Growth Related Genes And SNPs Based On The Small Yellow Croaker(Larimichthys Polyactis) Genome

This study analyzes the small yellow croaker?Larimichthys polyactis?genome based on two different strategies of high-throughput sequencing,and uses WGS to reassemble the small yellow croaker's genome on the original basis,based on 2b-RAD technology for population analysis of small yellow croakers from North and South populations,and further comparative genomics studies of large and small yellow croakers,The main result are as follows:1.Reassembly of the small yellow croaker genomeUsing original sequencing data from wild small yellow croakers in the East China Sea.after quality control of sequencing reads with new method,the small yellow croaker estimated genome size is 687Mb.Using the new version of Platanus?V1.2.4?,we got a genome has 692Mb closed to the estimated genome size.Remapping the used reads to the genome,A total of 98.93%?91.53%paired?of the sequencing data can be mapped to the genome.And the genomic BUSCO is 87.5%.Compared with two version of the genome,the genomic contig N50 and scaffold N50 have been greatly improved.the contig N50 and scaffold N50 for new genome has reached 7.9k and 146k from 3.6k and40k.After finish genome repeats and gene annotation.The repeating ratio of the small yellow croaker is 14.04%.Using homologous protein alignment prediction and de novo prediction methods,29950 genes were annotated in the small yellow croaker's genome.Based on the synteny results of the whole genome nucleic acid sequences,it was shown that the small yellow croaker genome had good Synteny with the large yellow croaker genome,and the synteny ratio reached 79.48%,and verification accuracy of small yellow croaker genome from the other hand.2.Compared with large yellow croakerCalculated Ka/Ks with single copy homologous gene between small yellow croaker and large yellow croaker.A total of 367 genes were significantly selected.There are 3 genes'protein were annotated as growth factor from total 367 genes.In the gene family analysis,the European Bass,Eastern Happy and zebrafish were analyzed together.The large yellow croaker and the small yellow croaker shared 14,782gene families,the small yellow croaker's unique gene family and the big croaker's unique gene family 1,880 Among them,13209 gene families are shared in Periformes,and the number of gene families shared only in large and small yellow croakers is 364.11 major categories have significant expansion in small yellow croaker gene expression including cell junction,purine metabolism,phagosome,receptor interaction,GnRH signaling pathway,gap junction,cell adhesion,ECM-receptor interaction,Ca²⁺signaling pathway,ABC transporter.3.Characterization of SNPs in L.polyactis based on 2b-RAD sequencingThis study included a total of 16 adult L.polyactis samples.We collected samples of DL1-5 and LS1-6 from local markets in Dalian?DL?and Lüshun?LS?,Liaoning Province,China,respectively that represent the wild stock?s?of Yellow-Bo Sea.The sequencing library was constructed using 2b-RAD multi-iso RAD technology.We scored a total of 1,374,008 putative SNP loci genome-wide.Further filtration yielded a final high-quality data set of 6,457 SNPs.These SNP markers presented sufficient power in detecting apparent genetic distinction among two wild samples from Yellow-Bo Sea and one captive sample from the East China Sea in L.polyactis.Using annotation,we identified seven SNPs that are presumed to have disruptive impacts in the proteins,probably causing protein truncation,loss of function or triggering nonsense mediated decay and diagnostic among the three genetically distinct samples.In addition,we detected strong inbreeding in L.polyactis possibly due to some population bottleneck and/or founder effect in the past decades.