The First High-Quality Reference Genome of Sika Deer Provides Insights into High-Tannin Adaptation

Abstract

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genome of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

Comprehensive transcriptome analysis of sika deer antler using PacBio and Illumina sequencing

“…Antler transcriptome sequencing. The RNA obtained from the antlers at growth stages (15,25,45, and 65 days) were combined to prepare the SMRTbell library (ANTLER1), and the RNA in ossification stages (100 and 130 days) to prepare another library (ANTLER2). We obtained 31.39 Gb of raw data and 14,495,425 subreads.…”

“…Therefore, several scientists have focused on exploring molecular regulatory mechanisms of regeneration, rapid growth, osteogenesis, and shedding of antlers using modern biological technologies (including transcriptomics, and proteomics) [12][13][14] . Furthermore, Xiumei Xing recently assembled a high-quality sika deer whole-genome sequence using combined technologies of SMRT, Illumina sequencing, and Hi-C, which significantly facilitated our work 15 . Antler growth is a classic "S" type curve, and its gene expression pattern undergoes major changes at different stages.…”

Duplication, Loss, and Evolutionary Features of Specific UDP-Glucuronosyltransferase Genes in Carnivora (Mammalia, Laurasiatheria)

“…The generally accepted “animal-plant warfare” hypothesis considers the evolution of the xenobiotic metabolism as one of major defense mechanisms in animals against daily exposure to xenobiotics; in this regard, plant secondary metabolites are likely among the major sources of evolutionary pressure [ 13 , 24 , 25 , 26 ]. Several studies have shown that herbivorous mammals and birds have experienced a huge expansion of UGT families [ 27 , 28 , 29 , 30 ]. In placental mammals, Kawai et al (2021) [ 31 ] recently demonstrated a relationship of herbivorous diet with a large number of UGT2B genes but not with UGT1A genes.…”

“…Moreover, a recent genomic analysis in woodrats (highly herbivorous) indicated significant duplication of UGT2Bs, in contrast to closely related omnivorous rats and deer mice [ 28 ]. Similarly, sika deer genomic analysis [ 29 ] suggested that genes in the UGT2B subfamily have a strong correlation with the adaptation of the species to a high-tannin diet. These reports underline the evolutionary importance of UGT2Bs in herbivorous adaptation.…”

Current Situation and Utilization of Velvet Deer Germplasm Resources in China

“…Obtaining a high-quality whole genome of a species is the prerequisite for genomic selection. The high-quality chromosome-level genome of sika deer has been published [ 53 ] and used as a reference genome for a genome-wide association study(GWAS). A total of 94 SNPs significantly related to velvet antler production performance have been obtained through genomic selection; they are located in the exon regions of OAS2 and ALYREF/THOC4 [ 54 ], and it is speculated that OAS2 and ALYREF/THOC4 may be related to the weight of velvet antlers [ 55 ].…”