Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq

Abstract

The fish gill, as one of the mucosal barriers, plays an important role in mucosal immune response. The fish swimbladder functions for regulating buoyancy. The fish swimbladder has long been postulated as a homologous organ of the tetrapod lung, but the molecular evidence is scarce. In order to provide new information that is complementary to gill immune genes, initiate new research directions concerning the genetic basis of the gill immune response and understand the molecular function of swimbladder as well as its relationship with lungs, transcriptome analysis of the fugu Takifugu rubripes gill and swimbladder was carried out by RNA-Seq. Approximately 55,061,524 and 44,736,850 raw sequence reads from gill and swimbladder were generated, respectively. Gene ontology (GO) and KEGG pathway analysis revealed diverse biological functions and processes. Transcriptome comparison between gill and swimbladder resulted in 3,790 differentially expressed genes, of which 1,520 were up-regulated in the swimbladder while 2,270 were down-regulated. In addition, 406 up regulated isoforms and 296 down regulated isoforms were observed in swimbladder in comparison to gill. By the gene enrichment analysis, the three immune-related pathways and 32 immune-related genes in gill were identified. In swimbladder, five pathways including 43 swimbladder-enriched genes were identified. This work should set the foundation for studying immune-related genes for the mucosal immunity and provide genomic resources to study the relatedness of the fish swimbladder and mammalian lung.

Figure 1. Sequencing reads mapped to various genomic regions. a, gill; b, swimbladder.

Figure 2. Distribution of genes based on RPKM. a, gill; b, swimbladder.

Figure 3. Gene Ontology (GO) (level 2) for the gill and swimbladder transcriptome under Molecular function, Cellular component and Biological process.

Figure 4. qRT-PCR validation of 18 genes that were differentially expressed between gill and swimbladder.

Dark red indicates the tissue of gill and medium slate blue indicates the swimbladder. a, Rh type C glycoprotein2; b, Ras-related protein Rab-19-like; c, Claudin-8-like; d, NAD(P)H dehydrogenase, quinone 1; e, Transmembrane protease serine 11D-like; g, Transmembrane protease serine 9-like; h, Trypsin-like; I, Transcription factor 21-like; j, Minichromosome maintenance complex component 4; k, IL2-inducible T-cell kinase; l, Microphthalmia-associated transcription factor; m, Nuclear receptor subfamily 4, group A, member 2; n, Tetraspanin 11; o, Ankyrin repeat domain-containing protein SOWAHA-like; p, Eukaryotic translation initiation factor 4A2; q, Kelch-like protein 13-like; r, Indian hedgehog protein-like; s, Neuromedin U receptor 1. Asterisk indicates statistical significant level of P<0.05.