Plant FIBer expression Database

Publications

How to cite FIBexDB

Mokshina N., Gorshkov O., Takasaki H., Onodera H., Sakamoto S., Gorshkova T., Mitsuda N.
FIBexDB: A New Online Transcriptome Platform to Analyze Development of Plant Cellulosic Fibers.
New Phytol., 231: 512-515 (2021)

Fund support

This project was supported by grants of the Russian Science Foundation (#19-14-00361, grant #20-44-070050) and
Strategic International Collaborative Research project promoted by the Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan.

Technical support

The design and user interface of this database were developed in collaboration with Yanagida T., Hosono K., Naraki Y., Space-Time Inc. Sapporo, Japan.



Publications used for FIBexDB construction

  1. Zhang N, Deyholos MK.
    RNA-Seq analysis of the shoot apex of flax (Linum usitatissimum) to identify phloem fiber specification genes. Front.
    Plant Sci. 2016; 7: 950.
    https://doi.org/10.3389/fpls.2016.00950
  2. Dmitriev AA, Kudryavtseva AV, Krasnov GS, Koroban NV, Speranskaya AS, Krinitsina AA, et al.
    Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress.
    BMC Plant Biol. 2016; 16: 237.
    https://doi.org/10.1186/s12870-016-0927-9
  3. Gorshkov O, Chernova T, Mokshina N, Gogoleva N, Suslov D, Tkachenko A, Gorshkova T.
    Intrusive growth of phloem fibers in flax stem: integrated analysis of miRNA and mRNA expression profiles.
    Plants 2019; 8: 47.
    https://doi.org/10.3390/plants8020047
  4. Gorshkova T, Chernova T, Mokshina N, Gorshkov V, Kozlova L, Gorshkov O.
    Transcriptome analysis of intrusively growing flax fibers isolated by laser microdissection.
    Sci. Rep. 2018; 8: 14570.
    https://doi.org/10.1038/s41598-018-32869-2
  5. Gorshkov O, Mokshina N, Ibragimova N, Ageeva M, Gogoleva N, Gorshkova T.
    Phloem fibres as motors of gravitropic behaviour of flax plants: level of transcriptome.
    Funct Plant Biol. 2017; 45: 203-214.
    https://doi.org./10.1071/FP16348
  6. Dmitriev AA, Krasnov GS, Rozhmina TA, Novakovskiy RO, Snezhkina AV, Fedorova MS, Yurkevich OY, Muravenko OV, Bolsheva NL, Kudryavtseva AV, Melnikova NV.
    Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.).
    BMC Plant Biol. 2017; 17: 253.
    https://doi.org/10.1186/s12870-017-1192-2
  7. Dmitriev AA, Krasnov GS, Rozhmina TA, Kishlyan NV, Zyablitsin AV, Sadritdinova AF, Snezhkina AV, Fedorova MS, Yurkevich OY, Muravenko OV, Bolsheva NL, Kudryavtseva AV and Melnikova NV
    Glutathione S-transferases and UDP-glycosyltransferases are involved in response to aluminum stress in Flax.
    Front. Plant Sci. 2015; 7: 1920.
    https://doi.org/10.3389/fpls.2016.01920
  8. Gerttula S, Zinkgraf M, Muday GK, Lewis DR, Ibatullin FM, Brumer H, Hart F, Mansfield SD, Filkov V, Groover A.
    Transcriptional and hormonal regulation of gravitropism of woody stems in Populus.
    Plant Cell 2015; 27: 2800-2813.
    https://doi.org/10.1105/tpc.15.00531
  9. Felten J, Vahala J, Love J, Gorzsas A, Ruggeberg M, Delhomme N, Lesniewska J, Kangasjarvi J, Hvidsten TR, Mellerowicz EJ, Sundberg B.
    Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen.
    New Phytol. 2018; 218: 999-1014.
    https://doi.org/10.1111/nph.15078
  10. Filichkin SA, Hamilton M, Dharmawardhana PD, Singh SK, Sullivan C, Ben-Hur A, Reddy A, Jaiswal P.
    Abiotic stresses modulate landscape of Poplar transcriptome via alternative splicing, differential intron retention, and isoform ratio switching.
    Front. Plant Sci. 2018; 9: 5.
    https://doi.org/10.3389/fpls.2018.00005
  11. Swamy PS, Hu H, Pattathil S, Maloney VJ, Xiao H, Xue LJ, Chung JD, Johnson VE, Zhu Y, Peter GF, Hahn MG, Mansfield SD, Harding SA, Tsai CJ.
    Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behaviour in Populus.
    J. Exp. Bot. 2015; 66: 6507-6518.
    https://doi.org/10.1093/jxb/erv383
  12. Hu H, Gu X, Xue LJ, Swamy PS, Harding SA, Tsai CJ.
    Tubulin C-terminal post-translational modifications do not occur in wood forming tissue of Populus.
    Front. Plant Sci. 2016; 7: 1493.
    https://doi.org/10.3389/fpls.2016.01493
  13. Shi R, Wang JP, Lin Y. et al.
    Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa.
    Planta 2017; 245: 927-938.
    https://doi.org/10.1007/s00425-016-2640-1
  14. Galinousky D, Mokshina N, Padvitski T, Ageeva M, Bogdan V, Kilchevsky A, Gorshkova T.
    The toolbox for fiber flax breeding: a pipeline from gene expression to fiber quality.
    Front. Genet. 2020; 11: 1431.
    https://doi.org/10.3389/fgene.2020.589881
  15. Petrova A, Kozlova L, Gorshkov O, Nazipova A, Ageeva M, Gorshkova T.
    Cell wall layer induced in xylem fibers of flax upon gravistimulation is similar to constitutively formed cell walls of bast fibers.
    Front. Plant Sci. 2021; 12: 485.
    https://doi.org/10.3389/fpls.2021.660375