title: De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing.
abstract: Production and supply of quality planting material is significant to coconut cultivation but is one of the major constraints in coconut productivity. Rapid multiplication of coconut through in vitro techniques, therefore, is of paramount importance. Although somatic embryogenesis in coconut is a promising technique that will allow for the mass production of high quality palms, coconut is highly recalcitrant to in vitro culture. In order to overcome the bottlenecks in coconut somatic embryogenesis and to develop a repeatable protocol, it is imperative to understand, identify, and characterize molecular events involved in coconut somatic embryogenesis pathway. Transcriptome analysis (RNA-Seq) of coconut embryogenic calli, derived from plumular explants of West Coast Tall cultivar, was undertaken on an Illumina HiSeq 2000 platform. After de novo transcriptome assembly and functional annotation, we have obtained 40,367 transcripts which showed significant BLASTx matches with similarity greater than 40 % and E value of ≤10(-5). Fourteen genes known to be involved in somatic embryogenesis were identified. Quantitative real-time PCR (qRT-PCR) analyses of these 14 genes were carried in six developmental stages. The result showed that CLV was upregulated in the initial stage of callogenesis. Transcripts GLP, GST, PKL, WUS, and WRKY were expressed more in somatic embryo stage. The expression of SERK, MAPK, AP2, SAUR, ECP, AGP, LEA, and ANT were higher in the embryogenic callus stage compared to initial culture and somatic embryo stages. This study provides the first insights into the gene expression patterns during somatic embryogenesis in coconut.
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India. mkraju.cpcri@gmail.com.
authors.forename: M K
authors.initials: MK
authors.lastname: Rajesh
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India.
authors.forename: T P
authors.initials: TP
authors.lastname: Fayas
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India.
authors.forename: S
authors.initials: S
authors.lastname: Naganeeswaran
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India.
authors.forename: K E
authors.initials: KE
authors.lastname: Rachana
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India.
authors.forename: U
authors.initials: U
authors.lastname: Bhavyashree
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India.
authors.forename: K K
authors.initials: KK
authors.lastname: Sajini
authors.affiliation: Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute, Kasaragod, 671124, Kerala, India.
authors.forename: Anitha
authors.initials: A
authors.lastname: Karun
mesh_terms: D003059:Cocos / Q000235:genetics* / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D058977:Molecular Sequence Annotation; D058439:Plant Somatic Embryogenesis Techniques; D060888:Real-Time Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
keywords: Coconut; RNA-Seq; Recalcitrant; Somatic embryogenesis; Transcriptome