Genome Sequencing,Assembly,annotation And Evolution Characteristics Analysis Of Red-backed Vole(Eothenomys Miltus)

Eothenomys miletus is a typical wild rodent species in the family Cricetidae,order Rodentia.E.miletus is mainly distributed in the Hengduan mountains region.The species is a major reservoir for plague and hantavirus.E.miletus is a dominant species of rats and widely distributes in Yunnan.In this study,we sequenced the genome of the E.miletus and generate a high-resolution chromosome-assigned genome assembly for E.miletus using a hybrid approach of Illumina sequencing,single-molecule sequencing and Hi-C sequencing.Then,by comparative analysis we revealed genetic underpinnings of the E.miletus feature.1.We generated a chromosome level genome of E.miletus using 163.36 Gb Illumina,309.56 Gb Pacbio and 359.68 Gb Hi-C data,which was appropriately 2.97 Gb.The length of contig N50 and scaffold N50 were 5.07 Mbp and 98.00 Mbp respectively.The total sequencing depth was 302×,which guaranteed high single-base correctness of E.miletus genome.CEGMA and BUSCO assessment showed that E.miletus genome covered 93.15% in core eukaryotic genes set and 94.9% in vertebrate conserved genes set indicating the integrity of the genome assembly was high.2.To better annotation of genes,we preformed the transcriptome sequencing of tissues including the brain,liver,spleen,lung and kidney.E.miletus genome contained 21,482 protein-encoding genes,of which 99.4% genes with predicted function.In additional,repetitive sequences and non-coding RNAs covered 39.54%and 0.06% in the genome respectively.3.The divergence time between E.miletus and Microtus ochrogaster was estimated to be about 3.9 million years ago(MYA).We identified 545 expanded gene families,424 extracted gene families and 2,241 positived select genes.We hypothesized these genes play an important role in the adaptive evolution of its diet,activity,mating,and immunity.In this study,the E.miletus genome was generated using three sequencing technologies.De novo assembly and annotation were performed.Using comparative genomic analysis,phylogenetic tree,species divergence time,adaptation evolution genes were obtained.It explained the unique traits and characteristics of E.miletus as an important pathogen host.