A high-quality reference genome of male sika deer and annotation results

We designed a new assembly strategy, which was used to assemble high-quality reference genome of male sika deer. Detailly, three genomes of <i>Cervus nippon</i> have previously been reported which include one female and two male genomes . However, contiguity and accuracy have greatly difference among three genome and assemble quality lower than new assemble genome, especially the female sika deer genome have mistaken when scaffold into chromosome that bring misunderstands for genomic analysis . Here, we combined two genomes sequencing data of male sika deer which include illuminate short reads 143Gb(~55X) 、Pacbio hifi longs reads 96.4Gb(~37X)、Oxford Nanopore longs reads 161Gb (~64X) and Hi-C paired-end reads 269Gb(~104X) acquired a gap less reference genome of male sika deer which genome sizes is 2.7 Gb, with contig N50 reach to 89Mb and have 11 T2T chromosomes . In addition, compared to the previously assemble, our improved assembly quality based on genome completeness (99.41%) as measured by the proportion of short-reads that map to the assembly: genome coverage (98.73%) and coverage of BUSCO (Benchmarking Universal Single-Copy Orthologs) genes for vertebrata (97.8%). the assembly quality value (QV) was estimated as 43.98 by an approach of reference-free and k-mer–based approach, exceeding the Vertebrate Genome Project standard of QV40. Together, these results indicate that our new assembly genome of male sika deer has higher accuracy, completeness, and contiguity. The resvised genome size is 2.7Gb, the repeat seqence is 44.9% and annotated 23,284 coding protein genes.