Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species

Xiaolin Liao,Peng Xu,Guoqing Lu,Xiaowen Sun,Lei Cheng,Songlin Chen,Michael Wachholtz,Marc Robinson-Rechavi

doi:10.1371/journal.pone.0062308

Xiaolin Liao, Peng Xu + Show 6 more

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https://doi.org/10.1371/journal.pone.0062308

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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.

Highlights

Crucian carp (Carassius auratus), belonging to the family Cyprinidae (Telestei), is widely distributed on the Eurasian continent [1]
The tissue liver was found with the largest number of raw reads (700,677), whereas the kidney tissue was found with the longest average length per read (321 bp)
In this study we investigated the genes involved in glycolysis and gluconeogenesis in crucian carp, comparative analysis of these genes among hypoxia tolerant animals, along with the study of other important genes such as hypoxia-inducible transcription factor (HIF) [33,34] may offer clues for the molecular adaptation involved in hypoxia tolerance

Summary

Introduction

Crucian carp (Carassius auratus), belonging to the family Cyprinidae (Telestei), is widely distributed on the Eurasian continent [1]. Crucian carp is popular as a food fish in China and elsewhere. Several strains of crucian carp have been developed in China based upon its unique reproductive characters (e.g., gynogenesis) [3,4,5]. Crucian carp has three different ploidy types in the wild, including diploid, triploid and tetraploid, each with a different reproductive mode [6]. Diploid crucian carp produce bisexual diploid offspring through bisexual reproduction; the tetraploid ones produce all-female offspring via gynogenesis. Dual reproductive modes exist in triploid crucian carp. Unisexual gynogenesis by heterogenous spermatozoa activation produces all-female offspring whereas bisexual reproduction generates bisexual triploid progenies [5,6]. Crucian carp have been considered as a potential model for the study of evolutionary developmental biology (Evo-Devo) [5]

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