title: Detection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset.
abstract: 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).
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
authors.forename: Ahmed M
authors.initials: AM
authors.lastname: Shokry
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
authors.forename: Saleh
authors.initials: S
authors.lastname: Al-Karim
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Ramadan
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Genetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypt.
authors.forename: Nour
authors.initials: N
authors.lastname: Gadallah
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
authors.forename: Sanaa G
authors.initials: SG
authors.lastname: Al Attas
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JS
authors.lastname: Sabir
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
authors.forename: Sabah M
authors.initials: SM
authors.lastname: Hassan
authors.affiliation: Arid Lands Agricultural Research Institute, Ain Shams University, Cairo, Egypt.
authors.forename: Magdy A
authors.initials: MA
authors.lastname: Madkour
authors.affiliation: School of Agriculture, Purdue University, West Lafayette, Indiana, USA.
authors.forename: Ray
authors.initials: R
authors.lastname: Bressan
authors.affiliation: Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
authors.forename: Magdy
authors.initials: M
authors.lastname: Mahfouz
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt. Electronic address: bahieldin55@gmail.com.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Bahieldin
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D031107:Calotropis / Q000235:genetics*; D030541:Databases, Genetic; D055864:Droughts; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D018749:RNA, Plant
keywords: 3D Modeling; Abiotic stress; BLAST; GTP-EFTU