Analysis of public RNA-seq data in studies of flax fiber biogenesis

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Abstract

In this work we used publicly available raw RNA-seq data to elucidate mechanisms of flax fiber biogenesis by measuring expression of cell-wall related genes (cellulose synthase, cellulose synthase-like and chitinase-like genes) in stem of flax (Linum usitatissimum cv. Bethune). Using public RNA-sequence data we have quantified and characterised the expression of the specific cell-wall genes in the top, middle and bottom parts of the Bethune flax stem. The most prominent findings are: Secondary cell-wall cellulose synthase (CesA) genes are expressed differentially in phloem and xylem in all parts of Bethune stem, in contrast with primary cell-wall cellulose synthase genes. Total expression level of cellulose synthase-like (Csl) genes is tissue invariant (although, CslG and CslE are differentially expressed) and smaller than the total expression of cellulose synthase genes. The CslD2D3 subgroup dominates total expression of CslD genes in both xylem and phloem. Expression levels of all expressed chitinase-like (Ctl) genes are tissue dependent in all parts of stem. Total expression level of chitinase-like genes is much higher than expression of cellulose synthase and cellulose synthase-like genes in both tissues.

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  • 1. Gorshkova T Brutch N Chabbert B Deyholos M Hayashi T Lev-Yadun S Mellerowicz EJ Morvan C Neutelings G Pilate G. Plant Fiber Formation: State of the Art Recent and Expected Progress and Open Questions. Critical Reviews In Plant Sciences 2012; 31 (3): 201-228.

  • 2. Bray NL Pimentel H Melsted P Pachter l. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 2016; 34: 525-527.

  • 3. Pimentel HJ Bray N Puente S Melsted P Pachter L. Differential analysis of RNA-Seq incorporating quantification uncertainty bioRxiv 2016; 058164.

  • 4. Wagner GP Kin K Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci 2012; 131: 281.

  • 5. Wang ZW Hobson N Galindo L Zhu SL Shi DH McDill J et al. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J 2012; 72: 461-473.

  • 6. Mikshina P Chernova T Chemikosova S Ibragimova N Mokshina N Gorshkova T. Cellulosic Fibers: Role of Matrix Polysaccharides in Structure and Function Cellulose - Fundamental Aspects Dr. Theo G.M. Van De Ven (Ed.) 2013; InTech.

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