In silico comparisons of the Ethylene Response Factor 1 (ERF1) gene between Malaysian wild banana (Musa acuminata ssp. malaccensis) and Pisang Klutuk Wulung (Musa balbisiana)

Kamalesha, Gede and Dwivany, Fenny Martha and Nugrahapraja, Husna and Putri, Rika Rahma (2022) In silico comparisons of the Ethylene Response Factor 1 (ERF1) gene between Malaysian wild banana (Musa acuminata ssp. malaccensis) and Pisang Klutuk Wulung (Musa balbisiana). Pertanika Journal of Science & Technology (Malaysia), 45 (2). pp. 519-545. ISSN 2231-8526

Musa balbisiana (B genome) has been observed to have a higher tolerance of biotic and abiotic stresses than Musa acuminata (A genome). Ethylene Response Factor 1 (ERF1) is a gene activator for pathogenesis-related proteins (PR proteins) such as basic chitinases and beta-1,3-glucanase. There are numerous ERF1 gene studies about Oryza sativa, but information about the banana ERF1 gene, especially in the B genome (Musa balbisiana “Pisang Klutuk Wulung”), has still not been explored thoroughly. Using annotated genomic data in an A genome (Musa acuminata ssp. malaccensis) and genomic data in a B genome (Musa balbisiana “Pisang Klutuk Wulung”), research on the ERF1 gene can be conducted at the gene sequences and amino acid sequences levels. The Musa acuminata (A genome) ERF1 gene nucleotide sequence was retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The Musa balbisiana (B genome) ERF1 gene nucleotide sequence was identified with the nucleotide Basic Local Alignment Search Tool (BLASTn) using an A genome ERF1 gene sequence as a query. Both ERF1 gene nucleotide sequences and amino acid sequences in the A and B genomes were annotated and compared. Seven annotated genome ERF1 gene sequences from the A and B genomes were identified with the probability that these genes were actively transcribed in cell activity. ERF1 gene comparisons between the A and B genomes showed that nucleotide composition, gene structure, gene position in each respective chromosome, ERF clusterization, identified motif, and amino acid composition in each of the identified motifs have similar characteristics.

Full text available from: Official URL: http://www.pertanika.upm.edu.my/resources/files/Pe...

Abstract

Musa balbisiana (B genome) has been observed to have a higher tolerance of biotic and abiotic stresses than Musa acuminata (A genome). Ethylene Response Factor 1 (ERF1) is a gene activator for pathogenesis-related proteins (PR proteins) such as basic chitinases and beta-1,3-glucanase. There are numerous ERF1 gene studies about Oryza sativa, but information about the banana ERF1 gene, especially in the B genome (Musa balbisiana “Pisang Klutuk Wulung”), has still not been explored thoroughly. Using annotated genomic data in an A genome (Musa acuminata ssp. malaccensis) and genomic data in a B genome (Musa balbisiana “Pisang Klutuk Wulung”), research on the ERF1 gene can be conducted at the gene sequences and amino acid sequences levels. The Musa acuminata (A genome) ERF1 gene nucleotide sequence was retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The Musa balbisiana (B genome) ERF1 gene nucleotide sequence was identified with the nucleotide Basic Local Alignment Search Tool (BLASTn) using an A genome ERF1 gene sequence as a query. Both ERF1 gene nucleotide sequences and amino acid sequences in the A and B genomes were annotated and compared. Seven annotated genome ERF1 gene sequences from the A and B genomes were identified with the probability that these genes were actively transcribed in cell activity. ERF1 gene comparisons between the A and B genomes showed that nucleotide composition, gene structure, gene position in each respective chromosome, ERF clusterization, identified motif, and amino acid composition in each of the identified motifs have similar characteristics.

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Item Type:	Article
AGROVOC Term:	Musa balbisiana
AGROVOC Term:	Musa acuminata
AGROVOC Term:	bananas
AGROVOC Term:	genomes
AGROVOC Term:	ethylene
AGROVOC Term:	plant growth substances
AGROVOC Term:	phylogenetic analysis
AGROVOC Term:	plant genetics
AGROVOC Term:	genomics
Geographical Term:	Indonesia
Uncontrolled Keywords:	AP2/ERF domain, comparative genomics, ethylene response factor 1, sequence annotation
Depositing User:	Ms. Azariah Hashim
Date Deposited:	27 Jan 2025 02:51
Last Modified:	27 Jan 2025 02:51
URI:	http://webagris.upm.edu.my/id/eprint/1926

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