Abstract
BackgroundRepetitive 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.ResultsWe 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.ConclusionsWe 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.
Highlights
Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes
After LTRdigest analyses, we identified 11,640 putative full-length long terminal repeat (LTR)-REs with polypurine tract (PPT), or primer-binding site (PBS) sites, or at least one typical protein domain (Additional file 1)
In conclusion, this study presents a comprehensive description of the repetitive sequence organization of spinach, an important vegetable and dioecious plant species
Summary
Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. A substantial fraction of plant genomes is occupied by repetitive DNA, which mainly includes transposable elements (TEs) and satellite DNAs. TEs are DNA fragments that have the ability to move from one part of a genome to another, often accounting for a large proportion of the plant genome. TEs are DNA fragments that have the ability to move from one part of a genome to another, often accounting for a large proportion of the plant genome They are categorized into two distinct classes based on structural feature and transposition pattern. Given that REs can increase their copy numbers after being transposed, they are usually the most abundant repetitive elements, especially long terminal repeat (LTR) REs. For example, in maize, REs and LTR-REs constitute 75.6 and 70.1% of the genome, respectively, whereas DNA transposons occupy 8.6% [1]. It consists of a large number of repeat units (50–1000 bp) that are organized in tandem arrays [4]
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