Construction And Application Of Common Carp Genome Database

Cyprinidae is a kind of freshwater fish,which is widely distributed all over the world.As a world leading country of carp culturing,C hina attaches great importance to the research of carp.Common carp have 100 chromosomes because of its special allotetraploid process.The development of carp genomic resources is becoming more and more mature.The whole genome sequencing of common carp has been completed as early as 2014,while other genomic developments includ ing gene maps,physical maps,SNPs and EST markers are also in full swing.And the amount of relevant genetic information is increasing.It is urgent to integrate these data to construct a genome database for further study of genetic characteristics of common carp.In the early stage,the research team supplemented and updated the carp genome data to obtain a new version of the common carp genome.Compared with the published genomes on NCBI,it was found that the new genome is closer to zebrafish,medaka and other reference species in gene length,exon length and protein length,which proves that the new genome has improved in gene integrity.At the same time,the laboratory has made progress in the genetic function annotation of carp,population genomic variation,body color gene expression,etc.,and accumulated a lot of relevant data.In this study,these sequences and annotation information were screened and integrated into a My SQL database,which was finally constructed into a Common carp genome database(Cc GDB).Based on the newly constrcucted genome database,Ubuntu’s open source system platform,My SQ L database system,Apache web server and PHP language were used as the framework of the platform.The Bioinformatics Research Platform of the Common carp Genomic Database was finally established(http://www.fishbrowser.org/database/Commoncarp＿genome/),realizing the storage,development and sharing of carp genome data resources.PHP+My SQ L method will be used to quickly retrieve the common carp gene function.A variety of search methods can be used for querying genetic information,including gene ID search,GO and KEGG search,and gene annotation keyword search.The search results show the sequence information,gene family information,homologous classification information and annotation information of GO and K EGG annotated by Common carp.Cc GDB provides an online Blast function for the Common carp genome sequence,transcript sequence and amino acid sequence,which allows users to upload their sequence to align.The download page also provides Common carp genomic data for users to download.In order to further demonstrate the application of the carp genome database in scientific research,the use of the Progesterone receptor(Pgr)gene was described in this study to illustrate the use of the database.Pgr is a receptor mediating the regulation of progesterone on fish gonad development and germ cell maturation.For now,only few research focus on the Pgr in polyploid fish.It is valuable to study the expression and function of Pgr in replicating genes by carp.After constructing the common carp genome database,the BLAST function was used to compare the zebrafish Pgr protein with the carp transcriptome and to find the two genes of carp Pgr.The results showed that the carp Pgr1 and Pgr2 belonged to the steroid hormone receptor gene family(TF106510),and they all have transcriptional regulation and participate in transcription factor activity,KEGG pathway predicts that Pgr1 and Pgr2 control oocyte meiosis and Progesterone-mediated oocyte maturation.In order to verify the results of the database analysis,the full length of the two Pgr genes were cloned from ovary using the RACE(rapid-amplification of c DNA ends)technique.Bioinformatics analysis showed that they had a nucleotide identity of 91% and a protein identity of 90%,Both consist of zinc finger domain and homologous superfamily of nuclear hormone receptor domains.The evolutionary analysis also showed that the carp Pgr gene was conserved in evolution.q RT-PCR analysis demonstrated that Pgr1 and Pgr2 had higher expression levels in gonads than in the other tissues,suggesting that both genes might be associated with common carp gonad development.They had higher expression levels in sperms and oocytes than in embryos after induced by spawning drugs,indicating that they might be involved in germ cell maturation.In the most examined status,higher Pgr1 expression level was revealed compared with Pgr2.The results show that the establishment of the database provides an important theoretical basis for the study of the function and expression of the carp gene.The establishment of the carp geno me database platform not only provides a solid foundation for the study of carp function and comparative genomics but also helps in the exploration of carp genome data and in-depth discovery of the link between carp evolution and replication genes.In addition,by integrating the new genomic genome and annotation data,the database will boost genome-assistant breeding and selection on domesticated common carp.