Genome Assembly And Population History Of Siniperca Chuatsi And Siniperca Knerii

Mandarin fish(Sinipercidae)is a kind of fish with high economic and cultural value unique to East Asia.It has a long history of cultural precipitation and is often recorded in history.Among them,Chinese mandarin fish(Siniperca chuatsi)is an important freshwater economic fish in China.Its annual output exceeded 300,000 tons in 2016,and its annual output value exceeded 20 billion yuan.Most of the mandarin fish species are endemic to China.Among them,S.chuatsi is now distributed in the Yangtze River,Pearl River,Minjiang River,Jiulong River,Qiantang River and Heilongjiang River.It is a species that is distributed in northern and southern China.The big-eyed mandarin fish(Siniperca knerii)is now distributed in the Pearl River,Minjiang River,Jiulong River,Yangtze River and Huaihe River,which is a southern species in China.Earlier,wild mandarin fish populations in China were relatively rich in resources,but since the 1970s,due to overfishing,water pollution and other factors,wild mandarin fish populations have declined sharply,and most of the populations north of the Yangtze River are facing extinction.Danger.Mandarin fishes are the top predators in freshwater water systems,and have high value for studying the origin and evolutionary history of East Asian fish species.Therefore,they have been used for species identification,taxonomy and breeding of fishes of Mandarin fish.Has a long research history.However,we lack sufficient understanding of the complete genetic information and population history of this group,especially in the absence of more genome-wide data,which has brought many inconveniences to genetic-related research.Secondly,the lack of research on the history of the population also makes a lack of understanding of the impact of geological history on the species.In addition to research on the mandarin fish itself,fish genome assembly also faces many difficulties,such as high content of repeated sequences and short genome assembly length.For the above problems,we conducted the following three aspects of research.The first part is the assembly of the genome of S.chuatsi and S.knerii.There has been no report of whole genome data for the fishes of the genus Mandarin fish,which has led to the lack of complete genomic data support for studies on population history and comparative genomes.In this study,large fragments of DNA were used to build a library containing hundreds of thousands of large pieces of DNA information through 10X Genomics database construction technology.NGS sequencing was used to obtain highly accurate sequence information.Finally,de Burijn Graph algorithm was used to combine large pieces of DNA information Obtain high-quality physical maps of the S.chuatsi and S.knerii.Through the above steps,we obtained high-quality genomes with Scaffold N50 values of 2.09 MB and 12.64 MB,respectively,with genome size of 678.99 MB and 677.73 MB,and repeated sequence contents of 16.33%and 5.41%.The genome was evaluated by BUSCO software,and 90%and 97%of the complete BUSCO gene was assembled for the S.chuatsi and S.knerii.The results show that the resulting genome has a high level in terms of both length and gene structural integrity.After obtaining highquality genomes,through annotations,32109 genes were obtained in the S.chuatsi and 28440 genes in S.knerii.For both genomes,more than 90%of the genes had at least one functional annotation in the database result.The second part is based on the optimization of 10X Genomics genome assembly method and the exploration of the scope of the technology.10X Genomics is based on microfluidic technology,which uses oil to wrap millions of large pieces of DNA(>50 kbp)with the reaction system to form about 1 million tiny droplets,each of which is an independent expansion.Increase the reaction system.The unique feature of 10X Genomics is that in the formation of these reaction systems,each droplet has an independent oligonucleotide tag(Barcode),which can be traced back to which large fragment they come from,using this information to form a short Link-reads can finally obtain information about large DNA fragments.However,there are no reports on the use range and capability limit of the technology,and no relevant information has been found in the official document recommendations.Therefore,on the basis of this technology,we first optimize the genome assembly.We first use the official recommended large DNA addition amount and software parameters for assembly,and then carry out gradient tests for both.The final result is:for the fish of the genus Mandarin fish,0.16 ng of large DNA is added,and the input of reads with 60 times the genome size is the best.After optimization,the data obtained by sequencing was further analyzed,and it was finally obtained that the technology has poor assembly quality for genomes with high content of repeated sequences,but it is better than simple short-segment sequencing assembly;for large DNA in each Barcode,It can only be up to 9 times the sequencing depth and cannot assemble a complete 50 kb large fragment.In terms of amplification reaction time,as the time increases,the degree of droplet rupture will also deepen.In 3 hours of reaction,20%of the droplets will rupture,and in 5 hours of reaction time,40%of the droplets will rupture.These results provide an optimized direction for the use of 10X Genomics technology and can be better applied to fish genome research.In the third part,we study the group history of S.knerii.We use the PSMC algorithm to study the history of the S.knerii population.The algorithm is based on the most recent common ancestor of heterozygous genes.At a certain moment in the past,if the population is large,there will be more common ancestor genes at that moment.The S.knerii is mainly distributed in the south of the Yangtze River.There is a famous ice age in the area-the Dali Ice Age,which lasted from 57,000 to 16,000 years ago.We calculated through the PSMC algorithm that during the Dali ice age,the population of the S.knerii had a significant decline,and the population increased after the ice age.This result also satisfies the refuge hypothesis.We can see that during the Dali ice age,the big eye mandarin was only distributed in a few places in southern China where the environment was suitable,and it spread to the entire southern water system here after the ice age.This study reveals for the first time the population history information of the S.knerii,and provides strong data support for the evolution history,genetic structure and population structure of the species.