The grass carp (Ctenopharyngodon idellus) is an important farmed fish, accounting for ~16% of global freshwater aquaculture and possesses 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. As the first step, Institute of Hydrobiology, Chinese Academy of Sciences (IHB), 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 provides 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. As above, 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 was published in Nature Genetics with the title of "The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation".

Figure  Female scaffolds anchored on the genetic map. (a) The scaffolds were anchored on a published consensus linkage map.The blue lines indicate the length of each linkage group to which the markers are mapped. Map distances between markers are depicted on a Kosambi centiMorgan scale. Orange bars represent the anchored scaffolds. The black lines linking markers and scaffolds show the locations of the markers on the scaffolds. The length of each scaffold is shown relative to a 5-Mb scale bar. (b) Syntenic relationship between the zebrafish chromosomes and the grass carp linkage groups. Linkage group 22 is aligned to zebrafish chromosomes 2 and 15, and linkage group 24 is aligned to zebrafish chromosomes 10 and 22. (c) Gene collinearity between zebrafish and grass carp. The zebrafish chromosomes are represented by blue blocks (for example, DR01). The grass carp scaffolds (length > 50 kb) are represented by orange blocks. Aligned genes are connected by green lines. The lengths of the chromosomes and scaffolds are shown relative to a 10-Mb scale bar. (d) FISH study of linkage group 24. The yellow marker CID1435 is located on the region aligned to zebrafish chromosome 10, and the red marker CID0538 is aligned to zebrafish chromosome 22. Scale bar, 5 μm.  (Figure by IHB)