Data from: The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)
Li, Shu-Fen et al. (2019), Data from: The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.), Dryad, Dataset, https://doi.org/10.5061/dryad.4053d31
Background: Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated.
Results: We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes.
Conclusions: We reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction.