ArticleBMC genomics2013
Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 47 citations in OpenAlex.
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- The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats.Planta · 2022Article
- Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes.Frontiers in plant science · 2022Article
- Identification, characterization and expression analysis of lineage-specific genes within mangrove species Aegiceras corniculatum.Molecular genetics and genomics : MGG · 2021Article
- Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea PlantFrontiers in genetics · 2021Article
- Identification of Orphan Genes in Unbalanced Datasets Based on Ensemble Learning.Frontiers in genetics · 2020Article
- Mining ofInternational journal of molecular sciences · 2018Article
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- GFDP: the gene family database in poplar.Database : the journal of biological databases and curation · 2018Article
- A database for orphan genes in Poaceae.Experimental and therapeutic medicine · 2017Article
- Linking species habitat and past palaeoclimatic events to evolution of the teleost innate immune system.Proceedings. Biological sciences · 2017Article
- Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?BMC bioinformatics · 2016Article
- Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis.BMC evolutionary biology · 2016Article
- The identification of additional zebrafish DICP genes reveals haplotype variation and linkage to MHC class I genes.Immunogenetics · 2016Article
- Correlated expression of retrocopies and parental genes in zebrafish.Molecular genetics and genomics : MGG · 2016Article
- Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.BMC genomics · 2015Article
- Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis).BMC genomics · 2015Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsIn 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.
conclusionsOur 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.