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 cro...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-01-01
|
| Series: | Mobile DNA |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13100-019-0147-6 |
| _version_ | 1819018725985091584 |
|---|---|
| author | Shu-Fen Li Yu-Jiao Guo Jia-Rong Li Dong-Xu Zhang Bing-Xiao Wang Ning Li Chuan-Liang Deng Wu-Jun Gao |
| author_facet | Shu-Fen Li Yu-Jiao Guo Jia-Rong Li Dong-Xu Zhang Bing-Xiao Wang Ning Li Chuan-Liang Deng Wu-Jun Gao |
| author_sort | Shu-Fen Li |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T03:24:00Z |
| format | Article |
| id | doaj.art-5a337e664d404a3b9a6affcb09eb0af3 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-21T03:24:00Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-5a337e664d404a3b9a6affcb09eb0af32022-12-21T19:17:38ZengBMCMobile DNA1759-87532019-01-0110111510.1186/s13100-019-0147-6The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.)Shu-Fen Li0Yu-Jiao Guo1Jia-Rong Li2Dong-Xu Zhang3Bing-Xiao Wang4Ning Li5Chuan-Liang Deng6Wu-Jun Gao7College of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Science, Shanxi Datong UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityAbstract 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.http://link.springer.com/article/10.1186/s13100-019-0147-6Repetitive sequenceSatellite DNASex chromosomeSpinachTransposable elements |
| spellingShingle | Shu-Fen Li Yu-Jiao Guo Jia-Rong Li Dong-Xu Zhang Bing-Xiao Wang Ning Li Chuan-Liang Deng Wu-Jun Gao The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.) Mobile DNA Repetitive sequence Satellite DNA Sex chromosome Spinach Transposable elements |
| title | The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.) |
| title_full | The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.) |
| title_fullStr | The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.) |
| title_full_unstemmed | The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.) |
| title_short | The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach (Spinacia oleracea L.) |
| title_sort | landscape of transposable elements and satellite dnas in the genome of a dioecious plant spinach spinacia oleracea l |
| topic | Repetitive sequence Satellite DNA Sex chromosome Spinach Transposable elements |
| url | http://link.springer.com/article/10.1186/s13100-019-0147-6 |
| work_keys_str_mv | AT shufenli thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT yujiaoguo thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT jiarongli thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT dongxuzhang thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT bingxiaowang thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT ningli thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT chuanliangdeng thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT wujungao thelandscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT shufenli landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT yujiaoguo landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT jiarongli landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT dongxuzhang landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT bingxiaowang landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT ningli landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT chuanliangdeng landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal AT wujungao landscapeoftransposableelementsandsatellitednasinthegenomeofadioeciousplantspinachspinaciaoleraceal |