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Comparative Genomics of Copia and Gypsy Retroelements in Three Banana Genomes: A, B, and S Genomes

Sigit Nur Pratama, Fenny Martha Dwivany and Husna Nugrahapraja

Pertanika Journal of Tropical Agricultural Science, Volume 44, Issue 4, November 2021

DOI: https://doi.org/10.47836/pjtas.44.4.01

Keywords: Banana, B, A, and S genomes, reverse transcriptase, transposable elements

Published on: 2 November 2021

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%, 20.78%, 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.

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