IHB OpenIR  > 水生生物多样性与资源保护研究中心  > 期刊论文
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish
Yang, Liandong1,2; Zou, Ming1,2; Fu, Beide1,2; He, Shunping1; He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
2013-01-31
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume14
AbstractBackground: 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.; 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.
SubtypeArticle
KeywordTeleost Lineage-specific Gene Transcriptome Zebrafish Embryogenesis
Department[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
DOI10.1186/1471-2164-14-65
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Funding OrganizationNational Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807] ; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807] ; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807] ; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807]
Indexed BySCI
Language英语
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS SubjectBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000316005800001
WOS KeywordTAXONOMICALLY RESTRICTED GENES ; HUMAN PROTEIN FUNCTION ; RAY-FINNED FISHES ; TELEOST FISH ; RNA-SEQ ; ORPHAN GENES ; DROSOPHILA-MELANOGASTER ; EVOLUTIONARY ANALYSIS ; ARABIDOPSIS-THALIANA ; BACTERIAL GENOMES
Funding OrganizationNational Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807] ; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807] ; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807] ; National Natural Science Foundation of China [31090254, U1036603]; Chinese Academy of Sciences [KSCX2-YW-Z-0807]
Citation statistics
Cited Times:27[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/19267
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorHe, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Hubei, Peoples R China.
Affiliation1.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
GB/T 7714
Yang, Liandong,Zou, Ming,Fu, Beide,et al. Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish[J]. BMC GENOMICS,2013,14.
APA Yang, Liandong,Zou, Ming,Fu, Beide,He, Shunping,&He, SP .(2013).Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish.BMC GENOMICS,14.
MLA Yang, Liandong,et al."Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish".BMC GENOMICS 14(2013).
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