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

Plant fibers constitute a major part of renewable biomass and are valuable resource for various industries, composite material chemistry, bioconversion processes. specialized long cells with thick cell walls that convenient model investigating fundamental issues such as individual biogenesis, wall formation, specialization. usually accumulate secondary walls, which contain lignin, cellulose, hemicelluloses like xylan, laid over thin primary walls. Some types those found in the phloem fiber crops bending parts hardwood tree species deposit cellulose-enriched tertiary onto (Gorshkova et al., 2018). The wall, also called gelatinous layer (G-layer), plays an important mechanical role; tension wood it serves to pull upward inclined trunk or branch (Gardiner 2014); annual crops, help keep narrow stems vertical position. does not lignin xylan – advantage plant because these polymers hamper saccharification efficiency cellulose lignocellulose. biogenesis trees has been studied separately, despite potentially common underlying mechanisms. Thus, comprehensive comparison from different sources is required identify basic mechanisms, if present, determine possible differences. To tackle this issue, we chose two plants, flax (Linum usitatissimum L.) poplar (Populus spp.), : (1) they widely used studying (2) even though both plants form their fibers, origins mechanisms induction 2018); (3) genomes were fully sequenced (Tuskan 2006; Wang 2012). Primary constitutively during normal development, while xylary only when induced by environmental factors. Each system its advantages: bundles can be easily isolated, giving unique possibility analyze distinct single type at certain developmental stage. transcriptomic studies have conducted fiber-containing samples other (Guerriero 2017; Xie 2020); however, datasets purified available any species. In wood, development occurs joint reactions several types. Analogically, xylem located pulling stem side after inclination (Ibragimova 2017), providing very similar permitting interspecies intraspecies comparisons deposition regulation. emergence NGS (next generation sequencing) technology boosted biological subjects, including leading accumulation vast array big data sets, most analyzed individually properly compared. utilize more efficiently, unified open database needs created. There some databases containing information about gene expression poplar: AspWood (Sundell 2017) PopGenIE (Sjödin 2009). However, do include formation. By contrast, there no all. We therefore combined normalized created new database, ‘FIBexDB’ (fiber database; https://ssl.cres-t.org/fibex/), storing our published newly obtained extracted publicly resources. FIBexDB key participants formation peculiarities inherent each contains connected but independent databases, one three entrances, namely flax, poplar, top pages (Fig. 1a). For collected RNA-sequencing (RNA-Seq) 61 nine projects, comprising transcriptomes seven tissue (shoot apical meristem, stages core parenchyma, tissue, hypocotyls, roots, leaves), cultivars subspecies, well mutant (reduced fibers) (Supporting Information Fig. S1; Tables S1, S2). RNA-Seq 88 leaves, wild-type transgenic poplars, treatments related S2; S3, S4). bridge genes species, regarding homologous relationships between Arabidopsis stored. ways use FIBexDB: browsing patterns multiple finding coexpressed (gene search; 1b); upregulated/downregulated particular situations/tissues (differentially expressed (DEG) finder; 1c). Gene searched identifier (ID) ‘Lus10028848’ ‘Potri.002G080700’ symbol. This search accept symbols locus identifiers, ‘BGAL12’ ‘AT4G26140’, shows corresponding and/or 1b). page (individual view) coding sequence, symbol present genes, paralogous 1b), helpful examine whether show patterns. pattern condition shown line graph addition, calculated dataset employed presented described coexpression network Cytoscape (Shannon 2003) using homology amino acid sequences connect view, less extent omitted make number than 50. labeled flax/poplar If encodes transcription factor (TF), rectangle name TF family indicated list genes. further clarity, colors representing subnetworks classified igraph software (Csardi & Nepusz, 2006). example, LusBGAL12 (Lus10028848) encoding ?-galactosidase, significant role (Roach 2011), specific fibers. closest Potri.006G144500 high wood. Instead, another ?-galactosidase (Potri.002G080700, PtrBGAL16) upregulation enriched Both Lus10028848 Potri.002G080700 RG-I rhamnosyltransferase GT106 rhamnogalacturonan lyase proteins involved synthesis modification; indicates PtrBGAL16 functions origin. sets TFs (maximum 300 each) 19 9 respectively, share (counterparts). allows users perform kind analysis easily. via DEG finder DEGs 87 153 combinations DEseq2 package (Love 2014) R statistical simply clicking graphical icons schematic pictures gene. A feature set conditions simultaneously, poplar. case, whose counterparts meet function, ‘counterparts’ means best-hit Blast search. find Furthermore, hierarchical k-means clustering (de Hoon 2004) few clicks largely aimed analyzing profiles tissues where massively produced; focus envisaged database. With developed analysis, provide insights into complex processes, biosynthesis, transcriptional regulatory us compare primary, secondary, As develop many under physiological situations, adding relevant molecular players ones samples. welcome collaboration field improving updating authors thank Prof. M. Deyholos (University British Columbia, Canada) who provided seeds rdf background cultivar sample unpublished study. T. Yanagida, K. Hosono, Y. Naraki (Space-Time Inc., Sapporo, Japan) design user interface Robbie Lewis, MSc, Edanz Group (https://en-author-services.edanz.com/ac) editing draft manuscript. work was supported grants Russian Science Foundation (grant no. 19-14-00361; gravistimulated grant 20-44-07005, analysis) Strategic International Collaborative Research project JPJ0088379) promoted Ministry Agriculture, Forestry Fisheries, Tokyo, Japan. acknowledge financial support government assignment FRC Kazan Scientific Center RAS (N Mokshina, OG, TG normalization discussion). No conflict interest declared. N Mitsuda entire HO SS ideas interface. HT, Mokshina assisted normalization. designed supervised Mitsuda, wrote All edited made comments on S1 Schematic diagram collection analysis. given S2. S2 based data. S3 S4 Table List experiments Please note: Wiley Blackwell responsible content functionality Supporting supplied authors. Any queries (other missing material) should directed New Phytologist Central Office. publisher supporting content) author article.