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Kausar MA, Narayan J, Mishra N, Akhter Y, Singh R, Khalifa AM, El-Hag ABM, Ahmed RME, Tyagi N, Mahfooz S. Studying Human Pathogenic Cryptococcus Gattii Lineages by Utilizing Simple Sequence Repeats to Create Diagnostic Markers and Analyzing Diversity. Biochem Genet 2024:10.1007/s10528-024-10812-7. [PMID: 38773043 DOI: 10.1007/s10528-024-10812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/11/2024] [Indexed: 05/23/2024]
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.
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Affiliation(s)
- Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Ha'il, Hail, 2440, Saudi Arabia.
| | - Jitendra Narayan
- CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Nishtha Mishra
- Department of Chemistry, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Rajeev Singh
- Department of Environmental Science, Jamia Millia Islamia Central University, New Delhi, 110025, India
| | - Amany Mohammed Khalifa
- Department of Pathology, College of Medicine, University of Ha'il, Hail, 2440, Saudi Arabia
| | | | | | - Neetu Tyagi
- Bone Biology Laboratory, Department of Physiology, University of Louisville, Louisville, USA
| | - Sahil Mahfooz
- Department of Industrial Microbiology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India.
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Kausar MA, Narayan J, Agarwal P, Singh P, Ahmed RME, El-Hag ABM, Khalifa AM, Mohammed NARK, Singh R, Mahfooz S. Distribution and conservation of simple sequence repeats in plant pathogenic species of Zymoseptoria and development of genomic resources for its orphaned species. Antonie Van Leeuwenhoek 2024; 117:11. [PMID: 38170404 DOI: 10.1007/s10482-023-01915-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
To better understand the structure and evolution of the genomes of four plant pathogenic species of Zymoseptoria, we analyzed the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in their whole genome and transcriptome sequences. In this study, SSRs are defined as repeats of more than 12 bases in length. The genome and transcriptome sequences of Zymoseptoria ardabiliae show the highest RA (201.1 and 129.9) and RD (3229.4 and 1928.2) of SSRs, while those of Zymoseptoria pseudotritici show the lowest RA (167.2 and 118.5) and RD (2482.2 and 1687.0). The majority of SSRs in the genomic and transcriptome sequences of species were trinucleotide SSRs, while dinucleotide SSRs were the least common. The most common trinucleotide motifs in the transcriptomic sequences across all species were those that encoded the amino acid arginine. As per our motif conservation study, Zymoseptoria tritici (12.4%) possessed the most unique motifs, while Z. pseudotritici (3.9%) had the fewest. Overall, only 38.1% of the motifs were found to be conserved among the species. Gene enrichment studies reveal that three of the species, Z. ardabiliae, Zymoseptoria brevis, and Z. pseudotritici, have SSRs in their genes related to cellular metabolism, while the remaining Z. tritici harbors SSRs in genes related to DNA synthesis and gene expression. In an effort to improve the genetic resources for the orphan species of pathogenic Zymoseptoria, a total of 73,134 primers were created. The genomic resources developed in this study could help with analyses of genetic relatedness within the population and the development of species-specific markers.
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Affiliation(s)
- Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Hail, 2440, Hail, Saudi Arabia.
| | - Jitendra Narayan
- CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Preeti Agarwal
- CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Pallavi Singh
- Department of Biotechnology, Dr APJ Abdul Kalam Technical University, Lucknow, 226031, India
| | | | | | - Amany Mohammed Khalifa
- Department of Pathology, College of Medicine, University of Hail, 2440, Hail, Saudi Arabia
| | | | - Rajeev Singh
- Department of Environmental Science, Jamia Millia Islamia Central University, 110025, New Delhi, India
| | - Sahil Mahfooz
- The Academic Editors, Saryu Enclave, Awadh Vikas Yojna, Lucknow, 226002, India.
- Department of Industrial Microbiology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India.
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Rasoarahona R, Wattanadilokchatkun P, Panthum T, Jaisamut K, Lisachov A, Thong T, Singchat W, Ahmad SF, Han K, Kraichak E, Muangmai N, Koga A, Duengkae P, Antunes A, Srikulnath K. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes. Chromosome Res 2023; 31:29. [PMID: 37775555 DOI: 10.1007/s10577-023-09738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/11/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.
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Affiliation(s)
- Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kitipong Jaisamut
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixes, Av. General Norton de Matos, S/N, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, S/N, 4169-007, Porto, Portugal
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, (CASTNAR, NRU-KU, Thailand), Bangkok, 10900, Thailand.
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand.
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Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment of genetic diversity of National Genebank of India and synteny with other related cucurbits. J Appl Genet 2022; 63:237-263. [PMID: 35106708 DOI: 10.1007/s13353-022-00684-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/06/2022] [Accepted: 01/15/2022] [Indexed: 10/19/2022]
Abstract
Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower, and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identification, and phylogenetic studies. Next-generation sequencing has revolutionized the approaches for discovery, assessment, and validation of molecular markers. We conducted a genome-wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data obtained from NCBI. By performing in silico mining of microsatellite repeat motifs, we developed 45,066 perfect SSR markers. Of which 207 markers were successfully validated and 120 (57.97%) polymorphic primer pairs were utilized for an in-depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6%, and 4.3% of di-, penta-, and hexa-nucleotide repeats in the bottle gourd genome, respectively. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%), and 11 of watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery, and for breeding in bottle gourd and other cucurbits species. KEY MESSAGE: Development of 45,066 perfect microsatellite markers as a valuable tool for marker assisted selection (MAS) in plant breeding.
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