Chongqing Engineering Laboratory of Green Planting and Deep Processing of Three Gorges Reservoir Famous-region Drug, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404120, P. R. China.
Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P. R. China.
Aging (Albany NY). 2020 Mar 10;12(5):4445-4462. doi: 10.18632/aging.102895.
Forest musk deer (, FMD) is an endangered artiodactyl species, male FMD produce musk. We have sequenced the whole genome of FMD, completed the genomic assembly and annotation, and performed bioinformatic analyses. Our results showed that microsatellites (SSRs) displayed nonrandomly distribution in genomic regions, and SSR abundances were much higher in the intronic and intergenic regions compared to other genomic regions. Tri- and hexanucleotide perfect (P) SSRs predominated in coding regions (CDSs), whereas, tetra- and pentanucleotide P-SSRs were less abundant. Trifold P-SSRs had more GC-contents in the 5'-untranslated regions (5'UTRs) and CDSs than other genomic regions, whereas mononucleotide P-SSRs had the least GC-contents. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs had different distributions in different genomic regions. The RCN of trinucleotide P-SSRs had increased significantly in the CDSs compared to the transposable elements (TEs), intronic and intergenic regions. The analysis of coefficient of variability (CV) of P-SSRs showed that the RCN of mononucleotide P-SSRs had relative higher variation in different genomic regions, followed by the CV pattern of RCN: dinucleotide P-SSRs > trinucleotide P-SSRs > tetranucleotide P-SSRs > pentanucleotide P-SSRs > hexanucleotide P-SSRs. The CV variations of RCN of the same mono- to hexanucleotide P-SSRs were relative higher in the intron and intergenic regions, followed by that in the TEs, and the relative lower was in the 5'UTR, CDSs and 3'UTRs. 58 novel polymorphic SSR loci were detected based on genotyping DNA from 36 captive FMD and 22 SSR markers finally showed polymorphism, stability, and repetition.
林麝（，FMD）是一种濒危的偶蹄目物种，雄性 FMD 产生麝香。我们已经对 FMD 的整个基因组进行了测序，完成了基因组组装和注释，并进行了生物信息学分析。我们的结果表明，微卫星（SSR）在基因组区域中呈现非随机分布，并且在内含子和基因间区域中 SSR 的丰度明显高于其他基因组区域。三核苷酸和六核苷酸完美（P）SSR 主要存在于编码区（CDS）中，而四核苷酸和五核苷酸 P-SSR 则较少。三核苷酸 P-SSR 在 5'非翻译区（5'UTR）和 CDS 中比其他基因组区域具有更高的 GC 含量，而单核苷酸 P-SSR 的 GC 含量最低。相同的单核苷酸到六核苷酸 P-SSR 的重复拷贝数（RCN）在不同的基因组区域中具有不同的分布。与转座元件（TE）、内含子和基因间区域相比，三核苷酸 P-SSR 的 RCN 在 CDS 中显著增加。P-SSR 系数变异（CV）分析表明，单核苷酸 P-SSR 的 RCN 在不同基因组区域中的变异相对较高，其次是 RCN 的 CV 模式：二核苷酸 P-SSR > 三核苷酸 P-SSR > 四核苷酸 P-SSR > 五核苷酸 P-SSR > 六核苷酸 P-SSR。相同的单核苷酸到六核苷酸 P-SSR 的 RCN 的 CV 变化在内含子和基因间区域中相对较高，其次是在 TE 中，相对较低的是在 5'UTR、CDS 和 3'UTR 中。基于 36 只圈养 FMD 的 DNA 分型，检测到 58 个新的多态性 SSR 位点，最终有 22 个 SSR 标记显示出多态性、稳定性和重复性。
