Survey Sequence And Analysis Of The Black Carp Genome

Black carp(Mylopharyngodon piceus)is one of the four traditional fishes in China.As an important cyprinid in the Yangtze River Basin,black carp is characteristic of large body size,fast growth and delicious meat.Lack of a reference genome of black carp restrict the deepening of research on artificial reproduction,nutrition,disease resistance and resource distribution in black carp.At present,many cyprinid fishes’ genomes have been sequenced.These species have a close relationship to black carp in phylogeny,sharing similar genome size and structure.The following conclusions are drawn:(1)A total of 69 Gb Illumina sequencing reads were generated to assemble a survey black carp genome,which has a scaffold N50 length of 9,583 bp and a genome size of957 MB.The BUSCO test estimated the genome completeness at around 90%.(2)Genome annotation revealed that the black carp genome carries 347 Mb repetitive sequence,accounting for 34.8% of the genome in length,including DNA transposon(22.6%),LTR Retrotransposon(1.1%),LINE(1.7%),SINE(1.5%).The predicted non-coding RNA genes and simple repeating sequences occupied 0.15% and 5.7% of the genome.Referencing the zebrafish genome,the gene modeling annotated 27541protein-coding genes,with an average length of 1,132 bp.The BUSCO test estimated the completeness of the gene model set at around 90.8%.There was a high gene collinearity between black carp and zebrafish that 3,145 black carp scaffolds were syntenic to the corresponding regions of the zebrafish chromosomes.(3)Gene clustering found that black carp,frog,grass carp,Hooksnout carp,zebrafish,cod,medaka,fugu,Tetraodon,weever and stickleback shared 21,884 gene families.After fossil calibration,it is estimated that black carp diverged from grass carp 13 million years ago,while diverged from zebrafish about 57 million years ago.We identified rapidly expanded gene clusters among the 11 genomes,of which the annotations by the KEGG Pathway database found that these clusters of large body-size fishes,such black carp and grass carp,were mainly involved in pathways of bone growth,hormone adjustment,circadian rhythms and cell differentiation.Among them,the axon guidance pathway employed a large number of genes in black carp.This pathway triggers changes in cytoskeletal tissue to determine the direction of the growth cone.Comparatively,zebrafish had little annotated hits in body-size-related pathways.We selected the genes of the rapidly expanded clusters annotated to be involved in the development-related pathways of black carp,grass carp and fugu to predict protein function interaction networks.The prediction outputs of black carp and grass carp were both annotated as the signaling pathways to promote the development,while the genes of fugu were involved in the pathways of growth hormone biosynthesis and secretion and action,which inhibited GH(Growth hormone)secretion and caused difference in body size.(4)In analysis of the typical gene families,it was found that the Toll-like receptor signaling pathway of zebrafish involved many extended clusters,as well as immune-related clusters.Prediction of conserved function domain of Toll-like receptor genes illustrated that black carp and grass carp may have intracellular and extracellular pathogen identification systems,while zebrafish only have extracellular pathogen identification system,implicating recognition of external bacterial infection is more important to zebrafish.In short,the draft genome assemblies fill in the gap of genome data in black carp,which provides the important reference data for the study of immunology,evolutionary biology,developmental biology and developmental toxicology.