Genome Informatics Facility, Department of Biotech, Iowa State University, Ames, Iowa, United States of America.
Infectious Bacterial Diseases Research Unit, National Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America.
PLoS One. 2021 Apr 28;16(4):e0249899. doi: 10.1371/journal.pone.0249899. eCollection 2021.
Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella abortus in the Greater Yellowstone area. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and Hi-C sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. We conclude by comparing cattle immune system-related genes to the elk genome, revealing eight putative gene losses in elk.
落基山麋鹿（Cervus canadensis）种群对养牛业具有重要的经济意义，因为它们是大黄石地区布鲁氏菌流产（Brucella abortus）的主要宿主。由于细胞适应性免疫反应微不足道，针对麋鹿种群中细胞内细菌疾病的疫苗接种尝试并未成功。由于缺乏基因组资源，因此难以更好地了解为什么疫苗接种不能诱导保护性免疫。为了克服这一限制，使用 PacBio、Illumina 和 Hi-C 测序技术，总覆盖率为 686 倍，将麋鹿基因组组装成 35 个假染色体。生成了强大的基因注释，产生了 18,013 个基因模型和 33,422 个 mRNAs。使用与红鹿和牛基因组的同线性来评估组装的准确性，确定了几个染色体重排、融合和裂变。由于该基因组组装和注释为鹿科物种的基因组功能探索提供了基础，我们通过探索与免疫系统相关的基因的保守性来展示其用途。我们通过将牛的免疫系统相关基因与麋鹿基因组进行比较，得出了麋鹿中存在 8 种可能的基因缺失的结论。
