Studying Human Pathogenic Cryptococcus Gattii Lineages by Utilizing Simple Sequence Repeats to Create Diagnostic Markers and Analyzing Diversity

IF 1.6 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Mohd Adnan Kausar, Jitendra Narayan, Nishtha Mishra, Yusuf Akhter, Rajeev Singh, Amany Mohammed Khalifa, Amel Bakri Mohammed El-Hag, Ruba Mustafa Elsaid Ahmed, Neetu Tyagi, Sahil Mahfooz
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引用次数: 0

Abstract

In this study, we compared the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) among the lineages of human pathogenic Cryptococcus gattii using an in-silico approach to gain a deeper understanding of the structure and evolution of their genomes. C. gattii isolate MF34 showed the highest RA and RD of SSRs in both the genomic and transcriptomic sequences, followed by isolate WM276. In both the genomic (50%) and transcriptomic (65%) sequences, trinucleotide SSRs were the most common SSR class. A motif conservation study found that the isolates had stronger conservation (56.1%) of motifs, with isolate IND107 having the most (5.7%) unique motifs. We discovered the presence of SSRs in genes that are directly or indirectly associated with disease using gene enrichment analysis. Isolate-specific unique motifs identified in this study could be utilized as molecular probes for isolate identification. To improve genetic resources among C. gattii isolates, 6499 primers were developed. These genomic resources developed in this study could help with diversity analysis and the development of isolate-specific markers.

Abstract Image

利用简单序列重复创建诊断标记并分析多样性,研究人类致病隐球菌加特氏菌系。
在这项研究中,我们采用了一种内模拟方法,比较了人类致病隐球菌加特菌系中简单序列重复序列(SSR)的发生率、相对丰度(RA)和密度(RD),以深入了解其基因组的结构和进化。在基因组和转录组序列中,C. gattii 分离物 MF34 的 SSR 的 RA 和 RD 最高,其次是分离物 WM276。在基因组(50%)和转录组(65%)序列中,三核苷酸 SSR 是最常见的 SSR 类别。图案保护研究发现,分离株的图案保护较强(56.1%),其中 IND107 分离株的独特图案最多(5.7%)。通过基因富集分析,我们发现与疾病直接或间接相关的基因中存在 SSR。本研究中发现的特异性独特图案可用作鉴定分离株的分子探针。为改善 C. gattii 分离物之间的基因资源,开发了 6499 个引物。本研究开发的这些基因组资源有助于多样性分析和分离物特异性标记的开发。
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来源期刊
Biochemical Genetics
Biochemical Genetics 生物-生化与分子生物学
CiteScore
3.90
自引率
0.00%
发文量
133
审稿时长
4.8 months
期刊介绍: Biochemical Genetics welcomes original manuscripts that address and test clear scientific hypotheses, are directed to a broad scientific audience, and clearly contribute to the advancement of the field through the use of sound sampling or experimental design, reliable analytical methodologies and robust statistical analyses. Although studies focusing on particular regions and target organisms are welcome, it is not the journal’s goal to publish essentially descriptive studies that provide results with narrow applicability, or are based on very small samples or pseudoreplication. Rather, Biochemical Genetics welcomes review articles that go beyond summarizing previous publications and create added value through the systematic analysis and critique of the current state of knowledge or by conducting meta-analyses. Methodological articles are also within the scope of Biological Genetics, particularly when new laboratory techniques or computational approaches are fully described and thoroughly compared with the existing benchmark methods. Biochemical Genetics welcomes articles on the following topics: Genomics; Proteomics; Population genetics; Phylogenetics; Metagenomics; Microbial genetics; Genetics and evolution of wild and cultivated plants; Animal genetics and evolution; Human genetics and evolution; Genetic disorders; Genetic markers of diseases; Gene technology and therapy; Experimental and analytical methods; Statistical and computational methods.
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