Development Of Gene Differential Expression Analysis And Molecular Markers Of Schizopygopsis Younghusbandi Based On Transcriptome Sequencing Date

Schizopygopsis younghusbandi is a special fish of the Tibet Plateau,widely distributed in the Yarlung Zangbo River basin,has great ecological and economic value.As the object of this study.First,using the RNA-seq to obtain a wealth of transcriptome information,after bioinformatics analysis,a large number of functional genes have been discovered.Next,the differences in the transcriptome information between the spotted and non-spotted surface of Schizopygopsis younghusbandi were compared and analyzed.Finally,a large number of SSR loci were discovered,the characteristics of SSR were analyzed,and polymorphic primer design screening was performed.The main conclusions obtained are as follows:1.Transcriptome sequencing of a mixture of skin,muscle,fin,liver,and kidney samples of spotted and unpopulated Schizopygopsis younghusbandi with Illumina HiSeq sequencing platforms,The raw reads was filtered,stitched and assembled to obtain 671947 transcripts,mean length 643 bp,N50 993 bp,N90 264 bp;unigenes 444530,mean length 817 bp,N50 1228 bp,N90 347 bp.2.Function annotation and classification for 444530 unigenes,182298 unigenes annotations succeed in Nr,41% of all unigenes,30217(6.79%)unigenes getting comments in all databases;Classification by GO annotation is divided into 3 major categories of 56 biological functions,Most of the annotations in the cellular process;Signal transduction mechanisms group is the largest of the 26 functional groups in the KOG classification;KEGG analysis for the 5 major branches,32 small branches,231 pathways.3.Screening for differentially expressed genes,1268 up,1185 down;then perform GO enrichment and KEGG enrichment for these genes,obtained a large number of biological functions and metabolic pathways related to immune diseases.4.The SSR locus search was performed on the transcriptome information of Schizopygopsis younghusbandi by MISA,183556 SSR loci were retrieved.The highest number of dinucleotide repeat type SSRs is 85,780(44.4%),There are a maximum of 77,206 A/T repeat primitives,followed by 55,630 AC/GT repeat primitives.5.Primer batch design of 183556 SSR loci using Primer3,60 pairs of primers were randomly selected for PCR amplification of genomic DNA of a certain Schizopygopsis younghusbandi,45 pairs of primers have been successfully amplified bands,the effective primer ratio is 75%,selection of 29 pairs of single bright primers for polymorphism analysis.6.Amplification of 29 pairs of primers in 10 genomic DNA of Lhasa squid from different locations,capillary electrophoresis of Amplified Products,24 pairs of primers showed polymorphism;The 24 SSR loci have 2-9 alleles,all 5.7;Ho was 0.3-1,average Ho was 0.67;He is 0.255-0.820,average He is 0.686;PIC is 0.222-0.827,average 0.645;24 SSR loci with high polymorphism,4 with moderate polymorphism and 1 with low polymorphism.