LTR retrotransposons from the Citrus x clementina genome: characterization and application

Dongliang Du,Jude W Grosser,Fred G Gmitter,Qibin Yu,Xiaoyun Du,Matthew R Mattia,Yuan Yu,Ming Huang,Yanbo Wang

doi:10.1007/s11295-018-1257-x

Abstract

Long terminal repeat retrotransposons (LTR-RTs) are a large portion of most plant genomes, and can be used as a powerful molecular marker system. The first citrus reference genome (Citrus x clementina) has been publicly available since 2011; however, previous studies in citrus have not utilized the whole genome for LTR-RT marker development. In this study, 3959 full-length LTR-RTs were identified in the C. x clementina genome using structure-based (LTR_FINDER) and homology-based (RepeatMasker) methods. LTR-RTs were first classified by protein domain into Gypsy and Copia superfamilies, and then clustered into 1074 families based on LTR sequence similarity. Three hundred fifty Copia families were grouped into four lineages: Retrofit, Tork, Sire, and Oryco. One hundred seventy-eight Gypsy families were sorted into six lineages: Athila, Tat, Renia, CRM, Galadriel, and Del. Most LTR-RTs (3218 or 81.3%) were anchored to the nine Clementine mandarin linkage groups, accounting for 9.74% of chromosomes currently assembled. Accessions of 25 Rutaceae species were genotyped using 17 inter-retrotransposon amplified polymorphism (IRAP) markers developed from conserved LTR regions. Sequence-specific amplified polymorphism (SSAP) makers were used to distinguish ‘Valencia’ and ‘Pineapple’ sweet oranges (C. x sinensis), and 24 sweet orange clones. LTR-RT markers developed from the Clementine genome can be transferred within the Rutaceae family demonstrating that they are an excellent tool for citrus and Rutaceae genetic analysis.

Highlights

Retrotransposons (RT) are a type of transposable element (TE) that moves through the genome via an RNA intermediate in a process that resembles Bcopy and paste^ (Wicker et al 2007)
We identified and characterized fulllength Long terminal repeat retrotransposons (LTR-RTs) in the C. x clementina genome for use as molecular markers
A total of 3959 full-length long terminal repeats (LTRs)-RTs were identified in the Clementine genome (Online Resources 2 and 3)

Summary

Introduction

Retrotransposons (RT) are a type of transposable element (TE) that moves through the genome via an RNA intermediate in a process that resembles Bcopy and paste^ (Wicker et al 2007). Several types of LTR-RT molecular markers have been developed, such as inter-retrotransposon amplified polymorphism (IRAP), sequence-specific amplified polymorphism (SSAP), retrotransposon-microsatellite amplified polymorphism (REMAP), insertion site-based polymorphism (ISBP), and retrotransposon-based insertion polymorphism (RBIP) (Flavell et al 1998; Kalendar et al 1999; Paux et al 2010; Waugh et al 1997). IRAP markers amplify the intervening region between two retrotransposons to show polymorphisms (Kalendar et al 2011; Kalendar et al 1999). SSAP exploits LTR-RT polymorphisms by amplifying the region between a retrotransposon and adjacent restriction site in the genome creating additional polymorphisms that can be used to differentiate closely related accessions (Syed et al 2005). The development of next-generation sequencing technologies has allowed for huge numbers of retrotransposon sequences to be generated, providing new opportunities for molecular marker development (Barghini et al 2014; Cossu et al 2012; Du et al 2010; Xu and Du 2013; Zhang et al 2012)

Objectives

Methods

Results

Conclusion