Teleosts, which roughly constitute 96% of all living fishes and half of the extant vertebrate, are the most phenotypically diversified and species-rich group of all the vertebrate species. The vast morphological and species diversity of teleosts have received intense attention worldwide because of their importance in both scientific research and aquaculture.  

However, the genomic basis of the complex phenotype of teleosts during evolution remains obscure, despite the increasing amount of genome and transcriptome sequence data available. By the approach of bioinformatics and comparative genomics, Yang Liandong (Phd student), under the supervision of Prof. He Shunping from the Research Group of Fish Phylogenetics and Biogeography at Institute of Hydrobiology, Chinese Academy of Sciences (IHB), 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.  

These findings, recently published in BMC genomics (http://www.biomedcentral.com/1471 -2164/14/65/abstract), provides valuable information leading towards a better understanding of the molecular mechanisms of the genomic basis of teleost phenotypic complexity for future studies.