Comparative Genomics of Copia and Gypsy retroelements in three banana genomes: A B and S genomes

Dwivany Fenny Martha, . and Pratama Sigit Nur, . and Nugrahapraja Husna, . Comparative Genomics of Copia and Gypsy retroelements in three banana genomes: A B and S genomes. pp. 697-711. ISSN 1511-3701

In plants the proportion of transposable elements (TEs) is generally dominated by long terminal repeat (LTR) retroelements. Therefore it significantly impacts on genome expansion and genetic and phenotypic variation namely Copia and Gypsy. Despite such contribution TEs characterisation in an important crop such as banana Musa balbisiana (B genome) Musa acuminata (A genome) and Musa schizocarpa (S genome) remains poorly understood. This study aimed to compare B A and S genomes based on repetitive element proportions and copy numbers and determine the evolutionary relationship of LTR using phylogenetic analysis of the reverse transcriptase (RT) domain. Genome assemblies were acquired from the Banana Genome Hub (banana-genome-hub.southgreen.fr). Repetitive elements were masked by RepeatMasker 4.0.9 before Perl parsing. Phylograms were constructed according to domain analysis using DANTE (Domain-based ANnotation of Transposable Elements) alignments were made using MAFFT 7 (multiple alignments using fast Fourier transform) and trees were inferred using FastTree 2. The trees were inspected using SeaView 4 and visualised with FigTree 1.4.4. We reported that B A and S genomes are composed of repetitive elements with 19.38 0.2078 and 25.96 respectively. The elements were identified with dominant proportions in the genome are LTR in which Copia is more abundant than Gypsy. Based on RT phylogenetic analysis LTR elements are clustered into 13 ancient lineages in which Sire (Copia) and Reina (Gypsy) are shown to be the most abundant LTR lineages in bananas.

Full text available from: Official URL: http://www.pertanika.upm.edu.my/pjtas/browse/regul...

Abstract

In plants the proportion of transposable elements (TEs) is generally dominated by long terminal repeat (LTR) retroelements. Therefore it significantly impacts on genome expansion and genetic and phenotypic variation namely Copia and Gypsy. Despite such contribution TEs characterisation in an important crop such as banana Musa balbisiana (B genome) Musa acuminata (A genome) and Musa schizocarpa (S genome) remains poorly understood. This study aimed to compare B A and S genomes based on repetitive element proportions and copy numbers and determine the evolutionary relationship of LTR using phylogenetic analysis of the reverse transcriptase (RT) domain. Genome assemblies were acquired from the Banana Genome Hub (banana-genome-hub.southgreen.fr). Repetitive elements were masked by RepeatMasker 4.0.9 before Perl parsing. Phylograms were constructed according to domain analysis using DANTE (Domain-based ANnotation of Transposable Elements) alignments were made using MAFFT 7 (multiple alignments using fast Fourier transform) and trees were inferred using FastTree 2. The trees were inspected using SeaView 4 and visualised with FigTree 1.4.4. We reported that B A and S genomes are composed of repetitive elements with 19.38 0.2078 and 25.96 respectively. The elements were identified with dominant proportions in the genome are LTR in which Copia is more abundant than Gypsy. Based on RT phylogenetic analysis LTR elements are clustered into 13 ancient lineages in which Sire (Copia) and Reina (Gypsy) are shown to be the most abundant LTR lineages in bananas.

[error in script]

Item Type:	Article
AGROVOC Term:	Bananas
AGROVOC Term:	Musa balbisiana
AGROVOC Term:	Musa acuminata
AGROVOC Term:	genomics
AGROVOC Term:	Phylogeny
AGROVOC Term:	analysis
AGROVOC Term:	Reverse transcriptase
AGROVOC Term:	Transposable elements
Depositing User:	Mr. AFANDI ABDUL MALEK
Last Modified:	24 Apr 2025 00:55
URI:	http://webagris.upm.edu.my/id/eprint/10148

Actions (login required)

View Item