Malik Asif Hussain, Jitendra Narayan, Anil Kumar Dwivedi, Nuha Abdel Rahman Khalil Mohammed, Mohd Adnan Kausar, Sadaf Anwar, Rajeev Singh, Amany Mohammed Khalifa, Sahil Mahfooz
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引用次数: 0
摘要
这项研究旨在对四种不同的新生隐球菌分离物的基因组和转录组序列中简单序列重复序列(SSR)的出现、相对密度(RD)和丰度(RA)进行比较分析。在全基因组序列中,发现新生隐球菌分离物 JEC21 的 SSR 的 RA(165.3)和 RD(2471.8)最高。相反,在转录组序列中,C. neoformans 分离物 KN99 显示出最大的 SSR RA(145.5)。在各类 SSR 中,三核苷酸重复序列在基因组序列(50%)和转录组序列(65%)中的出现率均高于其他重复序列。分离物之间的基调保守性分析表明,41.1%的基调在新变形杆菌分离物之间是保守的。该研究还发现了一些独特的主题,这些主题有可能成为分子探针,用于鉴定分离株。研究人员共为隐球菌分离物创建了 8117 个引物,以丰富其基因组资源。本研究创建的基因组资源有可能有助于多样性分析和创建针对单个分离物的标记。
Elucidation of SSR polymorphism in human pathogenic fungi Cryptococcus neoformans with focus on isolate-specific marker generation and genetic diversity assessment
This work aimed to conduct a comparative analysis of the occurrence, relative density (RD) and abundance (RA) of simple sequence repeats (SSRs), within the genomic and transcriptomic sequences of four different isolates of Cryptococcus neoformans. Among the whole genome sequences, it was observed that the C. neoformans isolate JEC21 exhibited the most elevated RA (165.3) and RD (2471.8) of SSRs. Conversely, among the transcriptome sequences, the C. neoformans isolate KN99 displayed the greatest RA (145.5) of SSRs. Among the classes of SSRs, trinucleotide repeats exhibited a higher prevalence in both the genomic sequences (50%) and transcriptome sequences (65%) over other repeats. Motif conservation analysis among the isolates demonstrated that 41.1% of motifs were conserved among the isolates of C. neoformans. The study also found unique motifs that could potentially serve as molecular probes for the purpose of isolate identification. A total of 8117 primers were created for the isolates of Cryptococcus to enrich it with genomic resources. The genomic resources created in this study have the potential to aid in the diversity analysis and the creation of markers specific to individual isolates.
期刊介绍:
Established in 1946, Biologia publishes high-quality research papers in the fields of microbial, plant and animal sciences. Microbial sciences papers span all aspects of Bacteria, Archaea and microbial Eucarya including biochemistry, cellular and molecular biology, genomics, proteomics and bioinformatics. Plant sciences topics include fundamental research in taxonomy, geobotany, genetics and all fields of experimental botany including cellular, whole-plant and community physiology. Zoology coverage includes animal systematics and taxonomy, morphology, ecology and physiology from cellular to molecular level.