Transcriptome analysis of crucian carp (Carassius auratus), an important aquaculture and hypoxia-tolerant species

Abstract

The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation. However, so far the genomics and transcriptomics data available for this species are still scarce. We performed de novo transcriptome sequencing of four cDNA libraries representing brain, muscle, liver and kidney tissues respectively, each with six specimens. The removal of low quality reads resulted in 2.62 million raw reads, which were assembled as 127,711 unigenes, including 84,867 isotigs and 42,844 singletons. A total of 22,273 unigenes were found with significant matches to 14,449 unique proteins. Around14,398 unigenes were assigned with at least one Gene Ontology (GO) category in 84,876 total assignments, and 6,382 unigenes were found in 237 predicted KEGG pathways. The gene expression analysis revealed more genes expressed in brain, more up-regulated genes in muscle and more down-regulated genes in liver as compared with gene expression profiles of other tissues. In addition, 23 enzymes in the glycolysis/gluconeogenesis pathway were recovered. Importantly, we identified 5,784 high-quality putative SNP and 11,295 microsatellite markers which include 5,364 microsatellites with flanking sequences ≥50 bp. This study produced the most comprehensive genomic resources that have been derived from crucian carp, including thousands of genetic markers, which will not only lay a foundation for further studies on polyploidy origin and anoxic survival but will also facilitate selective breeding of this important aquaculture species.

Figure 1. Comparison of DNA contents based on flow cytometry in crucian carp (a, b and c), with color crucian carp (d) used as a diploid reference.

Figure 2. Crucian carp transcriptome assembly and analysis pipeline, with corresponding numbers (in parentheses) obtained at each step.

Figure 3. Length distribution of isotigs (blue) and singletons (red) of crucian carp transcriptome.

Figure 4. Full and partial cDNAs indentified in crucian carp as compared with zebrafish whole transcriptome.

Figure 5. Functional classification of crucian carp unigenes based on three main Gene Ontology (GO) categories: biological process, molecular function and cellular component.

Figure 6. Differential gene expression analysis between four different tissues of crucian carp.

Figure 7. Glycolysis/gluconeogenesis KEGG map populated with transcripts coding for corresponding enzymes.

The enzymes identified are shown in red boxes and their abundances of transcripts in different tissues are shown in Table 6 .

Figure 8. Classification of single nucleotide polymorphisms (SNPs) identified in the crucian carp transcriptome.