Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

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

	Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
	Guo, Baocheng 1,2; Zou, Ming 1,2; Gan, Xiaoni 1,2,3; He, Shunping 1
刊名	BMC GENOMICS
	2010-06-23
卷号	11 页码:-
关键词	TETRAODONTIFORM FISHES REPETITIVE ELEMENTS INTRON SIZE DNA CONTENT GENE COTTON FUGU DUPLICATION DROSOPHILA GOSSYPIUM
ISSN号	1471-2164
通讯作者	He, SP, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Fish Phylogenet & Biogeog Grp, Wuhan 430072, Peoples R China
中文摘要	Background: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. Results: Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89%) and that in the Te. nigroviridis genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp). Conclusion: Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between D. holocanthus and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between D. holocanthus and the smooth pufferfish.
英文摘要	Background: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish.
学科主题	Biotechnology & Applied Microbiology; Genetics & Heredity
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biotechnology & Applied Microbiology ; Genetics & Heredity
研究领域[WOS]	Biotechnology & Applied Microbiology ; Genetics & Heredity
关键词[WOS]	TETRAODONTIFORM FISHES ; REPETITIVE ELEMENTS ; INTRON SIZE ; DNA CONTENT ; GENE ; COTTON ; FUGU ; DUPLICATION ; DROSOPHILA ; GOSSYPIUM
收录类别	SCI
资助信息	National Natural Science Foundation of China [30530120, 2007CB411601]
语种	英语
WOS记录号	WOS:000280399000001
公开日期	2010-12-23
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/13469]
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, Key Lab Aquat Biodivers & Conservat, Fish Phylogenet & Biogeog Grp, Wuhan 430072, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100039, Peoples R China 3.Chinese Acad Sci, Wuhan Inst Virol, Wuhan 430071, Peoples R China
推荐引用方式 GB/T 7714	Guo, Baocheng,Zou, Ming,Gan, Xiaoni,et al. Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing[J]. BMC GENOMICS,2010,11:-.
APA	Guo, Baocheng,Zou, Ming,Gan, Xiaoni,&He, Shunping.(2010).Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing.BMC GENOMICS,11,-.
MLA	Guo, Baocheng,et al."Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing".BMC GENOMICS 11(2010):-.