Molecular Entomology 2024, Vol.15, No.5, 192-199 http://emtoscipublisher.com/index.php/me 193 2 Genetic Insights into Sitophilus oryzae 2.1 Genomic studies and their findings Recent genomic studies on Sitophilus oryzae have provided significant insights into its genetic makeup, revealing a genome rich in Transposable Elements (TEs), which constitute about 72% of its genome (Figure 1) (Parisot et al., 2021). This high percentage of TEs is associated with the insect's endosymbiotic state and has implications for its adaptability and evolution. The genome sequencing efforts have also highlighted a high gene expansion rate in S. oryzae compared to other beetles, which may contribute to its success as a pest. Additionally, the genetic diversity of S. oryzae has been studied across different geographic locations, showing low mitochondrial diversity typical of stored product pests, which may be influenced by repeated phosphine fumigations. Figure 1 A Proportion of repeat content inS. oryzae’s genome (Adopted from Parisot et al., 2021) Image caption: The majority of repeats detected in S. oryzae are represented by Class II (TIR) elements, LINEs (Class I), and unclassified repeats (unknown). NR: non repetitive. B Variation of genome size and TE content in 62 insect species and S. oryzae. Coleopteran species are depicted in dark blue, and S. oryzae in light blue. S. oryzae is clearly a TE-rich genome. C TE proportion across 11 insect species, including six coleoptera. PLEs are included in the LINE superfamilies, DIRS in LTRs, and RC, CRY, MAV and TIR in the DNA superfamilies. NR: non repetitive. S. oryzae harbors the largest TE content among Coleopterans and most insect species studied to date. Within Coleoptera, there is a large variation in TE content and type, with A. planipennis, L. decemlineata, and O. taurus carrying an abundant LINE content, while S. oryzae, T. castaneum, and A. glabripennis show larger DNA content. D Classification of the 570 Mbs of TEs present in the S. oryzae genome. Most TIR families detected were not classified into known superfamilies. RTE LINE and Gypsy LTR elements are the most abundant superfamilies among retrotransposons. Around 21% of repeats in S. oryzae’s genome were not classified by our pipeline, and remain unknown (gray). E Distribution of TIR length sequences (right) detected by einverted and the internal region present between both TIRs (left) for complete consensus of TIR superfamilies (color) and unknown TIR families (gray) (Adopted from Parisot et al., 2021)
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