Full-Length LTR Retrotransposons in the Genome of Citrus × Clementina

Long terminal repeat retrotransposons (LTR-RTs) make up a large fraction of most plant genomes, and they play important roles in genome evolution. A total of 3,959 full-length LTR-RTs were identified in the sequenced Citrus x clementina genome using both structure-based (LTR_FINDER) and homology-based (RepeatMasker) methods. They were first classified into three superfamilies (Ty3-gypsy, Ty1-copia, or unknown) according to protein-domain organization, and then clustered into 1,074 families, based on their LTR sequence similarity. Three hundred fifty Copia families were grouped into four lineages: Retrofit, Tork, Sire and Oryco. One hundred seventy-eight Gypsy families fell into six lineages: Athila, Tat, Renia, CRM, Galadriel and Del. Most LTR elements (3,218 , or 81.3%) were anchored to 9 linkage groups of Clementine, accounting for 9.74% of the currently assembled chromosomes. Transcript level of these elements was analyzed using RNA-seq datasets of four samples. Only103 elements (2.6%) had an expression level above one read per kilobase of exon per million mapped reads (RPKM). Thirty LTR-RTs were used to genotype a sample of 25 Citrus accessions. The cluster analysis detected the existence of several clusters among Citrus accessions. Our results demonstrated the effectiveness of these LTR-RTs in analyzing Citrus phylogenetic relationships.