Can-SINE dynamics in the giant panda and three other Caniformia genomes
Abstract Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Canifo...
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | Mobile DNA |
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| Online Access: | http://link.springer.com/article/10.1186/s13100-018-0137-0 |
| _version_ | 1818581765404491776 |
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| author | Changjun Peng Lili Niu Jiabo Deng Jianqiu Yu Xueyan Zhang Chuang Zhou Jinchuan Xing Jing Li |
| author_facet | Changjun Peng Lili Niu Jiabo Deng Jianqiu Yu Xueyan Zhang Chuang Zhou Jinchuan Xing Jing Li |
| author_sort | Changjun Peng |
| collection | DOAJ |
| description | Abstract Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes. Conclusions Our results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes. |
| first_indexed | 2024-12-16T07:38:41Z |
| format | Article |
| id | doaj.art-99a718f490a74c6b8187dc799cf52466 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-16T07:38:41Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-99a718f490a74c6b8187dc799cf524662022-12-21T22:39:08ZengBMCMobile DNA1759-87532018-11-019111410.1186/s13100-018-0137-0Can-SINE dynamics in the giant panda and three other Caniformia genomesChangjun Peng0Lili Niu1Jiabo Deng2Jianqiu Yu3Xueyan Zhang4Chuang Zhou5Jinchuan Xing6Jing Li7Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of SichuanSichuan Wild Animal Research Institute, Chengdu ZooSichuan Wild Animal Research Institute, Chengdu ZooSichuan Wild Animal Research Institute, Chengdu ZooKey Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of SichuanSichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan UniversityDepartment of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New JerseyKey Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of SichuanAbstract Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes. Conclusions Our results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes.http://link.springer.com/article/10.1186/s13100-018-0137-0Caniformia speciesCan-SINEsTransposable element activityPutative panda-specific elements |
| spellingShingle | Changjun Peng Lili Niu Jiabo Deng Jianqiu Yu Xueyan Zhang Chuang Zhou Jinchuan Xing Jing Li Can-SINE dynamics in the giant panda and three other Caniformia genomes Mobile DNA Caniformia species Can-SINEs Transposable element activity Putative panda-specific elements |
| title | Can-SINE dynamics in the giant panda and three other Caniformia genomes |
| title_full | Can-SINE dynamics in the giant panda and three other Caniformia genomes |
| title_fullStr | Can-SINE dynamics in the giant panda and three other Caniformia genomes |
| title_full_unstemmed | Can-SINE dynamics in the giant panda and three other Caniformia genomes |
| title_short | Can-SINE dynamics in the giant panda and three other Caniformia genomes |
| title_sort | can sine dynamics in the giant panda and three other caniformia genomes |
| topic | Caniformia species Can-SINEs Transposable element activity Putative panda-specific elements |
| url | http://link.springer.com/article/10.1186/s13100-018-0137-0 |
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