development and defense.

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Section: Methodsmentioning

confidence: 99%

Section: Cluster 1: Lectin Genes Downregulated In Flax Root Tips In R...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Petrova

Mokshina

2022

Plants

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“…The comprehensive dataset of flax accessions from the Russian Federal Research Center for Bast Fiber has been recently published by Rozhmina et al ( 247 ). FIBexDB is a database based on transcriptomic data for flax where the expression pattern for genes and co-expression network are available and pairwise comparison can be made ( 248 ).…”

Section: Effective Utilization Of Linum Genetic Re...mentioning

confidence: 99%

Diversity of Linum genetic resources in global genebanks: from agro-morphological characterisation to novel genomic technologies – a review

et al. 2023

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Linseed or flaxseed is a well-recognized nutritional food with nutraceutical properties owing to high omega-3 fatty acid (α-Linolenic acid), dietary fiber, quality protein, and lignan content. Currently, linseed enjoys the status of a ‘superfood’ and its integration in the food chain as a functional food is evolving continuously as seed constituents are associated with lowering the risk of chronic ailments, such as heart diseases, cancer, diabetes, and rheumatoid arthritis. This crop also receives much attention in the handloom and textile sectors as the world’s coolest fabric linen is made up of its stem fibers which are endowed with unique qualities such as luster, tensile strength, density, bio-degradability, and non-hazardous nature. Worldwide, major linseed growing areas are facing erratic rainfall and temperature patterns affecting flax yield, quality, and response to biotic stresses. Amid such changing climatic regimes and associated future threats, diverse linseed genetic resources would be crucial for developing cultivars with a broad genetic base for sustainable production. Furthermore, linseed is grown across the world in varied agro-climatic conditions; therefore it is vital to develop niche-specific cultivars to cater to diverse needs and keep pace with rising demands globally. Linseed genetic diversity conserved in global genebanks in the form of germplasm collection from natural diversity rich areas is expected to harbor genetic variants and thus form crucial resources for breeding tailored crops to specific culinary and industrial uses. Global genebank collections thus potentially play an important role in supporting sustainable agriculture and food security. Currently, approximately 61,000 germplasm accessions of linseed including 1,127 wild accessions are conserved in genebanks/institutes worldwide. This review analyzes the current status of Linum genetic resources in global genebanks, evaluation for agro-morphological traits, stress tolerance, and nutritional profiling to promote their effective use for sustainable production and nutrition enhancement in our modern diets.

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“…Results: The results will be presented on the example of flax phloem fibers -the crucial elements of plant biomechanical system -that in the course of cell development consequently deposit three different cell wall types performing corresponding changes in cell wall machinery. The analysis of transcriptomic data was considerably facilitated by the developed online platform FIBexDB [3] that also helped to characterize individual genes and reveal their coexpression. Though the transcript amount of a certain gene is not always proportional to the amount of corresponding protein and especially to its activity, the changes in transcriptome patterns are very informative to realize the peculiarities of general cell metabolism and to detect the key molecular players, with various cell wall related enzymes and the involved transcription factors among them.…”

mentioning

confidence: 99%

Transcriptomics as an effective tool to study plant cell wall formation and function

Gorshkova¹

2022

The Thirteenth International Multiconference

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FIBexDB: a new online transcriptome platform to analyze development of plant cellulosic fibers

Cited by 9 publications

References 15 publications

Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Diversity of Linum genetic resources in global genebanks: from agro-morphological characterisation to novel genomic technologies – a review

Transcriptomics as an effective tool to study plant cell wall formation and function

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