The grass carp (Ctenopharyngodon idellus) is an important farmed fish, accounting for ~16% of global freshwater aquaculture and possessing a vegetarian diet. However, the lack of a complete genome sequence has made it difficult to conduct in-depth investigation on grass carp biology and breeding for better quality fish.

Researchers from Institute of Hydrobiology of Chinese Academy of Sciences, National Center for Gene Research of Chinese Academy of Sciences, Sun Yat-Sen University and other institutions reported a draft genome sequence and transcriptomic analysis of grass carp, adding this important species to the other sequenced teleosts: cod, fugu, medaka, tetraodon, stickleback and zebrafish. This information provided genomic insights into the evolutionary history of the grass carp and its unique vegetarian diet adaptation.

Adopting a whole-genome shotgun sequencing strategy and a modified de novo Phusion-meta assembly pipeline, the final assemblies of a gynogenetic female adult grass carp (0.90 Gb) and a wild, water-captured male adult (1.07 Gb) genomes were constructed. Based on 27 Gb of RNA-seq data and homologous gene information from zebrafish, a total of 27,263 protein-coding genes were annotated in the female genome. In addition, 114 scaffolds were anchored on 24 linkage groups, covering 573 Mb (64%) of the female assembly with 17,456 (64%) annotated genes localized.

Compared with 12 other vertebrate genomes, grass carp had the closest relationship to zebrafish. They shared 7,227 families, many immune-associated function domains in grass carp has undergone significant expansion. The estimated divergence time between zebrafish and grass carp was around 49-54 million years ago. The gene collinearity and FISH analysis demonstrated that zebrafish chromosomes 10 and 22 corresponded to a single chromosome, LG 24, in grass carp, suggesting a chromosome fusion in grass carp genome during evolution.

By comparison of the assemblies between the male and female grass carp, a total length of 2.38 Mb which was male-specific and mainly localized on LG24 was identified. LG 24 had the largest physical size but the smallest genetic distance, indicating a significantly lower exchange rate in the process of meiosis. The fusion of LG24 in grass carp may be related to sex chromosome differentiation.

Grass carp are typically herbivorous. How grass carp effectively absorb nutrients from plants to support their rapid growth is an unanswered research question. Analysis of the genes predicted from the assemblies of these non-host reads did not find cellulose-digesting enzymes in gut, implicating that the grass carp intestine might not digest and absorb cellulose.

The analyses of transcriptome data revealed the genes with differential expression levels were significantly enriched in the pathways associated with the circadian rhythm in gut, steroid biosynthesis, terpenoid backbone biosynthesis and glycerophospholipid metabolism pathways in liver. Grass carp may maintain a continuous feeding rhythm in order for them to get enough nutrients from their food.

As a member of the Cyprinidae family and the only species of the genus Ctenopharyngodon, analysis of grass carp genome sequence will provide key technical support for exploring important economic trait-related genes and genetic improvement of farmed species, but also will lay an important foundation for theoretical studies related to fish genome evolution, sex determination and differentiation mechanisms.

The study entitled "The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation" was published in Nature Genetics.