Identification of novel SINEs from Cyprinidae and their evolutionary significance
Identification of novel SINEs from Cyprinidae and their evolutionary significance作者机构：Institute of Hydrobiology Chinese Academy of Sciences Wuhan 430072 China Graduate School Chinese Academy of Sciences Beijing 100039 China
出 版 物：《Progress in Natural Science:Materials International》 (自然科学进展·国际材料(英文))
年 卷 期：2007年第17卷第3期
页 面：270-279页
核心收录：
学科分类：0710[理学-生物学] 07[理学] 071002[理学-动物学]
基 金：Supported by the National Fund for Distinguished Young Scholars (Grant No. 30225008)
主 题：short interspersed nuclear elements (SINEs) master gene model Opsar Zb-SINEs and Cyprinidae.
摘 要：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 -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 bp. 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 tRNAAla gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA sequence or a tRNA -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.
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