Department of Biotechnology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, India,
Department of Computer Science & Engineering, UIET, CSJM University, Kanpur, India,
Public Health Genomics. 2021;24(1-2):1-13. doi: 10.1159/000512087. Epub 2021 Jan 5.
Microsatellites or simple sequence repeats (SSR) are related to genomic structure, function, and certain diseases of taxonomically different organisms.
To characterize microsatellites in two closely related Candida species by searching and comparing 1-6 bp nucleotide motifs and utilizing them to develop species-specific markers.
Whole-genome sequence was downloaded from the public domain, microsatellites were mined and analyzed, and primers were synthesized.
A total of 15,821 and 7,868 microsatellites, with mono-nucleotides (8,679) and trinucleotides (3,156) as most frequent microsatellites, were mined in Candida dubliniensis and Candida albicans, respectively. Chromosome size was found positively correlated with microsatellite number in both the species, whereas it was negatively correlated with the relative abundance and density of microsatellites. A number of unique motifs were also found in both the species. Overall, microsatellite frequencies of each chromosome in C. dubliniensis were higher than in C. albicans.
The features of microsatellite distribution in the two species' genomes revealed that it is probably not conserved in the genus Candida. Data generated in this article could be used for comparative genome mapping and understanding the distribution of microsatellites and genome structure between these closely related and phenotypically misidentified species and may provide a foundation for the development of a new set of species-specific microsatellite markers. Here, we also report a novel microsatellite-based marker for C. dubliniensis-specific identification.
微卫星或简单重复序列（SSR）与基因组结构、功能以及分类学上不同生物的某些疾病有关。
通过搜索和比较 1-6 个核苷酸基序来对两个密切相关的假丝酵母属物种中的微卫星进行特征描述，并利用这些基序开发物种特异性标记物。
从公共领域下载全基因组序列，挖掘和分析微卫星，并合成引物。
在白假丝酵母和杜氏假丝酵母中分别挖掘到了 15821 个和 7868 个微卫星，其中单核苷酸（8679 个）和三核苷酸（3156 个）是最常见的微卫星。发现两个物种的染色体大小与微卫星数量呈正相关，而与微卫星的相对丰度和密度呈负相关。在两个物种中还发现了一些独特的基序。总体而言，白假丝酵母中每条染色体的微卫星频率均高于杜氏假丝酵母。
两个物种基因组中微卫星分布的特征表明，假丝酵母属中可能不存在微卫星保守性。本文生成的数据可用于比较基因组作图以及理解这些密切相关且表型上易混淆的物种之间的微卫星和基因组结构的分布，这可能为开发一套新的物种特异性微卫星标记物提供基础。本文还报道了一种用于杜氏假丝酵母特异性鉴定的新型基于微卫星的标记物。
