Dataset Information

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.).

ABSTRACT: 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.

SUBMITTER: Li SF

PROVIDER: S-EPMC6337768 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (<i>Spinacia oleracea</i> L.).

Li Shu-Fen SF Guo Yu-Jiao YJ Li Jia-Rong JR Zhang Dong-Xu DX Wang Bing-Xiao BX Li Ning N Deng Chuan-Liang CL Gao Wu-Jun WJ

Mobile DNA 20190118

<h4>Background</h4>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 (<i>Spinacia oleracea</i> 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.< ...[more]

PMID: 30675191

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Project description:Sex chromosome evolution has mostly been studied in species with heteromorphic sex chromosomes. The Spinacia genus serves as an ideal model for investigating evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution while their forces have not been fully explored in Spinacia species. Here, we identified major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative sugar beet to elucidate the evolutionary processes of sex chromosome evolution using next-generation sequencing (NGS) data. Comparative analysis revealed that the repeat elements of Spinacia species are considerably higher than of sugar beet, especially the Ty3/Gypsy and Ty1/Copia retrotransposons. The long terminal repeat retroelements (LTR) Angela, Athila, and Ogre may be accounted for the higher proportion of repeats in the spinach genome. Comparison of the repeats proportion between female and male genomes of three Spinacia species indicated the different representation in Spinacia tetrandra samples but not in the S. oleracea or S. turkestanica samples. From these results, we speculated that emergence of repetitive DNA sequences may correlate the formation of sex chromosome and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes as heteromorphic sex chromosomes exclusively existed in Spinacia tetrandra. Three novel sugar beet-specific satellites were identified and confirmed by fluorescence in situ hybridization (FISH); six out of eight new spinach-specific satellites were mapped to the short arm of sex chromosomes. A total of 141 copies of SolSat01-171-s were found in the sex determination region (SDR). Thus, the accumulation of satellite DNA on the short arm of chromosome 1 may be involved in the sex chromosome evolution in Spinacia species. Our study provides a fundamental resource for understanding repeat sequences in Spinacia species and their roles in sex chromosome evolution.

Dataset Information

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.).

Publications

The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (<i>Spinacia oleracea</i> L.).

Similar Datasets

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