In Silico Characterisation and Primer Design of Late Embryogenesis abundant (LEA) gene in Kelampayan

Mohd Jais, Sarifuddin (2022) In Silico Characterisation and Primer Design of Late Embryogenesis abundant (LEA) gene in Kelampayan. [Final Year Project Report] (Unpublished)

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Abstract

Neolamarckia cadamba (Roxb.) Bosser is also known as the Kelampayan tree is a huge transitory tree along with its quick growth. Since the 1960s, it has been in great demand, mostly for the timber industry and for its medicinal properties. Late embryogenesis abundant (LEA) gene is the encoded protein that has a significant impact in the adaptation of plants to stress conditions. To date, the in silico characterisation of LEA gene has been carried out in many plants such as potatoes, rice, etc., but no information on the LEA gene has been reported in Kelampayana. In order to have a greater understanding of the LEA gene in Kelampayan, the in silico characterisation was conducted to characterised LEA gene in Kelampayan. Primer designing was conducted to design the primer of LEA gene in Kelampayan for many uses such as PCR. The methodology of this study was done in two sections with the first section being the in silico characterization of LEA gene. The characterization consists of the phylogenetic tree analysis using MEGA 11 Software, the Domain search using CD Search tool, and Motifs search using MEME Online Tool. The second section, primer design was designed using Primer Blast tool. From a total of 92 LEA nucleotide sequences, the phylogenetic tree shows three distinct groups of LEA gene, differentiated by their function in their respective species. In order to do the molecular experiment of the LEA gene, the primer should be obtained for the further study of LEA gene. The primer design also provides the most suitable primer for every nucleotide sequence of TLP in Kelampayan. From this study, the genetic information of TLP was clearly understood from the characterization process and the primer was designed successfully.

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