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.

Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes

“…Among the pathways, the greatest number of assembled unigenes was found to be involved in the metabolic pathways, which is consistent with the sliver carp transcriptome analysis (Fu and He, 2012), but this pattern didn't occur for the Crucian Carp (Liao et al, 2013). The previous study reported that glycolysis metabolism could compensate for insufficient levels of oxygen in freely diving birds and mammals (Butler and Jones, 1997).…”

“…Compared with other fish transcriptomes sequenced within Cypriniformes (Fu and He, 2012;Gao et al, 2012;Ji et al, 2012;Liao et al, 2013;Long et al, 2013;Zou et al, 2014), the de novo assembly and annotations of T. dalaica transcriptome were best (Table 2). In terms of the gene expression level, T. dalaica transcriptome showed the highest similarity to zebrafish, which can be explained by the fact that Triplophysa fishes and zebrafish belonging to the same order Cypriniformes.…”

“…To assess the quality of our assembled unigenes, we made comparisons with other fish transcriptomes sequenced within Cypriniformes, Carassius auratus, Megalobrama amblycephala, Hypophthalmichthys molitrix, Elopichthys bambusa and Cyprinus carpio (Fu and He, 2012;Gao et al, 2012;Ji et al, 2012;Liao et al, 2013;Long et al, 2013;Zou et al, 2014). Furthermore, cDNA template was prepared using highquality RNA with a first-strand DNA synthesis kit (Promega).…”

Transcriptome analysis of soiny mullet (Liza haematocheila) spleen in response to Streptococcus dysgalactiae

“…BLAST results revealed that 38,241 (53.25%), 42,570 (59.28%), and 33,190 (46.22%) unigenes significantly matched with the annotated sequences in NR, NT, and Swiss-Prot databases, respectively. The annotation of soiny mullet spleen transcriptome was comparable to turbot (Scophthalmus maximus) (44.84%) [24] and mud loach (Misgurnus anguillicaudatus) (43.76%) [25], while higher than that in crucian carp (17.44%) [26] and Japanese flounder 100-500 500-1000 1000-1500 1500-2000 >=2000…”

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

“…The difference between the total number of transcripts in native and invasive silver carp could be attributed to the number of tissues used for analysis and/or the number of raw reads produced. The transcriptomes of several other cyprinid species have been reported, including common carp, crucian carp, blunt snout bream ( Megalobrama amblycephala ), and many other species, and the number of annotated transcripts among them including bigheaded carps ranges from 22,000 to 25,000, except for blunt snout bream (Gao et al., 2012; Liao et al., 2013; Wang et al., 2012). Transcriptomes are known to vary in different tissues, developmental stages, and physiological conditions.…”