title: Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly.
abstract: Phytochrome-like genes in the wild plant species Rhazya stricta Decne were characterized using a de novo genome assembly of next generation sequence data. Rhazya stricta contains more than 100 alkaloids with multiple pharmacological properties, and leaf extracts have been used to cure chronic rheumatism, to treat tumors, and in the treatment of several other diseases. Phytochromes are known to be involved in the light-regulated biosynthesis of some alkaloids. Phytochromes are soluble chromoproteins that function in the absorption of red and far-red light and the transduction of intracellular signals during light-regulated plant development. De novo assembly of the nuclear genome of R. stricta recovered 45,641 contigs greater than 1000bp long, which were used in constructing a local database. Five sequences belonging to Arabidopsis thaliana phytochrome gene family (i.e., AtphyABCDE) were used to identify R. stricta contigs with phytochrome-like sequences using BLAST. This led to the identification of three contigs with phytochrome-like sequences covering AtphyA-, AtphyC- and AtphyE-like full-length genes. Annotation of the three sequences showed that each contig consists of one phytochrome-like gene with three exons and two introns. BLASTn and BLASTp results indicated that RsphyA mRNA and protein sequences had homologues in Wrightia coccinea and and Solanum tuberosum, respectively. RsphyC-like mRNA and protein sequence were homologous to Vitis vinifera and Vitis riparia. RsphyE-like mRNA coding and protein sequences were homologous to Ipomoea nil. Multiple-sequence alignment of phytochrome proteins indicated a homology with 30 sequences from 23 different species of flowering plants. Phylogenetic analysis confirmed that each R. stricta phytochrome gene is related to the same phytochrome gene of other flowering plants. It is proposed that the absence of phyB gene in R. stricta is due to RsphyA gene taking over the role of phyB.
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), PO Box 80141, Jeddah 21589, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JS
authors.lastname: Sabir
authors.forename: Nabih A
authors.initials: NA
authors.lastname: Baeshen
authors.forename: Ahmed M
authors.initials: AM
authors.lastname: Shokry
authors.forename: Nour O
authors.initials: NO
authors.lastname: Gadalla
authors.forename: Sherif
authors.initials: S
authors.lastname: Edris
authors.forename: Mohammed H
authors.initials: MH
authors.lastname: Mutwakil
authors.forename: Ahmed M
authors.initials: AM
authors.lastname: Ramadan
authors.forename: Ahmed
authors.initials: A
authors.lastname: Atef
authors.forename: Magdy A
authors.initials: MA
authors.lastname: Al-Kordy
authors.forename: Osama A
authors.initials: OA
authors.lastname: Abuzinadah
authors.forename: Fotouh M
authors.initials: FM
authors.lastname: El-Domyati
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
authors.forename: Ahmed
authors.initials: A
authors.lastname: Bahieldin
mesh_terms: D000470:Alkaloids / Q000378:metabolism; D029062:Apocynaceae / Q000235:genetics*; D019295:Computational Biology; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification; D030541:Databases, Genetic; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D010802:Phylogeny; D010834:Phytochrome / Q000235:genetics*; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D000470:Alkaloids; D018744:DNA, Plant; D012333:RNA, Messenger; D018749:RNA, Plant; D010834:Phytochrome
keywords: Alkaloids; BLASTp; PhyB; phyA; phyC; phyE