Successful Invasions of Short Internally Deleted Elements (SIDEs) and Its Partner CR1 in Lepidoptera Insects

Wang, Ping-Lan; Luchetti, Andrea; Ruggieri, Angelo; Xiong, Xiao-Min; Xu, Min-Rui-Xuan; Xiao-gu, Zhang; Zhang, Hua-Hao

doi:10.1093/gbe/evz174

Cited by 2 publications

(1 citation statement)

References 50 publications

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“…This more detailed analysis therefore shows that the TE invasion of H. metabus genome is primarily driven by a few TE families that are also among the most abundant ones in the closest species genome sequences. In particular, the LINE CR1 Zenon has been shown to successfully invade other lepidopteran species' genomes (Wang et al, 2019).…”

Section: Invasion Of Repetitive Elementsmentioning

confidence: 99%

Transposable element accumulation drives genome size increase inHylesia metabus(Lepidoptera: Saturniidae), an urticating moth species from South America

Perrier,

Allio,

Legeai

et al. 2024

Preprint

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We present the first nuclear genome assembly and a complete mitogenome forHylesia metabus(Arthropoda; Insecta; Lepidoptera; Saturniidae). The assembled nuclear genome sequence is 1,271 Mb long, which is among the 10 largest lepidopteran genome assemblies published to date. It is scaffolded in 31 pseudo chromosomes, has a BUSCO score of 99.5%, and has a highly conserved synteny compared to phylogenetically close species. Repetitive elements make up 67% of the nuclear genome and are mainly located in intergenic regions, among which LINEs were predominant, with CR1-Zenon being the most abundant. Phylogenetic and comparative analyses ofH. metabusassembly and 17 additional Saturniidae and Sphingidae assemblies suggested that an accumulation of repetitive elements likely led to the increased size ofH. metabus’genome. Gene annotation using Helixer identified 26,122 transcripts. The Z scaffold was identified using both a synteny analysis and variations of coverage for two resequenced male and femaleH. metabus. TheH. metabusnuclear genome and mitogenome assemblies can be found and browsed on the BIPAA website and constitute useful resources for future population and comparative genomics studies.

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Section: Invasion Of Repetitive Elementsmentioning

confidence: 99%

Transposable element accumulation drives genome size increase inHylesia metabus(Lepidoptera: Saturniidae), an urticating moth species from South America

Perrier,

Allio,

Legeai

et al. 2024

Preprint

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Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions

Martelossi,

Iannello,

Ghiselli

et al. 2024

Mobile DNA

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Background Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retrotransposons widespread across eukaryotes. They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their overall distribution and impact on host genome evolution are still unknown due to the extreme scarcity of transposon libraries for the clade. In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution. Results We found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a “mosaic” evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. Multiple SINEs were found to be highly similar between phylogenetically related species but separated by extremely long evolutionary timescales, up to ~ 400 million years. Studying their genomic distribution in a subset of five species, we observed different patterns of SINE enrichment in various genomic compartments as well as differences in the tendency of SINEs to form tandem-like and palindromic structures also within intronic sequences. Despite these differences, we observed that SINEs, especially older ones, tend to accumulate preferentially within genes, or in their close proximity, consistently with a model of survival bias for less harmful, short non-coding transposons in euchromatic genomic regions. Conclusion Here we conducted a wide characterization of tRNA-related SINEs in bivalves revealing their taxonomic distribution and LINE partnerships across the clade. Moreover, through the study of their genomic distribution in five species, we highlighted commonalities and differences with other previously studied eukaryotes, thus extending our understanding of SINE evolution across the tree of life. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-024-00332-x.

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Successful Invasions of Short Internally Deleted Elements (SIDEs) and Its Partner CR1 in Lepidoptera Insects

Cited by 2 publications

References 50 publications

Transposable element accumulation drives genome size increase inHylesia metabus(Lepidoptera: Saturniidae), an urticating moth species from South America

Transposable element accumulation drives genome size increase inHylesia metabus(Lepidoptera: Saturniidae), an urticating moth species from South America

Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions

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