A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

Abstract

Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A + T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA)n microsatellite loci, and was named the microsatellite-associated interspersed nuclear element ( MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA)n microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA)n microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA)n microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains. Abstract Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A ? T content (62.3%), lack of internal protein coding sequence, and secondary structure consisting of subterminal inverted repeats (SIRs). The O. nubilalis TE has inserted at (GAAA) n microsatellite loci, and was named the microsatellite-associated interspersed nuclear element (MINE-1). Non-autonomous MINE-1 superfamily members also were identified downstream of (GAAA) n microsatellites within Bombyx mori and Pectinophora gossypiella genomes. Of 316 (GAAA) n microsatellites from the B. mori whole genome sequence, 201 (63.6%) have associated autonomous or non-autonomous MINE-1 elements. Autonomous B. mori MINE-1s a encode a helicase and endonuclease domain RepHel-like protein (BMHELp1) indicating their classification as Helitron-like transposons and were renamed Helitron1_BM. Transposition of MINE-1 members in Lepidoptera has resulted in the disruption of (GAAA) n microsatellite loci, has impacted the application of microsatellite-based genetic markers, and suggests genome sequence that flanks TT/AA dinucleotides may be required for target site recognition by RepHel endonuclease domains.

Structural and functional liaisons between transposable elements and satellite DNAs

“…Repeats are variable in DNA sequence, copy number (2-10), and monomer length (50-500 bp) when compared among species (Yang and Barbash 2008). According to classification in Thomas et al (2014), elements called PERI from seven species of the Drosophila buzzatii cluster (Kuhn and Heslop-Harrison 2011), MINE-1 and MINE-2 from Lepidoptera (Coates et al 2010(Coates et al , 2011, DTC84 from the clam Donax trunculus (Šatović and Plohl 2013), pearl from the oyster (Gaffney et al 2003), MgE from Mytilus galloprovincialis (Kourtidis et al 2006a), and Tsp from the sea urchin (Cohen et al 1985) are all DINE-1 like elements. Recently, two different MITE elements (terMITE1 and terMITE2) were described in termites, both also containing variable number of internal tandem repeats which are 16 and 114-bp long, respectively (Luchetti 2015).…”

Helitrons , the Eukaryotic Rolling-circle Transposable Elements

“…These Helentrons have palindromic subTIRs in addition to a palindrome at the 3′ end, and so have three sets of palindromic sequences (11) like IS91 elements (for review see reference 46). Some families of Helitrons and Helentrons carry tandem repeats, like microsatellites and minisatellites (11,22,24,26,32,36,39,(48)(49)(50)(51). For some HINE families, the tandem repeats occupy ∼ 50% of the total length of the element (11).…”

“…Among animals, they are most prevalent in the genomes of insects and other invertebrates. In insects, they have been identified from Diptera, Lepidoptera, Hymenoptera, Coleoptera, Hemiptera, (11,32,56), Thysanoptera, Orthoptera, Megaloptera, Strepsitera, and Isoptera. In addition to insects, Helentron genes have been identified in the genome of the polydnavirus, Cotesia sesamia bracovirus associated with hymenopteran wasps (11).…”

A rearrangement of the Z chromosome topology influences the sex-linked gene display in the European corn borer, Ostrinia nubilalis

“…All PCR amplified fragments were separated on 1.5% agarose gels. PCR products from O. nubilalis females were purified using Gel/PCR DNA fragment extraction kits (IBI Scientific, Peosta, IA), cloned into pGEM-T (Promega, Madison, WI), and sequenced (Coates et al 2010). Ostrinia nubilalis sequences were queried against the glean_cds.txt and glean_pro.txt files using tblastx and tblastn algorithms, aligned in MEGA 4.0 (Tamura et al 2007) as described previously, and putative substitution mutations within restriction endonuclease sites were identified manually.…”