TRANSCRIPTOME ANALYZIS OF HIGHER PLANTS CELLULOSE SYNTHASE GENES USING RNA-SEQUENCING DATA
Abstract
In the given work the transcriptomes of different organs and tissues of western poplar, eucalyptus, soybean and common bean were studied. The expression level of cellulose synthase genes was notably different in the studied plant species and in different types of tissues and organs within plants. For common bean and eucalyptus transcriptome the domination of certain cellulose synthase genes was typical. These prevailing genes made up more than 50 % of the total expression pull of cellulose synthases. On the contrary, cellulose synthase expression pulls of western poplar and soybean were distributed between multiple genes. The different expression strategies of CesA-genes may reflect the phylogenetic process that occurred in the genomes studied.
About the Authors
Ts. A. Padvitski
Institute of Genetics and Cytology of the National Academy of Sciences of Belarus
Belarus
Master of Bioinformatics, Master of Biology, Junior researcher
Belarus
Master of Bioinformatics, Master of Biology, Junior researcher
D. V. Galinousky
Institute of Genetics and Cytology of the National Academy of Sciences of Belarus
Belarus
Ph. D. (Biology), Researcher
Belarus
Ph. D. (Biology), Researcher
N. V. Anisimova
Institute of Genetics and Cytology of the National Academy of Sciences of Belarus
Belarus
Ph. D. (Biology), Senior researcher
Belarus
Ph. D. (Biology), Senior researcher
L. V. Khotyleva
Institute of Genetics and Cytology of the National Academy of Sciences of Belarus
Belarus
Academician, D. Sc. (Biology), Professor, Chief researcher
Belarus
Academician, D. Sc. (Biology), Professor, Chief researcher
A. V. Kilchevsk
Institute of Genetics and Cytology of the National Academy of Sciences of Belarus
Belarus
Corresponding Member, D. Sc. (Biology), Professor, Head of Laboratory
Belarus
Corresponding Member, D. Sc. (Biology), Professor, Head of Laboratory
References
1. JGI Phytozome 10.3 [Electronic resource]. – Mode of access: http://phytozome.jgi.doe.gov. – Date of access: 12.10.2015.
2. Wang, Z. RNA-Seq: a revolutionary tool for transcriptomics / Z. Wang, M. Gerstein, M. Snyder // Nature reviews genetics. – 2009. – Vol. 10, N 1. – P. 57–63.
3. Giorgi, F. M. Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana /
4. F. M. Giorgi, C. Del Fabbro, F. Licausi // Bioinformatics. – 2013. – Vol. 29, N 6. – P. 717–724.
5. Chu, Y. RNA Sequencing: Platform Selection, Experimental Design, and Data Interpretation / Y. Chu, D. R. Corey // Nucleic Acid Therapeutics. – 2012. – Vol. 22, N 4. – P. 271–274.
6. Wakasa, Y. RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions / Y. Wakasa, Y. Oono, Sh. Yazawa // BMC Plant Biology. – 2014. – Vol. 14. – P. 101.
7. RNA-Seq Analysis of the Response of the Halophyte, Mesembryanthemum crystallinum (Ice Plant) to High Salinity /
8. H. Tsukagoshi [et al.] // PLoS ONE. – 2015. – Vol. 10, N 2. – e0118339. doi.org/10.1371/journal.pone.0118339.
9. Горшкова, Т. А. Растительная клеточная стенка как динамическая система / Т. А. Горшкова. – Москва, 2007. – 429 с.
10. RNA-Seq data from Phytozome [Electronic resource]. – Mode of access: http://phytozome.jgi.doe.gov/phytomine/aspect.do?name=Expression. – Date of access: 12.10.2015.
11. Biomart [Electronic resource]. – Mode of access: http://www.biomart.org/. – Date of access: 12.10.2015.
12. EMBL-EBL: Family: Cellulose_synt (PF03552) [Electronic resource]. – Mode of access: http://pfam.xfam.org/family/Cellulose_synt#tabview=tab0. – Date of access: 12.10.2015.
13. EMBL-EBL: MUSCLE. Multiple Sequence Alignment [Electronic resource]. – Mode of access: https://www.ebi.ac.uk/Tools/msa/muscle/. – Date of access: 12.10.2015.
14. EMBL-EBL: ClustalW2 – Phylogeny [Electronic resource]. – Mode of access: http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/. – Date of access: 12.10.2015.
15. ATGC: South of France bioinformatics platform [Electronic resource]. – Mode of access: http://www.atgc-montpellier.fr/phyml/. – Date of access: 12.10.2015.
16. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation / C. Trapnell [et al.] // Nat. Biotechnol. – 2010. – Vol. 28, N 5. – P. 511–515. doi.org/10.1038/nbt.1621.
17. Genome sequence of the palaeopolyploid soybean / J. Schmutz [et al.] // Nature. – 2010. – Vol. 463. – P. 178–183. doi.org/10.1038/nature08670.
Review
Views: 987
Email this article 