Ethylene response factor 1 (ERF1) in silico comparison between Malaysian dwarf banana (Musa acuminata ssp. Malaccensis) and “Pisang Klutuk Wulung” (Musa balbisiana)

• Main Author: Kamalesha, Gede
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/42693
• Institution: Institut Teknologi Bandung

Musa species is classified into 4 groups based on its genomic composition: Musa acuminata (A genome), Musa balbisiana (B genome), Musa schizocarpa (S genome), and Musa australimusa (T genome). Musa balbisiana (genome B) are known to have better resistance against abiotic and biotic stresses than Musa acuminata. One of protein involved in ethylene signal transduction of plants is response is ethylene response factor 1 (ERF1). ERF1 is a transcription factor for various genes involved in plant response, one of them is pathogen defense response. Information about these protein (ERF1) is limited in Musa genus. With published annotated genome of Musa acuminata subs. Malaccencis and genome draft in Musa balbisiana, identification and comparison of ERF1 between both species is possible. This study aims to elucidate defense response against pathogen mechanism of Musa balbisiana from molecular aspect. Nucleotide and protein sequence of ERF1 gene in Musa acuminata subs. Malaccensis was retrieved from Kyoto Encyclopedia of Genes and Genomes (KEGG). Musa balbisiana ERF1 nucleotide and protein sequence was retrieved from BLASTN program output using ERF1 Musa acuminata sequence as querry. Nucleotide sequence of ERF1 in Musa acuminata and Musa balbisiana was compared based on the following: identity or similarity with pairwise sequence alignment using Needleman-Wunsh algorithm, gene structure (exon and intron) using FGENESH+ program and gene position in chromosome. Protein sequences of ERF1 in Musa acuminata and Musa balbisiana were grouped based on Nakano ERF1 classification system based on phylogenetic tree construction with neighbour-joining method and motifs identification with MEME suite program. Seven ERF1 gene in A genome were retrieved from KEGG database with the following gene ID from NCBI (National Centre for Biotechnology Information): “103971653” (MaERF1_1), “103972093” (MaERF1_2), “103973681” (MaERF1_3), “103981246” (MaERF1_4), “103981564” (MaERF1_5), “103983138” (MaERF1_6), “103985947” (MaERF1_7). Seven ERF1 gene in B genome were identified and was named MbERF1_1, MbERF1_2, MbERF1_3, MbERF1_4, MbERF1_5, MbERF1_6, and MbERF1_7. Comparison analysis of nucleotide and amino acid sequence between A and B genome showed that nucleotide composition, gene structure, gene position on chromosome, ERF grouping, and motifs on MaERF1 (A genome) and MbERF1 (B genome) have similar characteristics.