Molecular evidence for adaptive evolution of olfactory-related genes in cervids

Comparative Genomics Reveal Phylogenetic Relationship and Chromosomal Evolutionary Events of Eight Cervidae Species

Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.

Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution

Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.

The Phenolic Compounds in the Young Shoots of Selected Willow Cultivars as a Determinant of the Plants' Attractiveness to Cervids (Cervidae, Mammalia)

This study examined the phenolic acids, flavonoids, and salicylates contents in young, 3-month-old shoots (including the leaves) of willow (Salix spp.). The cultivars were selected based on experiments carried out previously in Poland on fodder and energy willows. It was found, using the HPLC-MS/MS method, that the willow cultivars analyzed from three experimental plots, contained nine different phenolic acids, five salicylates and nine flavonoids, including four flavanols (quercetin, kaempferol, taxifolin and isorhamnetin), two flavanones (prunin, naringenin), two flavones (luteolin, apigenin) and one flavan-3-ol (catechin). The contents of individual compounds were not identical and depended on the cultivar from which they were isolated. The S. laurina 220/205 and S. amygdalina Krakowianka contained the greatest amounts of phenolic acids. The lowest quantities of these compounds were found in the S. viminalis Tur, S. pantaderana and S. cordata clone 1036. The highest concentration of flavonoids in young stems was found in S. fragilis clone 1043. The S. purpurea clone 1131 contained the highest amounts of salicylic compounds. Based on the results obtained from all experimental plots, it was shown that there is a negative correlation between the extent of browsing damage and the content of helicine and salicin from the group of salicylic compounds. A similar analysis between the phenolic acid concentration and the degree of willow browsing showed a positive correlation, especially between ferulic, trans-cinnamic, and synapinic acid. A negative correlation was found between the concentration of protocatechic acid content and browsing by cervids.