Detection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset
Type
ArticleAuthors
Shokry, Ahmed M.Al-Karim, Saleh
Ramadan, Ahmed M Ali
Gadallah, Nour
Al-Attas, Sanaa G.
Sabir, Jamal Sabir M
Hassan, Sabah Mohammed
Madkour, Loutfy H.
Bressan, Ray Anthony
Mahfouz, Magdy M.

Bahieldin, Ahmed M.
KAUST Department
Biological and Environmental Science and Engineering (BESE) DivisionBioscience Program
Center for Desert Agriculture
Laboratory for Genome Engineering
Plant Science
Plant Science Program
Date
2014-02Permanent link to this record
http://hdl.handle.net/10754/563379
Metadata
Show full item recordAbstract
The wild plant species Calotropis procera (C. procera) has many potential applications and beneficial uses in medicine, industry and ornamental field. It also represents an excellent source of genes for drought and salt tolerance. Genes encoding proteins that contain the conserved universal stress protein (USP) domain are known to provide organisms like bacteria, archaea, fungi, protozoa and plants with the ability to respond to a plethora of environmental stresses. However, information on the possible occurrence of Usp in C. procera is not available. In this study, we uncovered and characterized a one-class A Usp-like (UspA-like, NCBI accession No. KC954274) gene in this medicinal plant from the de novo assembled genome contigs of the high-throughput sequencing dataset. A number of GenBank accessions for Usp sequences were blasted with the recovered de novo assembled contigs. Homology modelling of the deduced amino acids (NCBI accession No. AGT02387) was further carried out using Swiss-Model, accessible via the EXPASY. Superimposition of C. procera USPA-like full sequence model on Thermus thermophilus USP UniProt protein (PDB accession No. Q5SJV7) was constructed using RasMol and Deep-View programs. The functional domains of the novel USPA-like amino acids sequence were identified from the NCBI conserved domain database (CDD) that provide insights into sequence structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM). © 2014 Académie des sciences.Citation
Shokry, A. M., Al-Karim, S., Ramadan, A., Gadallah, N., Al Attas, S. G., Sabir, J. S. M., … Bahieldin, A. (2014). Detection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset. Comptes Rendus Biologies, 337(2), 86–94. doi:10.1016/j.crvi.2013.12.008Sponsors
This project was funded by the Deanship of Scientific Research (DSR), King Abdulaziz University, Jeddah, under Grant No. 1432-3-15/HiCi. The authors, therefore, acknowledge with thanks DSR technical and financial support.Publisher
Elsevier BVJournal
Comptes Rendus BiologiesPubMed ID
24581802ae974a485f413a2113503eed53cd6c53
10.1016/j.crvi.2013.12.008
Scopus Count
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