Genome Assembly,Annotation And Comparative Genome Analysis Of Hemiculter Leucisculus(Basilewksy,1855) And Hemiculter Tchangi Fang

Hemiculter leucisculus(Basilewksy,1855)and Hemiculter tchangi Fang belong to Cypriniformes,Culterinae and Hemiculter,which are small freshwater fishes with strong reproductive and adaptive abilities.Among them,H.leucisculus is a widely distributed fish from brackish water to fresh water,which is omnivorous to plants,while H.tchangi is an omnivorous endemic species of animals in Sichuan in the upper reaches of the Yangtze River in China.This paper discusses the wide adaptability of H.leucisculus through comparative genome analysis.In this study,Hi Fi sequencing technology and Hi-C-assisted assembly strategy were used to assemble the whole genomes of H.leucisculus and H.tchangi.After annotation of genomes,the genetic differences between them were analyzed by comparing genomes,and compared with other Cyprinidae fishes,the phylogenetic tree was constructed,the divergence time of species and the gene families that contracted and expanded were inferred,and the extensive adaptability of H.leucisculus and the characteristics of H.tchangi as local species were analyzed from the perspectives of feeding habits and adaptability.The main results are as follows:(1)Genome-wide sequencing and assembly of H.leucisculus and H.tchangi.Based on the genome survey,their genomes were preliminarily investigated.It was preliminarily estimated that the genome size of H.leucisculus was about 1007.32 Mb,the heterozygosity rate was about 1.31%,the repetitive sequence content was about59.99%,and the genome size of H.tchangi was 988.84 Mb,the heterozygosity rate was about 0.77%,and the repetitive sequence content was about 59.58%.All of them belonged to complex genomes with high heterozygosity and high repetition.Based on the results of genome survey,the strategy of Hi Fi sequencing and Hi-C auxiliary assembly was formulated,and 1024.75 Mb H.leucisculus genome and 986.48 Mb H.tchangi genome were obtained.The integrity analysis of the two genomes by BUSCO showed that 96.4% and 96.9% of actinopterygii＿odb10 were assembled in the genome of H.leucisculus and H.tchangi,respectively,indicating that the genome integrity of the two genomes was good.(2)Annotating the genomes of H.leucisculus and H.tchangi,a total of 64.81%repeats were annotated in H.leucisculus genome,of which 6.18% were tandem repeats and 50.34% were scattered repeats;A total of 64.81% repeats,8.73% tandem repeats and 50.41% scattered repeats were recorded in the genome of H.tchangi.Based on the prediction of coding genes with the genome of masked repeats,28,524 coding genes and 27,076 coding genes were predicted respectively,of which 94.46% coding genes in the meal genome can be compared in the protein database,and 93.30% coding genes in H.tchangi have corresponding functional annotations.(3)Based on the results of genome annotation,the genomes of H.leucisculus and H.tchangi were compared and analyzed.The mitochondrial genome sequences of several species,such as Hemiculter,other fishes in Cyprinidae,Perciformes and so on,were downloaded from NCBI,and compared with the mitochondrial genome sequences of H.leucisculus and H.tchangi,so as to construct a phylogenetic tree based on mitochondrial genome.The protein sequences of H.leucisculus and H.tchangi were clustered with the protein sequences of zebrafish,Megalobrama amblycephala,Sinocyclocheilus,American golden perch,stickleback,puffer fish and published silver carp genomes in NCBI refseq database,and the species tree was constructed,the divergence time of species was inferred,and the contraction and expansion of gene families were counted.It is speculated that the meal and H.tchangi diverged between 4 million and 8 million years ago.Based on comparative genomics,through the adaptive evolution analysis of Hemiculter genus,it is found that the gene family related to H.leucisculus and H.tchangi reproduction has expanded significantly,and the enrichment analysis of its unique gene family GO enrichment shows that the hatching rate of H.tchangi fertilized eggs may be higher,and sperm may have stronger athletic ability for H.leucisculus.In addition,H.tchangi has significantly expanded in the family of vision-related genes,which provides a genetic basis for H.tchangi’s eating habits.In the H.leucisculus genome,there are many gene families in immunity,salinity adaptation,feeding behavior and multiple metabolic pathways significantly enriched,which provides a molecular basis for adapting to the changing environment.In this study,high-quality genomes of H.leucisculus and H.tchangi were obtained at chromosome level,and the strong reproductive ability and adaptability of H.leucisculus species were further discussed,which provided theoretical basis for further analyzing the adaptive evolution and hybridization mechanism of populations.