Genomics Comparison of Copia and Gypsy Retroelements in Musa balbisiana ‘Pisang Klutuk Wulung’, Musa acuminata ‘DH Pahang’, and Musa schizocarpa

• Main Author: Nur Pratama, Sigit
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/42148
• Institution: Institut Teknologi Bandung

Hitherto, characterization of repetitive banana sequence is still limited, including the Musa species: Musa balbisiana (B genome), Musa acuminata (A genome), and Musa schizocarpa (S genome). Nevertheless, repetitive elements and transposable elements (TEs) are considered important due to the fact that TEs have a large genome fraction and can be useful for genome mapping, evolutionary studies, omics studies, and marker-assisted selection. In plants, proportion of TEs is generally dominated by Long Terminal Repeat (LTR) retroelements, namely Copia and Gypsy. LTR elements are known to have impacts on genome expansion and genetic and phenotype variation. That said, this study was aimed to compare B, A, and S genome based on repetitive element proportions and copy number of transposable elements and to determine the evolutionary relationship of LTR retroelement (Ty1/Copia and Ty3/Gypsy) by means of 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 prior to perl parsing. Filograms were constructed according to domain analysis with DANTE, alignments with MAFFT 7, and trees inference with FastTree 2. The trees were inspected using SeaView 4 and visualized with FigTree 1.4.4. Respectively, B, A, and S genomes comprised repetitive elements with a proportion of 19.38%, 20.78%, 25.96%. Elements with dominant proportions in the genome are LTR (Copia and Gypsy). Copia on genome B has a copy number (CN) of 61,070 copies, genome A 68,857 copies, and genome S 95,849 copies. Gypsy has a CN on the B genome of 46,075 copies, a genome of 59,495 copies and the genome S 82,317 copies. Despite having a low genome proportion with less than 2%, tandem repeats were observed as elements with the highest CN. Copia Superfamily has a higher proportion of Gypsy on each banana chromosome in genome B and genome A with a total proportion of Copia 8.79% and Gypsy 7.51% in genome B, Copia 9.32% and Gypsy 8.21% in the genome A, and Copia 12.66% and Gypsy 9.7% in the S genome. To conclude, these elements have active transposition potential characters and their structures tend to be full-length with the divergence close to 0 and the ratio close to 1. In terms of RT phylogenetic analysis, LTR element can be clustered into 13 ancient lineages and grouped into clades of Copia and Gypsy superfamily, chromovirus and non-chromovirus lineages in Gypsy, and Sirevirus and Tork lineages in Copia. SIRE (Copia) and Reina (Gypsy) are shown to be the most abundant LTR families in bananas. To sum up, B, A, and S genomes have a proportion of repetitive elements with B < A < S with LTR (Copia and Gypsy) as elements with the highest proportion, Copia is more abundant than Gypsy and RT domain can be used to construct LTR (Copia and Gypsy) filograms in the B, A, and S genomes and to cluster the LTR families.