A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development

• Published in: BMC genomics 2024-06, Vol.25 (1), p.617-13, Article 617
• Main Authors: Wang, Qianghui, Han, Ruobing, Xing, Haihua, Li, Heping
• Format: Article
• Language: English
• Subjects: Accuracy; Animals; Antler development; Antlers - growth & development; Antlers - metabolism; Cbfa-1 protein; Cervus elaphus; Cervus nippon; Chromosome evolution; Chromosomes; Comparative analysis; Consensus genome; Conserved sequence; Deer; Deer - genetics; Deer - growth & development; DNA binding proteins; Evolution; Evolutionary genetics; Fertility; Gene expression; Gene Expression Profiling; Gene regulation; Genes; Genome; Genomes; Genomic analysis; Genomics; Genomics - methods; Haplotypes; Kinases; Male; Nucleotide sequence; Pax8 protein; Proteins; Sika deer; SIX gene family; Sox9 protein; TFs; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptome; Transcriptomes
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10522-9

Sika deer (Cervus nippon) holds significance among cervids, with three genomes recently published. However, these genomes still contain hundreds of gaps and display significant discrepancies in continuity and accuracy. This poses challenges to functional genomics research and the selection of an appropriate reference genome. Thus, obtaining a high-quality reference genome is imperative to delve into functional genomics effectively. Here we report a high-quality consensus genome of male sika deer. All 34 chromosomes are assembled into single-contig pseudomolecules without any gaps, which is the most complete assembly. The genome size is 2.7G with 23,284 protein-coding genes. Comparative genomics analysis found that the genomes of sika deer and red deer are highly conserved, an approximately 2.4G collinear regions with up to 99% sequence similarity. Meanwhile, we observed the fusion of red deer's Chr23 and Chr4 during evolution, forming sika deer's Chr1. Additionally, we identified 607 transcription factors (TFs) that are involved in the regulation of antler development, including RUNX2, SOX6, SOX8, SOX9, PAX8, SIX2, SIX4, SIX6, SPI1, NFAC1, KLHL8, ZN710, JDP2, and TWST2, based on this consensus reference genome. Our results indicated that we acquired a high-quality consensus reference genome. That provided valuable resources for understanding functional genomics. In addition, discovered the genetic basis of sika-red hybrid fertility and identified 607 significant TFs that impact antler development.