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

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.

A systematic revision of Capparaceae and Cleomaceae in Egypt: an evaluation of the generic delimitations of Capparis and Cleome using ecological and genetic diversity

“…Many studies confirmed that the retrotransposons marker, e.g., ISTR had a superior discrimination capacity and have the flexibility to detect several polymorphic loci per individual reaction [60]. Recently, Du et al [61] suggested that retrotransposons (RT) occupied 28.1 Mb of the genome sequence, accounting for 9.74% of the entire genome. These results indicated that ISTR had an abundant presence of Ty-1 Copia retrotransposons, which permit obtaining useful polymorphism among the tested genotypes of Capparaceae and Cleome germplasm.…”

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

“…LTR-RTs are extremely variable in size, ranging in plants from 4 kb to over 31–23 kb [39,40] (i.e., Ogre elements with >23 kb in length [41,42]) for functional and complete elements [12,42,43]. A key feature in this order is the presence of long terminal repeats (LTRs), which are two homologous (identical at the time of insertion) non-coding DNA sequences [44] located at both ends of the internal coding region and can range from a few hundred base pairs to more than 5 kb [26]. LTR-RTs contain one [45] or more open reading frames (ORF) [46] that are transcribed using host machinery [47] and code for gag and polyprotein ( pol ) genes.…”

Genetic Assessment of Some Egyptian Cultivated Citrus and its Relatives using Retrotransposons and Microsatellite

“…This is seems caused by the distinction of the LTR-REMAP marker system. In subsequent studies, (Biswas et al, 2010a: Du et al, 2018 described that LTR-REMAP markers exhibited higher levels of heterozygosity due to the high copy number of effective alleles and its widespread distribution of LTR in citrus. The moderate value of the effective number of alleles per locus for SSR markers in comparison to LTR-REMAP may suggest the presence of many unique or less frequent alleles (Biswas et al, 2010a,b andAmar et al, 2011).…”

“…Many studies confirmed that the LTR-REMAP marker had a superior discrimination capacity and have ability to discover more polymorphic locus per individual reaction (Biswas et al, 2010b). Recently, (Du et al, 2018) recommended that LTR-RTs occupied 28.1 Mb of the genome sequence, accounting for 9.74% of the whole genome. These results suggested that LTR-REMAP had an abundant presence of Ty-1 copia retrotransposons, which allow obtaining advantageous polymorphism between the tested genotypes of citrus germplasm.…”

“…Accordingly, these unique properties of retrotransposons have been utilized as genetic implements for plant genotyping (Mansour, 2008), intraspecific relationships, functional analyses of genes and the genetic diversity (Kalendar & Schulman, 2014). Unfortunately, LTR-REMAP based marker is still less studied in citrus research (Du et al, 2018).…”