| Chanodichthys erythropterus,a fierce carnivorous small Cyprinidae fish widely spread in East Asia.Because of its taste,fine flesh and high protein and low lipid characteristics,it is highly sought after by consumers in the market and has become the main economic fish species in many fishing grounds,with high farming value and commercial potential.However,in the last decade or so,overfishing to satisfy the consumer market,coupled with water pollution caused by various human activities,the natural population of the C.erythropterus has plummeted.Most studies on C.erythropterus have focused on feeding,reproduction and genetic studies based on simple molecular markers.A high-quality genomic resource is indispensable for a comprehensive and systematic study of issues such as adaptation and genetic breeding of the C.erythropterus.Based on the above,this study constructed a high-quality genome at the chromosome level of the C.erythropterus by Illumina sequencing,Nanopore sequencing and Hi-C technology,and used a comparative genomics approach to resolve this genome,focusing on pathways and genes associated with growth and immunity.The main results and conclusions of this study are as follows.(1)This study constructed a genome of approximately 1.09 GB in size,with contig N50 and scaffold N50 reaching 23.29 Mb and 42.4 Mb,and anchored to 24 chromosomes by Hi-C technology,with a 99.49% mounting rate.The genome BUSCO and CEGMA results reached98.5% and 97.98%,respectively,both indicating the high quality of this C.erythropterus genome.(2)Annotation of the C.erythropterus genome yielded repetitive sequences of about 557 Mb in size,accounting for 51.34% of the entire genome,with a high proportion of LTR(43.23%);A total of 33,706 genes were successfully predicted in the C.erythropterus genome,and 33,041(98.0%)of them were annotated functionally in various databases.(3)In this study,nine Osteichthyes species were selected for comparative genomic analysis,and a total of 4,222 shared single-copy gene families were obtained for subsequent analysis.Among the selected species,the C.erythropterus is the most closely related to the M.amblycephala,and the two are estimated to have diverged about 12.27 million years ago.The results of the covariance analysis with zebrafish showed that the C.erythropterus has good covariance with zebrafish and demonstrated that the C.erythropterus experienced a chromosomal fusion event.A total of 314 unique gene families,104 significant expand gene families and 305 positively selected genes were identified in this genome.GO and KEGG enrichment analyses showed that it was mostly associated with functions such as immune repair and innate immune response.Immune related genes such as FOXP3 and TNF were screened in positive selection analysis,which is presumed to be the reason for the ability of the C.erythropterus to adapt to multiple environments and become a dominant species important factors.(4)In order to identify genes related to growth and immunity in C.erythropterus,this study further compared C.erythropterus with C.auratus,C.idella and M.piceus in groups.The analysis revealed that genes related to growth and development such as BMP2 and PNX,and genes related to immune defense and resistance to stress such as CLEC4 E,ADAR and RHBG were positively selected in C.erythropterus.It is hypothesized that these may have potential effects on traits such as small body size,slower growth and strong adaptability in C.erythropterus.In conclusion,the results of the genome assembly,annotation and analysis obtained in this study will provide complete basic information for adaptation studies,population conservation and population genetics of C.erythropterus.In addition,it will advance genomic breeding programs in the C.erythropterus farming industry and providing new ideas for molecular breeding,species improvement and disease control of the C.erythropterus. |
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