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题名: Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish
作者: Yang, Liandong1, 2; Zou, Ming1, 2; Fu, Beide1, 2; He, Shunping1
通讯作者: He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
关键词: Teleost ; Lineage-specific gene ; Transcriptome ; Zebrafish embryogenesis
刊名: BMC GENOMICS
发表日期: 2013-01-31
DOI: 10.1186/1471-2164-14-65
卷: 14
收录类别: SCI
文章类型: Article
部门归属: [Yang, Liandong ; Zou, Ming ; Fu, Beide ; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China ; [Yang, Liandong ; Zou, Ming ; Fu, Beide] Univ Chinese Acad Sci, Beijing 100039, Peoples R China
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
资助者: National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807]
类目[WOS]: Biotechnology & Applied Microbiology ; Genetics & Heredity
研究领域[WOS]: Biotechnology & Applied Microbiology ; Genetics & Heredity
摘要: Background: The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explanation for the morphological complexity of teleosts, considering the relatively large number of extinct basal ray-finned fishes. Results: In this study, we performed comparative genomic analysis to discover the Conserved Teleost-Specific Genes (CTSGs) and orphan genes within zebrafish and found that these two sets of lineage-specific genes may have played important roles during zebrafish embryogenesis. Lineage-specific genes within zebrafish share many of the characteristics of their counterparts in other species: shorter length, fewer exon numbers, higher GC content, and fewer of them have transcript support. Chromosomal location analysis indicated that neither the CTSGs nor the orphan genes were distributed evenly in the chromosomes of zebrafish. The significant enrichment of immunity proteins in CTSGs annotated by gene ontology (GO) or predicted ab initio may imply that defense against pathogens may be an important reason for the diversification of teleosts. The evolutionary origin of the lineage-specific genes was determined and a very high percentage of lineage-specific genes were generated via gene duplications. The temporal and spatial expression profile of lineage-specific genes obtained by expressed sequence tags (EST) and RNA-seq data revealed two novel properties: in addition to being highly tissue-preferred expression, lineage-specific genes are also highly temporally restricted, namely they are expressed in narrower time windows than evolutionarily conserved genes and are specifically enriched in later-stage embryos and early larval stages. Conclusions: Our study provides the first systematic identification of two different sets of lineage-specific genes within zebrafish and provides valuable information leading towards a better understanding of the molecular mechanisms of the genomic basis of teleost phenotypic complexity for future studies.
英文摘要: Background: The genomic basis of teleost phenotypic complexity remains obscure, despite increasing availability of genome and transcriptome sequence data. Fish-specific genome duplication cannot provide sufficient explanation for the morphological complexity of teleosts, considering the relatively large number of extinct basal ray-finned fishes.
关键词[WOS]: TAXONOMICALLY RESTRICTED GENES ; HUMAN PROTEIN FUNCTION ; RAY-FINNED FISHES ; TELEOST FISH ; RNA-SEQ ; ORPHAN GENES ; DROSOPHILA-MELANOGASTER ; EVOLUTIONARY ANALYSIS ; ARABIDOPSIS-THALIANA ; BACTERIAL GENOMES
语种: 英语
WOS记录号: WOS:000316005800001
ISSN号: 1471-2164
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/19267
Appears in Collections:水生生物多样性与资源保护研究中心_期刊论文

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作者单位: 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China

Recommended Citation:
Yang, LD; Zou, M; Fu, BD; He, SP.Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish,BMC GENOMICS,2013,14():
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