Analysis of public RNA-seq data in studies of flax fiber biogenesis
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-sequ...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Sciendo
2017-05-01
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| Series: | The EuroBiotech Journal |
| Online Access: | https://doi.org/10.24190/ISSN2564-615X/2017/02.10 |
| _version_ | 1818587399557480448 |
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| author | Galinousky Dmitry Padvitski Tsimafei |
| author_facet | Galinousky Dmitry Padvitski Tsimafei |
| author_sort | Galinousky Dmitry |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-16T09:08:15Z |
| format | Article |
| id | doaj.art-904bf1501cd84372bc153aae6b5cff1f |
| institution | Directory Open Access Journal |
| issn | 2564-615X |
| language | English |
| last_indexed | 2024-12-16T09:08:15Z |
| publishDate | 2017-05-01 |
| publisher | Sciendo |
| record_format | Article |
| series | The EuroBiotech Journal |
| spelling | doaj.art-904bf1501cd84372bc153aae6b5cff1f2022-12-21T22:37:02ZengSciendoThe EuroBiotech Journal2564-615X2017-05-011217717910.24190/ISSN2564-615X/2017/02.10Analysis of public RNA-seq data in studies of flax fiber biogenesisGalinousky Dmitry0Padvitski Tsimafei1Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics & Cytology, Novosibirsk , BelarusLaboratory of Ecological Genetics and Biotechnology, Institute of Genetics & Cytology, Novosibirsk , BelarusIn 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.https://doi.org/10.24190/ISSN2564-615X/2017/02.10 |
| spellingShingle | Galinousky Dmitry Padvitski Tsimafei Analysis of public RNA-seq data in studies of flax fiber biogenesis The EuroBiotech Journal |
| title | Analysis of public RNA-seq data in studies of flax fiber biogenesis |
| title_full | Analysis of public RNA-seq data in studies of flax fiber biogenesis |
| title_fullStr | Analysis of public RNA-seq data in studies of flax fiber biogenesis |
| title_full_unstemmed | Analysis of public RNA-seq data in studies of flax fiber biogenesis |
| title_short | Analysis of public RNA-seq data in studies of flax fiber biogenesis |
| title_sort | analysis of public rna seq data in studies of flax fiber biogenesis |
| url | https://doi.org/10.24190/ISSN2564-615X/2017/02.10 |
| work_keys_str_mv | AT galinouskydmitry analysisofpublicrnaseqdatainstudiesofflaxfiberbiogenesis AT padvitskitsimafei analysisofpublicrnaseqdatainstudiesofflaxfiberbiogenesis |