Whole Genome Gine MAP Construction And Sex-determining Genes Mapping In Nibea Albiflora

Yellow drum(Nibea albiflora)is a commercially important marine fish in East China Sea,which belongs to the Perciformes order and the Sciaenidae family.Compared with large yellow croaker(Larimichthys crocea),the largest mariculture fish in China,yellow drum has higher growth rate and resistance to several epidemic diseases in the large yellow croaker such as the cryptocaryonosis(white spot disease)caused by Cryptocaryon irritans and the visceral white spot disease caused by Pseudomonas plecoglossicida,making it to be very interesting aquaculture species.The annual yield of the yellow drum continuously increased in recent years.In the dissertation,we assembled a draft genome and a fine-map genome of the yellow drum with a coverage of 98.2%,and conducted series of investigations including genome annotation,population and evolution analyses and dissected sex determination genes.The reference genome generated in this work will definitely facilitate studies of functional genes related to economically important traits,and genetic improvement carried out by genomic selection in the aquaculture industry of this species.The main research results and conclusions are as following.1)The mixed transcriptome analysis of yellow drum.In this section,we first sequenced the pooled RNA from 11 tissues or organs of yellow drum on an Illumina HiSeq 2500 platform,and de novo assembled a 98.3 Mb transcriptome.A total of 31,183 unigenes were obtained after removing redundant splices and keeping the longest transcript of each gene.And 26,728(85.7%)Unigenes were ultimately annotated in at least one database of nr,nt,Swiss-Prot and KOG,which would be used in future genome assembly and annotation.In addition,total of 15 growth-and 22 immune-related genes were identified,which will be important resources for relevant study.2)The draft genome assembly and population and evolution analysis in yellow drum.To assemble a reference genome,a homozygous yellow drum from two generations of gynogenesis was submitted for genomic sequencing on an Illumina HiSeq platform.The draft genome was assembled into 565.3 Mb,and 22,448 genes were identified using combined annotation methods,among which 21,614(96.3%)were functionally annotated in NCBI nr,trEMBL,Swiss-Prot,and KOG databases.The nucleotide diversity analysis proved that the current aquaculture populations of the yellow drum are still genetically diverse when comparing with gynogenesis fish and other species,whereas lower than the wild population of the yellow drum because of inbreeding.Evolutionary analyses revealed that yellow drum is close to the large yellow croaker,and diverged about 19.7 million years ago(MYA).And gene family expansion and contraction analyses found that the genes in myosin and SNF(sodium: neurotransmitter symporter)families were significantly expanded,that could explain yellow drum has better swimming ability and hunt activity than the large yellow croaker in the mariculture pools.3)The fine-map genome construction of yellow drum.The contigs in draft genome assembled using short reads were highly fragmented.To obtain a more complete genome,we further resequenced a male yellow drum adopting four advanced sequencing technologies-PacBio,Illumina,10 X Genomics and Hi-C-at high sequencing depth of 511.4? coverage.After assembling,we obtained a contig-scale genome with size of 578.8 Mb(N50: 19.17Mb),and high-quality chromosome-scale genome with size of 556.8 Mb(N50: 29.3 Mb).And 103 out of 513 contigs were reliably anchored onto 24 chromosomes with the help of Hi-C.Both the contig-and chromosome-scale genome reached considerable continuity compared with that in the draft genome.Sequence identity assessment revealed the high accuracy of contigs of our assembly,and the BUSCO evaluation demonstrated the preferable completeness of the reference genome.A total of 21,269 consensus genes were predicted in the yellow drum genome,among which 20,386(95.8%)were functionally annotated in several protein databases.4)The sex-determining genes mapping in yellow drum.A total of 34,082 single nucleotide polymorphisms(SNPs)were identified in 371 individuals sequenced with genotyping by sequencing(GBS)technology when aligned to the reference genome.We further mapped 18 significant sex-related SNPs via genome-wide association study(GWAS)in the candidate sex determination region.Based on comparative RNA-seq analysis between ovary and testis,we proposed that Fbxl17 and Dmrt1 as potential sex-determining genes in the yellow drum.The putative sex-determining mechanisms would shed light on the further sex determination studies in the yellow drum and other teleosts.