Haplotype-Resolved Genome of Sika Deer Reveals Allele-Specific Gene Expression and Chromosome Evolution

Abstract

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.

Genome-wide analysis reveals genomic diversity and signatures of selection in Qinchuan beef cattle

“…ROH lengths can provide insights into the history of inbreeding, where a shorter ROH reflects older inbreeding events, while a longer ROH suggests recent and close inbreeding [21]. In this study, European taurine (Angus and Hereford) exhibited the longest ROH, while Chinese indicine (Leiqiong and Wenling) and crossed cattle (QCC) showed the shortest ROH lengths.…”

“…In addition, in a genome-wide association analysis of key traits in chickens, CAMK4 was identified as a potentially important candidate for testicular growth [20]. In a high-quality haplotype of sika deer antlers based on chromosome-scale genomes, RPS6 was identified as one of several extended gene families that may help velvet antlers grow rapidly without causing cancer [21]. These genes may be related to the excellent meat production performance of QNC.…”

Analysis of Whole-Genome as a Novel Strategy for Animal Species Identification

“…In 2022, high-quality, chromosome-level genomes of C. nippon were published [ 20 , 21 ]. To investigate the effect of genome quality on the results of bioinformatic analysis, the sWGS data of C. nippon was compared with a published C. nippon genome.…”

“…23,25,26,27,32,33, and CK; II contains 4,5,6,14,15,16,17,24,28,29,30,31,34,and 35; III cont 2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 and CK; IV contains 1, 10, and 19; V contains1, 4, 5, 6, 10, 14, 15, 16, 17, 19, 24, 28, 29, 30, 34, 35, …”

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

“…However, it is currently uncertain in our study whether the chromosomal evolutionary event among the four species is chromosome fission or chromosome fusion. Nevertheless, some studies suggested that the chromosomal evolutionary pattern between sika deer and red deer was chromosome fission, which means the divergence time of sika deer is earlier than that of red deer [77]. And a study based on cytogenetics has suggested that chromosome fusion played a great role in karyotypic differentiation in Cervinae [78].…”