Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish

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.

Genome-wide identification of lineage-specific genes within Caenorhabditis elegans

“…5). The analysis of the GO categories shows that both the SSGs and GSGs functionally associated with transcription and growth factors present the most represented, which is similar to the results found in zebrafish [13]. In contrast, the proteins encoded by SSGs and GSGs that were involved in cation channel, ion channel, signal transducer, transcription regulation, and metal ion transport are underrepresented.…”

“…In contrast, the proteins encoded by SSGs and GSGs that were involved in cation channel, ion channel, signal transducer, transcription regulation, and metal ion transport are underrepresented. The analysis of the cellular roles revealed that the SSGs and GSGs relevant to translation and cell envelope are over-represented, similar to the findings in zebrafish and mice [13,43]. However, the LSGs involved in biosynthesis of cofactors and cellular processes represented the lowest proportion.…”

“…According to our results, the averages of the above features of the three gene sets are significantly different from each other (one-way ANOVA; p b 0.01). Similarly, SSGs exhibit the lowest values for each genetic feature, as observed in other species, such as Arabidopsis thaliana [5], zebrafish [13], and honey bee [11]. In contrast, the average GC content of the SSGs was the highest, which is similar to the results obtained in zebrafish [13] but opposite to those found in A. thaliana [5] and honey bee [11].…”

“…Similarly, SSGs exhibit the lowest values for each genetic feature, as observed in other species, such as Arabidopsis thaliana [5], zebrafish [13], and honey bee [11]. In contrast, the average GC content of the SSGs was the highest, which is similar to the results obtained in zebrafish [13] but opposite to those found in A. thaliana [5] and honey bee [11]. The transcriptional analysis based on EST and full-length cDNA revealed that 38.68% of SSGs, 60.27% of GSGs, and 82.74% of ECs have transcripts (t-test, p b 0.01).…”

“…However, study of these genes is helpful to aid in the comprehensive understanding of a species. With the increasing development of sequencing technologies, we have gained access to a number of genomes and transcriptomes from a wide range of species, which has aided the extensive study of the LSGs within mammals [8][9][10], insects [2,11,12], fish [13], plants [5,[14][15][16], and microbial species [17][18][19][20]. However, the LSGs in C. elegans have not yet been researched through genomewide methods.…”