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Identification of novel SINEs from Cyprinidae and their evolutionary significance
Han Yawei; He Shunping; Chen Yiyu; He, SP, Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China
2007-03-01
Source PublicationPROGRESS IN NATURAL SCIENCE
ISSN1002-0071
Volume17Issue:3Pages:270-279
AbstractShort interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.; Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.
SubtypeArticle
KeywordShort Interspersed Nuclear Elements (Sines) Master Gene Model Opsar Zb-sines And Cyprinidae
DepartmentChinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China; Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
Subject AreaMultidisciplinary Sciences
WOS HeadingsScience & Technology ; Technology
Indexed BySCI
Language英语
WOS Research AreaMaterials Science ; Science & Technology - Other Topics
WOS SubjectMaterials Science, Multidisciplinary ; Multidisciplinary Sciences
WOS IDWOS:000246193900006
WOS KeywordINTERSPERSED REPETITIVE ELEMENTS ; MOUSE GENOME ; MOLECULAR SYSTEMATICS ; EUKARYOTIC GENOMES ; MESSENGER-RNA ; ALU REPEATS ; SEQUENCES ; RETROTRANSPOSITION ; FAMILY ; LINES
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/8634
Collection期刊论文
Corresponding AuthorHe, SP, Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Han Yawei,He Shunping,Chen Yiyu,et al. Identification of novel SINEs from Cyprinidae and their evolutionary significance[J]. PROGRESS IN NATURAL SCIENCE,2007,17(3):270-279.
APA Han Yawei,He Shunping,Chen Yiyu,&He, SP, Chinese Acad Sci, Inst Hydrobiol, Wuhan 430072, Peoples R China.(2007).Identification of novel SINEs from Cyprinidae and their evolutionary significance.PROGRESS IN NATURAL SCIENCE,17(3),270-279.
MLA Han Yawei,et al."Identification of novel SINEs from Cyprinidae and their evolutionary significance".PROGRESS IN NATURAL SCIENCE 17.3(2007):270-279.
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