Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp

CORC > 水生生物研究所 > 中科院水生所知识产出（2009年前） > 水生生物多样性与资源保护研究中心 > 期刊论文

	Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp
	Chi, Wei 1,2; Tong, Chaobo 1,2; Gan, Xiaoni 1,2; He, Shunping 1
刊名	PLOS ONE
	2011-08-15
卷号	6 期号:8 页码:e23549
关键词	ARABIDOPSIS-THALIANA DUPLICATE GENES MICRORNA GENES C-ELEGANS EVOLUTION EXPRESSION DROSOPHILA RNAS SET RETROTRANSPOSONS
ISSN号	1932-6203
通讯作者	Chi, W (reprint author), Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan, Hubei, Peoples R China ; clad@ihb.ac.cn
中文摘要	MicroRNAs (miRNAs) are small non-coding RNA molecules that are processed from large 'hairpin' precursors and function as post-transcriptional regulators of target genes. Although many individual miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in teleost fishes. By using high throughput sequencing technology, we have identified 167 and 166 conserved miRNAs (belonging to 108 families) in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), respectively. We compared the expression patterns of conserved miRNAs by means of hierarchical clustering analysis and log2 ratio. Results indicated that there is not a strong correlation between sequence conservation and expression conservation, most of these miRNAs have similar expression patterns. However, high expression differences were also identified for several individual miRNAs. Several miRNA* sequences were also found in our dataset and some of them may have regulatory functions. Two computational strategies were used to identify novel miRNAs from un-annotated data in the two carps. A first strategy based on zebrafish genome, identified 8 and 22 novel miRNAs in bighead carp and silver carp, respectively. We postulate that these miRNAs should also exist in the zebrafish, but the methodologies used have not allowed for their detection. In the second strategy we obtained several carp-specific miRNAs, 31 in bighead carp and 32 in silver carp, which showed low expression. Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes.
英文摘要	MicroRNAs (miRNAs) are small non-coding RNA molecules that are processed from large 'hairpin' precursors and function as post-transcriptional regulators of target genes. Although many individual miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in teleost fishes. By using high throughput sequencing technology, we have identified 167 and 166 conserved miRNAs (belonging to 108 families) in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), respectively. We compared the expression patterns of conserved miRNAs by means of hierarchical clustering analysis and log2 ratio. Results indicated that there is not a strong correlation between sequence conservation and expression conservation, most of these miRNAs have similar expression patterns. However, high expression differences were also identified for several individual miRNAs. Several miRNA* sequences were also found in our dataset and some of them may have regulatory functions. Two computational strategies were used to identify novel miRNAs from un-annotated data in the two carps. A first strategy based on zebrafish genome, identified 8 and 22 novel miRNAs in bighead carp and silver carp, respectively. We postulate that these miRNAs should also exist in the zebrafish, but the methodologies used have not allowed for their detection. In the second strategy we obtained several carp-specific miRNAs, 31 in bighead carp and 32 in silver carp, which showed low expression. Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes.
学科主题	Life Sciences & Biomedicine - Other Topics
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	ARABIDOPSIS-THALIANA ; DUPLICATE GENES ; MICRORNA GENES ; C-ELEGANS ; EVOLUTION ; EXPRESSION ; DROSOPHILA ; RNAS ; SET ; RETROTRANSPOSONS
收录类别	SCI
资助信息	National Basic Research Program of China[2007CB411601]
语种	英语
WOS记录号	WOS:000293953700032
公开日期	2011-12-22
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/16397]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
作者单位	1.Chinese Acad Sci, Inst Hydrobiol, Lab Fish Phylogenet & Biogeog, Wuhan, Hubei, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Chi, Wei,Tong, Chaobo,Gan, Xiaoni,et al. Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp[J]. PLOS ONE,2011,6(8):e23549.
APA	Chi, Wei,Tong, Chaobo,Gan, Xiaoni,&He, Shunping.(2011).Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp.PLOS ONE,6(8),e23549.
MLA	Chi, Wei,et al."Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp".PLOS ONE 6.8(2011):e23549.