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Geethanjali S, Kadirvel P, Anumalla M, Hemanth Sadhana N, Annamalai A, Ali J. Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning. PLANTS (BASEL, SWITZERLAND) 2024; 13:2619. [PMID: 39339594 PMCID: PMC11435353 DOI: 10.3390/plants13182619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/18/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024]
Abstract
Genetic markers are powerful tools for understanding genetic diversity and the molecular basis of traits, ushering in a new era of molecular breeding in crops. Over the past 50 years, DNA markers have rapidly changed, moving from hybridization-based and second-generation-based to sequence-based markers. Simple sequence repeats (SSRs) are the ideal markers in plant breeding, and they have numerous desirable properties, including their repeatability, codominance, multi-allelic nature, and locus specificity. They can be generated from any species, which requires prior sequence knowledge. SSRs may serve as evolutionary tuning knobs, allowing for rapid identification and adaptation to new circumstances. The evaluations published thus far have mostly ignored SSR polymorphism and gene evolution due to a lack of data regarding the precise placements of SSRs on chromosomes. However, NGS technologies have made it possible to produce high-throughput SSRs for any species using massive volumes of genomic sequence data that can be generated fast and at a minimal cost. Though SNP markers are gradually replacing the erstwhile DNA marker systems, SSRs remain the markers of choice in orphan crops due to the lack of genomic resources at the reference level and their adaptability to resource-limited labor. Several bioinformatic approaches and tools have evolved to handle genomic sequences to identify SSRs and generate primers for genotyping applications in plant breeding projects. This paper includes the currently available methodologies for producing SSR markers, genomic resource databases, and computational tools/pipelines for SSR data mining and primer generation. This review aims to provide a 'one-stop shop' of information to help each new user carefully select tools for identifying and utilizing SSRs in genetic research and breeding programs.
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Affiliation(s)
- Subramaniam Geethanjali
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Palchamy Kadirvel
- Crop Improvement Section, ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad 500030, India
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños 4031, Laguna, Philippines
- IRRI South Asia Hub, Patancheru, Hyderabad 502324, India
| | - Nithyananth Hemanth Sadhana
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Anandan Annamalai
- Indian Council of Agricultural Research (ICAR), Indian Institute of Seed Science, Bengaluru 560065, India
| | - Jauhar Ali
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños 4031, Laguna, Philippines
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Panda S, Swain SK, Sahu BP, Sarangi R. Insights into genome plasticity and gene regulation in Orientia tsutsugamushi through genome-wide mining of microsatellite markers. 3 Biotech 2023; 13:366. [PMID: 37840877 PMCID: PMC10575825 DOI: 10.1007/s13205-023-03795-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Microsatellite markers are being used for molecular identification and characterization as well as estimation of evolution patterns due to their highly polymorphic nature. The repeats hold 40% of the entire genome of Orientia tsutsugamushi (OT), but not yet been characterized. Thus, we investigated the genome-wide presence of microsatellites within nine complete genomes of OT and analyzed their distribution pattern, composition, and complexity. The in-silico study revealed that the genome of OT enriched with microsatellites having a total of 126,187 SSRs and 10,374 cSSRs throughout the genome, of which 70% and 30% are represented within the coding and non-coding regions, respectively. The relative density (RD) and relative abundance (RA) of SSRs were 42-44.43/kb and 6.25-6.59/kb, while for cSSRs this value ranged from 7.06 to 8.1/kb and 0.50 to 0.55/kb, respectively. However, RA and RD were weakly correlated with genome size and incidence of microsatellites. The mononucleotide repeats (54.55%) were prevalent over di- (33.22%), tri- (11.88%), tetra- (0.27%), penta- (0.02%), hexanucleotide (0.04%) repeats, with poly (A/T) richness over poly (G/C). The motif composition of cSSRs revealed that maximum cSSRs were made up of two microsatellites having unique duplication patterns such as AT-x-AT and CG-x-CG. To our knowledge, this is the first study of microsatellites in the OT genome, where characterization of such variations in repeat sequences would be important in deciphering the origin, rate of mutation, and role of repeat sequences in the genome. More numbers of microsatellites represented within the coding region provide an insight into the genome plasticity that may interfere with gene regulation to mitigate host-pathogen interaction and evolution of the species.
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Affiliation(s)
- Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Subrat Kumar Swain
- Medical Research Laboratory, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
| | - Basanta Pravas Sahu
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha 751003 India
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Darshan K, Aggarwal R, Bashyal BM, Singh J, Saharan MS, Gurjar MS, Solanke AU. Characterization and development of transcriptome-derived novel EST-SSR markers to assess genetic diversity in Chaetomium globosum. 3 Biotech 2023; 13:379. [PMID: 37900266 PMCID: PMC10600081 DOI: 10.1007/s13205-023-03794-7] [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: 08/08/2022] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Chaetomium globosum Kunze, an internationally recognized biocontrol fungus. It mycoparasitizes various plant pathogens and produce antifungal metabolites to suppress the growth of pathogenic fungi. Lack of detailed genome level diversity studies has delimited the development and utilization of potential C. globosum strains. The present study was taken to reveal the distribution, identification, and characterization of expressed sequence tag-simple sequence repeats (EST-SSRs) in C. globosum. RNA-Seq experiment was performed for C. globosum potential isolate Cg2 (AY429049) using Illumina HiSeq 2500. Reference-guided de novo assembly yielded 45,582 transcripts containing 27,957 unigenes. We generated a new set of 8485 EST-SSR markers distributed in 5908 unigene sequences with one SSR locus distribution density per 6.1 kb. Six distinct classes of SSR repeat motifs were identified. The most abundant were mononucleotide repeats (51.67%), followed by tri-nucleotides (36.61%). Out of 5034 EST-SSR primers, 50 primer pairs were selected and validated for the polymorphic study of 15 C. globosum isolates. Twenty-two SSR markers showed average genetic polymorphism among C. globosum isolates. The number of alleles (Na) per marker ranges from 2 to 4, with a total of 74 alleles detected for 22 markers with a mean polymorphism information content (PIC) value of 0.4. UPGMA hierarchical clustering analysis generated three main clusters of C. globosum isolates and exhibited a lower similarity index range from 0.59 to 0.85. Thus, the newly developed EST-SSR markers could replace traditional methods for determining diversity. The study will also enhance the genomic research in C. globosum to explore its biocontrol potential against phytopathogens. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03794-7.
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Affiliation(s)
- K. Darshan
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Forest Protection Division, ICFRE-Tropical Forest Research Institute, Jabalpur, Madhya Pradesh 482021 India
| | - Rashmi Aggarwal
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Jagmohan Singh
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. S. Saharan
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. S. Gurjar
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Amolkumar U. Solanke
- ICAR-National Institute for Plant Biotechnology, ICAR-IARI, New Delhi, 110012 India
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Kashyap PL, Kumar S, Kumar RS, Sharma A, Khanna A, Kajal, Raj S, Jasrotia P, Singh G. Comparative analysis of nine Tilletia indica genomes for the development of novel microsatellite markers for genetic diversity and population structure analysis. Front Microbiol 2023; 14:1227750. [PMID: 37520344 PMCID: PMC10374028 DOI: 10.3389/fmicb.2023.1227750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Karnal bunt (KB; Tilletia indica) is the prime quarantine concern for quality wheat production throughout the world. The most effective approach to dealing with this biotic stress is to breed KB-resistant wheat varieties, which warrants a better understanding of T. indica genome architecture. In India, the North Western Plain Zone is the prime hot spot for KB disease, but only limited efforts have been made to decipher T. indica diversity at the genomic level. Microsatellites offer a powerful and robust typing system for the characterization and genetic diversity assessment of plant pathogens. At present, inadequate information is available with respect to the development of genome-derived markers for revealing genetic variability in T. indica populations. In current research, nine complete genome sequences of T. indica (PSWKBGH_1, PSWKBGH_2, PSWKBGD_1_3, RAKB_UP_1, TiK_1, Tik, DAOMC236408, DAOMC236414, and DAOMC236416) that exist in the public domain were explored to know the dynamic distribution of microsatellites. Comparative genome analysis revealed a high level of relative abundance and relative density of microsatellites in the PSWKBGH_1 genome in contrast to other genomes. No significant correlation between microsatellite distribution for GC content and genome size was established. All the genomes showed the dominance of tri-nucleotide motifs, followed by mono-, di-, tetra-, hexa-, and penta-nucleotide motifs. Out of 50 tested markers, 36 showed successful amplification in T. indica isolates and produced 52 different alleles. A PCR assay along with analysis of the polymorphic information content (PIC) revealed 10 markers as neutral and polymorphic loci (PIC 0.37). The identified polymorphic SSR loci grouped a geographically distinct T. indica population of 50 isolates representing seven Indian regions (Jammu, Himachal Pradesh, Punjab, Haryana, Uttarakhand, Uttar Pradesh, and Rajasthan) into four distinct clusters. The results of the analysis of molecular variance identified 94% genetic variation within the population and 6% among the population. Structure analysis also confirmed the existence of four genetically diverse groups containing admixtures of T. indica isolates across populations. In nutshell, the current study was successful in identifying novel, neutral and polymorphic microsatellite markers that will be valuable in offering deep insight into the evolutionary relationship and dynamics of the T. indica population for devising effective KB management strategies in wheat.
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Losada LCDML, Monteiro RC, de Carvalho JA, Hagen F, Fisher MC, Spruijtenburg B, Meis JF, de Groot T, Gonçalves SS, Negroni R, Kano R, Bonifaz A, de Camargo ZP, Rodrigues AM. High-Throughput Microsatellite Markers Development for Genetic Characterization of Emerging Sporothrix Species. J Fungi (Basel) 2023; 9:354. [PMID: 36983522 PMCID: PMC10054832 DOI: 10.3390/jof9030354] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Sporotrichosis is the main subcutaneous mycosis worldwide transmitted by animal or plant vectors and often escalates to outbreaks or epidemics. The current cat-transmitted sporotrichosis driven by Sporothrix brasiliensis has become a significant public health issue in South America. Transmission dynamics remain enigmatic due to the lack of development of polymorphic markers for molecular epidemiological analysis. This study used a high-throughput mining strategy to characterize simple sequence repeat (SSR) markers from Sporothrix genomes. A total of 118,140-143,912 SSR loci were identified (82,841-98,369 unique markers), with a 3651.55-3804.65 SSR/Mb density and a majority of dinucleotides motifs (GC/CG). We developed a panel of 15 highly polymorphic SSR markers suitable for genotyping S. brasiliensis, S. schenckii, and S. globosa. PCR amplification revealed 240 alleles in 180 Sporothrix isolates with excellent polymorphic information content (PIC = 0.9101), expected heterozygosity (H = 0.9159), and discriminating power (D = 0.7127), supporting the effectiveness of SSR markers in uncovering cryptic genetic diversity. A systematic population genetic study estimated three clusters, corresponding to S. brasiliensis (population 1, n = 97), S. schenckii (population 2, n = 49), and S. globosa (population 3, n = 34), with a weak signature of mixed ancestry between populations 1 and 2 or 3 and 2. Partitioning of genetic variation via AMOVA revealed highly structured populations (ΦPT = 0.539; Nm = 0.213; p < 0.0001), with approximately equivalent genetic variability within (46%) and between (54%) populations. Analysis of SSR diversity supports Rio de Janeiro (RJ) as the center of origin for contemporary S. brasiliensis infections. The recent emergence of cat-transmitted sporotrichosis in northeastern Brazil indicates an RJ-Northeast migration resulting in founder effects during the introduction of diseased animals into sporotrichosis-free areas. Our results demonstrated high cross-species transferability, reproducibility, and informativeness of SSR genetic markers, helping dissect deep and fine-scale genetic structures and guiding decision making to mitigate the harmful effects of the expansion of cat-transmitted sporotrichosis.
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Affiliation(s)
- Luiza Chaves de Miranda Leonhardt Losada
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Ruan Campos Monteiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Matthew C. Fisher
- Medical Research Council Center for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Bram Spruijtenburg
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Department I of Internal Medicine, Faculty of Medicine, University of Cologne, and Excellence Center for Medical Mycology, University Hospital Cologne, 50931 Cologne, Germany
| | - Theun de Groot
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
- Center of Expertise in Mycology Radboud University Medical Center/Canisius-Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands
| | - Sarah Santos Gonçalves
- Infectious Diseases Postgraduate Program, Center for Research in Medical Mycology, Federal University of Espírito Santo (UFES), Vitória 29043900, Brazil
| | - Ricardo Negroni
- Mycology Unit of the Infectious Diseases Hospital Francisco Javier Muñiz, Reference Center of Mycology of Buenos Aires City, Uspallata, Buenos Aires 2272, Argentina
| | - Rui Kano
- Teikyo University Institute of Medical Mycology (TIMM), 359 Otsuka, Tokyo 192-0395, Japan
| | - Alexandro Bonifaz
- Dermatology Service, Mycology Department, Hospital General de México, “Dr. Eduardo Liceaga”, Balmis 148, Colonia Doctores, Mexico City 03020, Mexico
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
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Sun X, Wang G, Yang J, Yu W, Xu J, Tang B, Ding G, Zhang D. Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae). Mol Biol Rep 2023; 50:4165-4173. [PMID: 36894769 DOI: 10.1007/s11033-023-08356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023]
Abstract
BACKGROUND As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind. METHODS AND RESULTS A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria. CONCLUSION This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.
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Affiliation(s)
- Xiaoli Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jie Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Wei Yu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Jiayue Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China
| | - Ge Ding
- Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, 224003, China
| | - Daizhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China.
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Jafarian H, Hardani AK, Asnafi AA, Zarei Mahmoudabadi A. Enzymatic and antifungal susceptibility profiles of Candida glabrata isolates from pediatric patients and their genetic diversity based on microsatellite length polymorphism. Lett Appl Microbiol 2022; 75:1569-1578. [PMID: 36087054 DOI: 10.1111/lam.13824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 11/27/2022]
Abstract
This study aimed to detect different genotypes of Candida glabrata isolates in pediatric patients with and without neutropenia utilizing microsatellite length polymorphism (MLP) and its correlation with drug resistance and enzymatic activity were assessed. Samples from neutropenic and non-neutropenic patients were collected from November 2020 to November 2021. Thirty-six C. glabrata strains were isolated and identified using classical and molecular methods. Then, C. glabrata isolates were genotyped by the MLP technique, and their antifungal susceptibility was performed based on the CLSI M27 guideline. Eighteen different multi-loci genotypes (G1 - G18) were detected based on MLP analysis. Analysis of molecular variance revealed high genetic variation within populations (94%) and low genetic differentiation among populations (6%). Also, 40% (n=4) of isolates from neutropenic patients were non-wild-type for posaconazole, and 30% (n=3) were resistant to caspofungin. Very strong hemolytic and proteinase activity were seen in 97.2 and 86.1% of isolates. Candida glabrata strains from neutropenic patients were genetically divergent from other populations. The minimum spanning tree shows that observed genotypes were mainly related to previously reported genotypes from Iran, Spain, and China.
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Affiliation(s)
- Hadis Jafarian
- Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Kamal Hardani
- Department of Pediatrics, School of Medicine, Abuzar Children Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Amin Asnafi
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Zarei Mahmoudabadi
- Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops. Int J Mol Sci 2022; 23:ijms23179847. [PMID: 36077247 PMCID: PMC9456221 DOI: 10.3390/ijms23179847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/03/2022] Open
Abstract
Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.
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Mandal K, Dutta S, Upadhyay A, Panda A, Tripathy S. Comparative Genome Analysis Across 128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution and Localized Evolution of Compartmentalized Genomes. Front Microbiol 2022; 13:806398. [PMID: 35369471 PMCID: PMC8967354 DOI: 10.3389/fmicb.2022.806398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of (TTTAGGG)n or (TTAGGGT)n rather than the canonical (TTAGGG)n. RxLR (arginine-any amino acid-leucine-arginine) motifs containing effectors diverge rapidly in Phytophthora and do not show any core common group. The RxLR effectors of some Phytophthora isolates have a tendency to form clusters with RxLRs from other species than within the same species. An analysis of the flanking intergenic distance clearly indicates a two-speed genome organization for all the Phytophthora isolates. Apart from effectors and the transposons, a large number of other virulence genes such as carbohydrate-active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP-binding cassette transporters (ABC), and ubiquitins are also present in the repeat-rich compartments. This indicates a rapid co-evolution of this powerful arsenal for successful pathogenicity. Whole genome duplication studies indicate that the pattern followed is more specific to a geographic location. To conclude, the large-scale genomic studies of Phytophthora have thrown light on their adaptive evolution, which is largely guided by the localized host-mediated selection pressure.
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Affiliation(s)
- Kajal Mandal
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Subhajeet Dutta
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Upadhyay
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Panda
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, United States
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Boiko S. Design of microsatellite markers for Schizophyllum commune (Agaricales, Basidiomycota) based on analysis of its genome. UKRAINIAN BOTANICAL JOURNAL 2022. [DOI: 10.15407/ukrbotj79.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Simple sequence repeats of DNA (SSRs) are the most popular source of genetic markers used in population genetics, phylogenetics, and genetic mapping. A large number of nucleotide repeats enriched in G and C were identified. 336 mononucleotide motifs with more than ten repeats were recorded. 2020 nucleotide repeats were identified, of which 97.4% are di- (68.2%) and trinucleotides (29.2%). The total number of unique SSR loci, to which primers pairs were developed, was 1920. PCR primer sequences for unique SSR loci of the S. commune genome are presented. Of the twenty-two SSR markers synthesized for the S. commune genome, amplicons formed 64% on freshly isolated DNA samples.
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Coffee Leaf Rust (Hemileia vastatrix) from the Recent Invasion into Hawaii Shares a Genotypic Relationship with Latin American Populations. J Fungi (Basel) 2022; 8:jof8020189. [PMID: 35205944 PMCID: PMC8877902 DOI: 10.3390/jof8020189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 12/10/2022] Open
Abstract
Hawaii has long been one of the last coffee-producing regions of the world free of coffee leaf rust (CLR) disease, which is caused by the biotrophic fungus Hemileia vastatrix. However, CLR was detected in coffee farms and feral coffee on the island of Maui in February 2020 and subsequently on other islands of the Hawaiian archipelago. The source of the outbreak in Hawaii is not known, and CLR could have entered Hawaii from more than 50 coffee-producing nations that harbor the pathogen. To determine the source(s) of the Hawaii inoculum, we analyzed a set of eleven simple sequence repeat markers (SSRs) generated from Hawaii isolates within a dataset of 434 CLR isolates collected from 17 countries spanning both old and new world populations, and then conducted a minimum spanning network (MSN) analysis to trace the most likely pathway that H. vastatrix could have taken to Hawaii. Forty-two multilocus genotypes (MLGs) of H. vastatrix were found in the global dataset, with all isolates from Hawaii assignable to MLG 10 or derived from it. MLG 10 is widespread in Central America and Jamaica, making this region the most probable source of inoculum for the outbreak in Hawaii. An examination of global weather patterns during the months preceding the introduction of CLR makes it unlikely that the pathogen was windborne to the islands. Likely scenarios for the introduction of CLR to Hawaii are the accidental introduction of spores or infected plant material by travelers or seasonal workers, or improperly fumigated coffee shipments originating from Central America or the Caribbean islands.
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Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans. Sci Rep 2022; 12:2359. [PMID: 35149731 PMCID: PMC8837645 DOI: 10.1038/s41598-022-05428-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/12/2022] [Indexed: 11/09/2022] Open
Abstract
Ilyonectria destructans is a pathogenic fungus causing root rot and other symptoms on trees and many crops. This paper analyses the mitochondrial genome of I. destructans and compares it with other published Nectriaceae mitogenomes. The I. destructans mitogenome appears as a circular DNA molecule of 42,895 bp and an overall GC content of 28.23%. It contains 28 protein-coding genes (15 core protein genes and 13 free-standing ORFs), two rRNAs and 27 tRNAs. The gene content and order were found to be conserved in the mitogenome of I. destructans and other Nectriaceae, although the genome size varies because of the variation in the number and length of intergenic regions and introns. For most core protein-coding genes in Nectriaceae species, Ka/Ks < 1 indicates purifying selection. Among some Nectriaceae representatives, only the rps3 gene was found under positive selection. Phylogenetic analyses based on nucleotide sequences of 15 protein-coding genes divided 45 Hypocreales species into six major clades matching the families Bionectriaceae, Cordycipitaceae, Clavicipitaceae, Ophiocordycipitaceae, Hypocreaceae and Nectriaceae. I. destructans appeared as a sister species to unidentified Ilyonectia sp., closely related to C. ilicicola, N. cinnabarina and a clad of ten Fusarium species and G. moniliformis. The complete mitogenome of I. destructans reported in the current paper will facilitate the study of epidemiology, biology, genetic diversity of the species and the evolution of family Nectriace and the Hypocreales order.
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Zhou D, Xu J, Dong J, Li H, Wang D, Gu J, Zhang KQ, Zhang Y. Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China. Microorganisms 2021; 9:1919. [PMID: 34576814 PMCID: PMC8465350 DOI: 10.3390/microorganisms9091919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species Arthrobotrys oligospora. However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of A. oligospora from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the A. oligospora population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of A. oligospora in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability.
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Affiliation(s)
- Duanyong Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
- School of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianyong Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Da Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Juan Gu
- School of Life Science, Yunnan University, Kunming 650032, China;
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China; (D.Z.); (J.D.); (H.L.); (D.W.)
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Dabral A, Shamoon A, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1623-1638. [PMID: 34305342 PMCID: PMC8285676 DOI: 10.1007/s12298-021-01035-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Proteaceae, a largely southern hemisphere family consisting of 80 genera distributed in Australia and southern Africa as its centres of greatest diversity, also extends well in northern and southern America. Under this family, Grevillea robusta is a fast-growing species got popularity in farm and avenue plantations. Despite the ecological and economic importance, the species has not yet been investigated for its genetic improvement and genome-based studies. Only a few molecular markers are available for the species or its close relatives, which hinders genomic and population genetics studies. Genetic markers have been intensively applied for the main strategies in breeding programs, especially for the economically important traits. Hence, it is of utmost priority to develop genomic database resources and species-specific markers for studying quantitative genetics in G. robusta. Given this, the present study aimed to develop de novo genome sequencing, robust microsatellites markers, sequence annotation and their validation in different stands of G. robusta in northern India. Library preparation and sequencing were carried out using Illumina paired-end sequencing technology. Approximately, ten gigabases (Gb) sequence data with 70.87 million raw reads assembled into 425,923 contigs (read mapped to 76.48%) comprising 455 Mb genome size (23 × coverage) generated through genome skimming approach. In total, 9421 simple sequence repeat (SSR) primer pairs were successfully designed from 13,335 microsatellite repeats. Afterward, a subset of 161 primer pairs was randomly selected, synthesized and validated. All the tested primers showed successful amplification but only 13 showed polymorphisms. The polymorphic SSRs were further used to estimate the measures of genetic diversity in 12 genotypes each from the states of Punjab, Haryana, Himachal Pradesh and Uttarakhand. Importantly, the average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.69, 0.356, 0.557 and 0.388, respectively. The availability of sequence information and newly developed SSR markers could potentially be used in various genetic analyses and improvements through molecular breeding strategies for G. robusta. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01035-w.
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Affiliation(s)
- Aman Dabral
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Rajendra K. Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand 248 006 India
| | - Harish S. Ginwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Maneesh S. Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
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15
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Lei Y, Zhou Y, Price M, Song Z. Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions. BMC Genomics 2021; 22:421. [PMID: 34098869 PMCID: PMC8186053 DOI: 10.1186/s12864-021-07752-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distribution patterns have been studied in most phylogenetic lineages, they are unclear in fish species. RESULTS Here, we present the first systematic examination of microsatellite distribution in coding and non-coding regions of 14 fish genomes. Our study showed that the number and type of microsatellites displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation and DNA replication slippage theories alone were insufficient to explain the distribution patterns. Our results showed that microsatellites are dominant in non-coding regions. The total number of microsatellites ranged from 78,378 to 1,012,084, and the relative density varied from 4925.76 bp/Mb to 25,401.97 bp/Mb. Overall, (A + T)-rich repeats were dominant. The dependence of repeat abundance on the length of the repeated unit (1-6 nt) showed a great similarity decrease, whereas more tri-nucleotide repeats were found in exonic regions than tetra-nucleotide repeats of most species. Moreover, the incidence of different repeated types appeared species- and genomic-specific. These results highlight potential mechanisms for maintaining microsatellite distribution, such as selective forces and mismatch repair systems. CONCLUSIONS Our data could be beneficial for the studies of genome evolution and microsatellite DNA evolutionary dynamics, and facilitate the exploration of microsatellites structural, function, composition mode and molecular markers development in these species.
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Affiliation(s)
- Yi Lei
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yu Zhou
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China.
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, People's Republic of China.
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Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species. J Fungi (Basel) 2021; 7:jof7040288. [PMID: 33921243 PMCID: PMC8070597 DOI: 10.3390/jof7040288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.
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Jain A, Sharma PC. Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families. INFECTION GENETICS AND EVOLUTION 2021; 92:104853. [PMID: 33839312 DOI: 10.1016/j.meegid.2021.104853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 04/04/2021] [Indexed: 11/15/2022]
Abstract
Microsatellites are nonrandom hypervariable iterations of one to six nucleotides, existing across the coding as well as noncoding regions of virtually all known genomes, arising primarily due to polymerase slippage and unequal crossing over during replication events. Two or more perfect microsatellites located in close proximity form compound microsatellites. We studied the distribution of compound microsatellites in 118 ssDNA virus genomes belonging to three economically important virus families, namely Anelloviridae, Circoviridae, and Parvoviridae, known to predominantly infect livestock and humans. Among these virus families, 0-58.49% of perfect microsatellites were involved in the formation of compound microsatellites, the majority being located in the coding regions. No clear relationship existed between the genomic features (genome size and GC%) and compound microsatellite characteristics (relative abundance and relative density). The majority of the compound microsatellites resulted from di-SSR couples. A strong positive relationship was observed between the maximum distance value and length of compound microsatellite, percentage of microsatellites involved in the compound microsatellite formation, and relative microsatellite density. The degree of variability among microsatellite characteristics studied was largely a species-specific phenomenon. A major proportion of compound microsatellites was represented by similar motif combinations. The findings of the present study will help in better understanding of the structural, functional, and evolutionary role of compound microsatellites prevailing in the smaller genomes.
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Affiliation(s)
- Ankit Jain
- Merck Life Science Pvt. Ltd, Sector-17, Chandigarh, India
| | - Prakash C Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka Sector-16 C, New Delhi 11078, India.
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Kimunye JN, Muzhinji N, Mostert D, Viljoen A, Bester-van der Merwe AE, Mahuku G. Genetic Diversity and Mating Type Distribution of Pseudocercospora fijiensis on Banana in Uganda and Tanzania. PHYTOPATHOLOGY 2021; 111:741-750. [PMID: 32931393 DOI: 10.1094/phyto-04-20-0138-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Black Sigatoka, caused by Pseudocercospora fijiensis, is a major foliar disease of banana and plantain worldwide. There are few available data regarding the genetic diversity and population structure of the pathogen in East Africa, which are needed to design effective and durable disease management strategies. We genotyped 319 single-spore isolates of P. fijiensis collected from seven regions in Uganda and Tanzania and five isolates from Nigeria using 16 simple sequence repeat markers and mating type-specific primers. Isolates from each country and region within the country were treated as populations and subpopulations, respectively. A total of 296 multilocus genotypes (MLGs) were recovered, representing a clonal fraction of 7%. Subpopulations had a moderate level of genetic diversity (Hexp = 0.12 to 0.31; mean, 0.29). Mating type distribution did not deviate from equilibrium (MAT1-1: MAT1-2, 1:1 ratio) in Uganda; however, in Tanzania the mating types were not in equilibrium (4:1 ratio). The index of association tests (IA and r̄d) showed that all populations were at linkage equilibrium (P > 0.05), thus supporting the hypothesis of random association of alleles. These findings are consistent with a pathogen that reproduces both clonally and sexually. Low and insignificant levels of population differentiation were detected, with 90% of the variation occurring among isolates within subpopulations. The high intrapopulation variation has implications in breeding for resistance to P. fijiensis because isolates differing in aggressiveness and virulence are likely to exist over small spatial scales. Diverse isolates will be required for resistance screening to ensure selection of banana cultivars with durable resistance to Sigatoka in East Africa.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Janet N Kimunye
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | - Norman Muzhinji
- Department of Applied and Natural Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
| | - Diane Mostert
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | - Altus Viljoen
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | | | - George Mahuku
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- International Institute of Tropical Agriculture, P.O. Box, 34441, Dar es Salaam, Tanzania
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Genome-wide in silico identification and characterization of Simple Sequence Repeats in diverse completed SARS-CoV-2 genomes. GENE REPORTS 2021; 23:101020. [PMID: 33521382 PMCID: PMC7835092 DOI: 10.1016/j.genrep.2021.101020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/06/2020] [Accepted: 12/29/2020] [Indexed: 12/19/2022]
Abstract
Simple sequence repeats (SSRs) or, Microsatellites are short repeat sequences that have been extensively studied in eukaryotic (plants) and prokaryotic (bacteria) organisms. Compared to other organisms, the presence and incidence of SSR on viral genomes are less studied. With the emergence of novel infectious viruses over the past few decades, it is imperative to study the genetic diversity in such viruses to predict their evolutionary and functional changes over time. Following the emergence of SARS-CoV-2, we have assembled 121 complete genomes reported from 31 countries across the six continents for the identification and characterization of SSR repeats. Using two independent SSR identification tools, we have found remarkable consistency in the diversity of microsatellites pattern (38–42 per genome) found in the 121 analyzed SARS-CoV-2 genomes indication their important role for genome stability. Among the identified motifs, trinucleotide and hexanucleotide repeats were found to be the most abundant form followed by mono- and di-nucleotide. There were no tetra- or penta-nucleotide repeats in the analyzed SARS-CoV-2 genomes. The discovery of microsatellites in SARS-CoV-2 genomes may become useful for the population genetics, evolutionary analysis, strain identification and genetic variation.
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Singh P, Nath R, Venkatesh V. Comparative Genome-Wide Characterization of Microsatellites in Candida albicans and Candida dubliniensis Leading to the Development of Species-Specific Marker. Public Health Genomics 2021; 24:1-13. [PMID: 33401274 DOI: 10.1159/000512087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/30/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Microsatellites or simple sequence repeats (SSR) are related to genomic structure, function, and certain diseases of taxonomically different organisms. OBJECTIVE 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. METHODS Whole-genome sequence was downloaded from the public domain, microsatellites were mined and analyzed, and primers were synthesized. RESULTS 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. CONCLUSION 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.
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Affiliation(s)
- Pallavi Singh
- Department of Biotechnology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, India, .,Department of Computer Science & Engineering, UIET, CSJM University, Kanpur, India,
| | - Ravindra Nath
- Department of Computer Science & Engineering, UIET, CSJM University, Kanpur, India
| | - Vimala Venkatesh
- Department of Microbiology, King George's Medical University, Lucknow, India
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Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome. Sci Rep 2020; 10:13852. [PMID: 32807836 PMCID: PMC7431841 DOI: 10.1038/s41598-020-70634-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/01/2020] [Indexed: 11/09/2022] Open
Abstract
Genome-wide in-silico identification of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036-1,181 microsatellites per strain. The further screening revealed the presence of 83-107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6-8.4 and 53.0-59.5 bp/kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6-0.8 and 12.1-17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD significantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-significantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)-x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. Finally, in-silico polymorphism was assessed, followed by in-vitro validation using PCR analysis and sequencing. The thirteen polymorphic SSR markers developed in this study were further characterized by mapping with the sequence present in the database. The results of the present study indicate that these SSRs could be a useful tool for identification, analysis of genetic diversity, and understanding the evolutionary status of the virus.
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Chen Y, Zhang ZK, He Y, Zhou C. A Large-Scale High-Density Weighted Structural Connectome of the Macaque Brain Acquired by Predicting Missing Links. Cereb Cortex 2020; 30:4771-4789. [PMID: 32313935 PMCID: PMC7391281 DOI: 10.1093/cercor/bhaa060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 01/21/2023] Open
Abstract
As a substrate for function, large-scale brain structural networks are crucial for fundamental and systems-level understanding of primate brains. However, it is challenging to acquire a complete primate whole-brain structural connectome using track tracing techniques. Here, we acquired a weighted brain structural network across 91 cortical regions of a whole macaque brain hemisphere with a connectivity density of 59% by predicting missing links from the CoCoMac-based binary network with a low density of 26.3%. The prediction model combines three factors, including spatial proximity, topological similarity, and cytoarchitectural similarity-to predict missing links and assign connection weights. The model was tested on a recently obtained high connectivity density yet partial-coverage experimental weighted network connecting 91 sources to 29 target regions; the model showed a prediction sensitivity of 74.1% in the predicted network. This predicted macaque hemisphere-wide weighted network has module segregation closely matching functional domains. Interestingly, the areas that act as integrators linking the segregated modules are mainly distributed in the frontoparietal network and correspond to the regions with large wiring costs in the predicted weighted network. This predicted weighted network provides a high-density structural dataset for further exploration of relationships between structure, function, and metabolism in the primate brain.
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Affiliation(s)
- Yuhan Chen
- National Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing 100875, China
- Department of Physics, Centre for Nonlinear Studies, and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong
| | - Zi-Ke Zhang
- College of Media and International Culture, Zhejiang University, Hangzhou 310058, China
- Alibaba Research Center for Complex Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yong He
- National Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China
- Beijing Key Laboratory of Brain Imaging and Connectomics, Beijing Normal University, Beijing 100875, China
| | - Changsong Zhou
- Department of Physics, Centre for Nonlinear Studies, and Beijing-Hong Kong-Singapore Joint Centre for Nonlinear and Complex Systems (Hong Kong), Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong
- Department of Physics, Zhejiang University, Hangzhou 310027, China
- Research Centre, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China
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Sasseron GR, Benchimol-Reis LL, Perseguini JMKC, Paulino JFC, Bajay MM, Carbonell SAM, Chiorato AF. Fusarium oxysporum f. sp. phaseoli genetic variability assessed by new developed microsatellites. Genet Mol Biol 2020; 43:e20190267. [PMID: 32478796 PMCID: PMC7263423 DOI: 10.1590/1678-4685-gmb-2019-0267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 03/11/2020] [Indexed: 11/22/2022] Open
Abstract
Fusarium oxysporum f. sp. phaseoli (Fop) J.B. Kendrich & W.C. Snyder is the causal agent of Fusarium wilt of common bean (Phaseolus vulgaris L.). The objective of this study was to develop microsatellite markers (SSRs) to characterize the genetic diversity of Fop. Two libraries enriched with SSRs were developed and a total of 40 pairs of SSRs were characterized. Out of these, 15 SSRs were polymorphic for 42 Fop isolates. The number of alleles varied from two to ten, with an average of four alleles per locus and an average PIC (Polymorphic Information Content) of 0.38. The genetic diversity assessed by microsatellites for Fop was low, as expected for an asexual fungus, and not associated with geographic origin, but they were able to detect enough genetic variability among isolates in order to differentiate them. Microsatellites are a robust tool widely used for genetic fingerprinting and population structure analyses. SSRs for Fop may be an efficient tool for a better understanding of the ecology, epidemiology and evolution of this pathogen.
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Affiliation(s)
- Graziéle R Sasseron
- Instituto Agrônomico (IAC), Centro de Pesquisa em Recursos Genéticos, Campinas, SP, Brazil
| | | | | | - Jean Fausto C Paulino
- Instituto Agrônomico (IAC), Centro de Pesquisa em Recursos Genéticos, Campinas, SP, Brazil
| | - Miklos M Bajay
- Universidade do Estado de Santa Catarina (UDESC), Centro de Educação Superior da Região Sul da (CERES), Departamento de Engenharia de Pesca e Ciências Biológicas (DEPB), Laguna, SC, Brazil
| | - Sérgio A M Carbonell
- Instituto Agrônomico (IAC), Centro de Análise e Pesquisa Tecnológica do Agronegócio dos Grãos e Fibras, Campinas, SP, Brazil
| | - Alisson F Chiorato
- Instituto Agrônomico (IAC), Centro de Análise e Pesquisa Tecnológica do Agronegócio dos Grãos e Fibras, Campinas, SP, Brazil
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Qi WH, Lu T, Zheng CL, Jiang XM, Jie H, Zhang XY, Yue BS, Zhao GJ. Distribution patterns of microsatellites and development of its marker in different genomic regions of forest musk deer genome based on high throughput sequencing. Aging (Albany NY) 2020; 12:4445-4462. [PMID: 32155132 PMCID: PMC7093171 DOI: 10.18632/aging.102895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/25/2020] [Indexed: 01/21/2023]
Abstract
Forest musk deer (Moschus berezovskii, 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.
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Affiliation(s)
- Wen-Hua Qi
- 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
| | - Ting Lu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P. R. China
| | - Cheng-Li Zheng
- Sichuan Institute of Musk Deer Breeding, Chengdu 611830, P. R. China
| | - Xue-Mei Jiang
- College of Environmental and Chemistry Engineering, Chongqing Three Gorges University, Chongqing 404120, P. R. China
| | - Hang Jie
- Chongqing Engineering Technology Research Center for GAP of Genuine Medicinal Materials, Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, P. R. China
| | - Xiu-Yue Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P. R. China
| | - Bi-Song Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, P. R. China
| | - Gui-Jun Zhao
- Chongqing Engineering Technology Research Center for GAP of Genuine Medicinal Materials, Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, P. R. China
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Li TT, Tang B, Bai X, Wang XL, Luo XN, Yan HB, Zhu HF, Jia H, Liu XL, Liu MY. Development of genome-wide polymorphic microsatellite markers for Trichinella spiralis. Parasit Vectors 2020; 13:58. [PMID: 32046770 PMCID: PMC7014596 DOI: 10.1186/s13071-020-3929-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/03/2020] [Indexed: 02/05/2023] Open
Abstract
Background Trichinella nematodes are globally distributed food-borne pathogens, in which Trichinella spiralis is the most common species in China. Microsatellites are a powerful tool in population genetics and phylogeographic analysis. However, only a few microsatellite markers were reported in T. spiralis. Thus, there is a need to develop and validate genome-wide microsatellite markers for T. spiralis. Methods Microsatellites were selected from shotgun genomic sequences using MIcroSAtellite identification tool (MISA). The identified markers were validated in 12 isolates of T. spiralis in China. Results A total of 93,140 microsatellites were identified by MISA from 9267 contigs in T. spiralis genome sequences, in which 16 polymorphic loci were selected for validation by PCR with single larvae from 12 isolates of T. spiralis in China. There were 7–19 alleles per locus (average 11.25 alleles per locus). The observed heterozygosity (HO) and expected heterozygosity (HE) ranged from 0.325 to 0.750 and 0.737 to 0.918, respectively. The polymorphism information content (PIC) ranged from 0.719 to 0.978 (average 0.826). Among the 16 loci, markers for 10 loci could be amplified from all 12 international standard strains of Trichinella spp. Conclusions Sixteen highly polymorphic markers were selected and validated for T. spiralis. Primary phylogenetic analysis showed that these markers might serve as a useful tool for genetic studies of Trichinella parasites.![]()
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Affiliation(s)
- Ting-Ting Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Bin Tang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue-Lin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue-Nong Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong-Fei Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Hong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Xiao-Lei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
| | - Ming-Yuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, People's Republic of China.
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Abstract
AbstractMicrosatellites or simple sequence repeats (SSRs) are among the genetic markers most widely utilized in research. This includes applications in numerous fields such as genetic conservation, paternity testing, and molecular breeding. Though ordered draft genome assemblies of camels have been announced, including for the Arabian camel, systemic analysis of camel SSRs is still limited. The identification and development of informative and robust molecular SSR markers are essential for marker assisted breeding programs and paternity testing. Here we searched and compared perfect SSRs with 1–6 bp nucleotide motifs to characterize microsatellites for draft genome sequences of the Camelidae. We analyzed and compared the occurrence, relative abundance, relative density, and guanine-cytosine (GC) content in four taxonomically different camelid species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. A total of 546762, 544494, 547974, and 437815 SSRs were mined, respectively. Mononucleotide SSRs were the most frequent in the four genomes, followed in descending order by di-, tetra-, tri-, penta-, and hexanucleotide SSRs. GC content was highest in dinucleotide SSRs and lowest in mononucleotide SSRs. Our results provide further evidence that SSRs are more abundant in noncoding regions than in coding regions. Similar distributions of microsatellites were found in all four species, which indicates that the pattern of microsatellites is conserved in family Camelidae.
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Dunn MJ, Anderson MZ. To Repeat or Not to Repeat: Repetitive Sequences Regulate Genome Stability in Candida albicans. Genes (Basel) 2019; 10:genes10110866. [PMID: 31671659 PMCID: PMC6896093 DOI: 10.3390/genes10110866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/15/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022] Open
Abstract
Genome instability often leads to cell death but can also give rise to innovative genotypic and phenotypic variation through mutation and structural rearrangements. Repetitive sequences and chromatin architecture in particular are critical modulators of recombination and mutability. In Candida albicans, four major classes of repeats exist in the genome: telomeres, subtelomeres, the major repeat sequence (MRS), and the ribosomal DNA (rDNA) locus. Characterization of these loci has revealed how their structure contributes to recombination and either promotes or restricts sequence evolution. The mechanisms of recombination that give rise to genome instability are known for some of these regions, whereas others are generally unexplored. More recent work has revealed additional repetitive elements, including expanded gene families and centromeric repeats that facilitate recombination and genetic innovation. Together, the repeats facilitate C. albicans evolution through construction of novel genotypes that underlie C. albicans adaptive potential and promote persistence across its human host.
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Affiliation(s)
- Matthew J. Dunn
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | - Matthew Z. Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +614-247-0058
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Varady ES, Bodaghi S, Vidalakis G, Douhan GW. Microsatellite characterization and marker development for the fungus Penicillium digitatum, causal agent of green mold of citrus. Microbiologyopen 2019; 8:e00788. [PMID: 30697963 PMCID: PMC6612547 DOI: 10.1002/mbo3.788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 01/24/2023] Open
Abstract
Penicillium digitatum is one of the most important postharvest pathogens of citrus on a global scale causing significant annual losses due to fruit rot. However, little is known about the diversity of P. digitatum populations. The genome of P. digitatum has been sequenced, providing an opportunity to determine the microsatellite distribution within P. digitatum to develop markers that could be valuable tools for studying the population biology of this pathogen. In the analyses, a total of 3,134 microsatellite loci were detected; 66.73%, 23.23%, 8.23%, 1.24%, 0.16%, and 0.77% were detected as mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats, respectively. As consistent with other ascomycete fungi, the genome size of P. digitatum does not seem to correlate with the density of microsatellite loci. However, significantly longer motifs of mono-, di-, and tetranucleotide repeats were identified in P. digitatum compared to 10 other published ascomycete species with repeats of over 800, 300, and 900 motifs found, respectively. One isolate from southern California and five additional isolates from other countries ("global isolates") were used to initially screen microsatellite markers developed in this study. Twelve additional isolates, referred to as the "local isolates," were also collected from citrus at the University of California Riverside agricultural experiment station and were subsequently used to screen the primers that sequenced well and were polymorphic based on the global isolates. Thirty-six primers were screened, and nine trinucleotide loci and one hexanucleotide locus were chosen as robust markers. These loci yielded two to seven alleles and will be useful to study population genetic structure of P. digitatum populations.
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Affiliation(s)
- Erika S. Varady
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCalifornia
- Department of Molecular Biology and BiochemistryUniversity of California IrvineIrvineCalifornia
| | - Sohrab Bodaghi
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCalifornia
| | - Georgios Vidalakis
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCalifornia
| | - Greg W. Douhan
- University of California Cooperative ExtensionTulareCalifornia
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Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00264-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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30
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Lelwala RV, Korhonen PK, Young ND, Scott JB, Ades PK, Gasser RB, Taylor PWJ. Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti. PLoS One 2019; 14:e0212248. [PMID: 31150449 PMCID: PMC6544218 DOI: 10.1371/journal.pone.0212248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/02/2019] [Indexed: 01/30/2023] Open
Abstract
Colletotrichum tanaceti is an emerging foliar fungal pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium). Despite being reported consistently from field surveys in Australia, the molecular basis of pathogenicity of C. tanaceti on pyrethrum is unknown. Herein, the genome of C. tanaceti (isolate BRIP57314) was assembled de novo and annotated using transcriptomic evidence. The inferred putative pathogenicity gene suite of C. tanaceti comprised a large array of genes encoding secreted effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its putative pathogenicity gene profiles with those of closely related species suggested that C. tanaceti likely has additional hosts to pyrethrum. The genome of C. tanaceti had a high repeat content and repetitive elements were located significantly closer to genes inferred to influence pathogenicity than other genes. These repeats are likely to have accelerated mutational and transposition rates in the genome, resulting in a rapid evolution of certain CAZyme families in this species. The C. tanaceti genome showed strong signals of Repeat Induced Point (RIP) mutation which likely caused its bipartite nature consisting of distinct gene-sparse, repeat and A-T rich regions. Pathogenicity genes within these RIP affected regions were likely to have a higher evolutionary rate than the rest of the genome. This "two-speed" genome phenomenon in certain Colletotrichum spp. was hypothesized to have caused the clustering of species based on the pathogenicity genes, to deviate from taxonomic relationships. The large repertoire of pathogenicity factors that potentially evolve rapidly due to the plasticity of the genome, indicated that C. tanaceti has a high evolutionary potential. Therefore, C. tanaceti poses a high-risk to the pyrethrum industry. Knowledge of the evolution and diversity of the putative pathogenicity genes will facilitate future research in disease management of C. tanaceti and other Colletotrichum spp.
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Affiliation(s)
- Ruvini V. Lelwala
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jason B. Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia
| | - Peter K. Ades
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul W. J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Du XH, Wang H, Sun J, Xiong L, Yu J. Hybridization, characterization and transferability of SSRs in the genus Morchella. Fungal Biol 2019; 123:528-538. [PMID: 31196522 DOI: 10.1016/j.funbio.2019.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/18/2019] [Accepted: 05/03/2019] [Indexed: 11/25/2022]
Abstract
Recently, Morchella importuna, M. sextelata, M. eximia, M. exuberans, Mel-13, and Mel-21 have been successfully cultivated in China and planting areas rapidly expanded because of their economic importance. Effective molecular markers are urgently needed for accurately identifying morel cultivars. Microsatellites are widely utilized for strain authentication in many fungal groups. To our knowledge, for the first time we characterized the distribution of microsatellites (simple sequence repeats, SSRs) in the M. importuna genome with 12902 SSRs and reported the first set of SSRs developed for Morchella species. Mono-nucleotides (66.2 %) were the most frequent motifs, followed by tri- (15.4 %), di- (12.1 %), tetra- (3.7 %), penta- (1.3 %) and hexa-nucleotides (1.3 %). We tested the cross-species amplification of 180 SSRs on 24 samples from the six species and high cross-species transferability of SSRs (87.7 %) was found. Among twenty-two microsatellites selected for genetic diversity analysis on 127 samples from the six species, fifteen to twenty polymorphic loci were identified in M. importuna, M. sextelata, M. eximia, M. exuberans, Mel-13 and Mel-21. Interspecific hybridization events were detected among morel species, indicating the potential application of morel crossbreeding. Ninety-one cultivated samples were characterized as new cultivars with different genotypes, but cultivar names used for these by farmers was confusing, with misnaming, synonyms and homonyms. Our results are not only helpful for cultivar identification and morel breeding programs in China, but also provide molecular tools for genetic studies in morels.
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Affiliation(s)
- Xi-Hui Du
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.
| | - Hanchen Wang
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Jingjing Sun
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Lunyi Xiong
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
| | - Jingjing Yu
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China
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Li D, Zhang H, Peng S, Pan S, Tan Z. Conserved microsatellites may contribute to stem-loop structures in 5', 3' terminals of Ebolavirus genomes. Biochem Biophys Res Commun 2019; 514:726-733. [PMID: 31078274 PMCID: PMC7092875 DOI: 10.1016/j.bbrc.2019.04.192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/25/2019] [Accepted: 04/28/2019] [Indexed: 12/12/2022]
Abstract
Microsatellites (SSRs) are ubiquitous in coding and non-coding regions of the Ebolavirus genomes. We synthetically analyzed the microsatellites in whole-genome and terminal regions of 219 Ebolavirus genomes from five species. The Ebolavirus sequences were observed with small intraspecies variations and large interspecific variations, especially in the terminal non-coding regions. Only five conserved microsatellites were detected in the complete genomes, and four of them which well base-paired to help forming conserved stem-loop structures mainly appeared in the terminal non-coding regions. These results suggest that the conserved microsatellites may be evolutionary selected to form conserved secondary structures in 5′, 3′ terminals of Ebolavirus genomes. It may help to understand the biological significance of microsatellites in Ebolavirus and also other virus genomes. Conserved microsatellites mainly occurred in 5′, 3′ terminal non-coding regions. Conserved microsatellites may contribute to conserved stem-loop structures. Conserved microsatellites might be preserved under greater evolutionary pressure.
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Affiliation(s)
- Douyue Li
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Hongxi Zhang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Shan Peng
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Saichao Pan
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Zhongyang Tan
- Bioinformatics Center, College of Biology, Hunan University, Changsha, China.
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Alam CM, Iqbal A, Sharma A, Schulman AH, Ali S. Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family. Front Genet 2019; 10:207. [PMID: 30923537 PMCID: PMC6426759 DOI: 10.3389/fgene.2019.00207] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 02/26/2019] [Indexed: 01/21/2023] Open
Abstract
The incidence, distribution, and variation of simple sequence repeats (SSRs) in viruses is instrumental in understanding the functional and evolutionary aspects of repeat sequences. Full-length genome sequences retrieved from NCBI were used for extraction and analysis of repeat sequences using IMEx software. We have also developed two MATLAB-based tools for extraction of gene locations from GenBank in tabular format and simulation of this data with SSR incidence data. Present study encompassing 147 Mycobacteriophage genomes revealed 25,284 SSRs and 1,127 compound SSRs (cSSRs) through IMEx. Mono- to hexa-nucleotide motifs were present. The SSR count per genome ranged from 78 (M100) to 342 (M58) while cSSRs incidence ranged from 1 (M138) to 17 (M28, M73). Though cSSRs were present in all the genomes, their frequency and SSR to cSSR conversion percentage varied from 1.08 (M138 with 93 SSRs) to 8.33 (M116 with 96 SSRs). In terms of localization, the SSRs were predominantly localized to coding regions (∼78%). Interestingly, genomes of around 50 kb contained a similar number of SSRs/cSSRs to that in a 110 kb genome, suggesting functional relevance for SSRs which was substantiated by variation in motif constitution between species with different host range. The three species with broad host range (M97, M100, M116) have around 90% of their mono-nucleotide repeat motifs composed of G or C and only M16 has both A and T mononucleotide motifs. Around 20% of the di-nucleotide repeat motifs in the genomes exhibiting a broad host range were CT/TC, which were either absent or represented to a much lesser extent in the other genomes.
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Affiliation(s)
- Chaudhary Mashhood Alam
- Luke/BI Plant Genome Dynamics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Ingenious e-Brain Solutions, Gurugram, India
| | - Asif Iqbal
- PIRO Technologies Private Limited, New Delhi, India
| | - Anjana Sharma
- Department of Biomedical Sciences, SRCASW, University of Delhi, New Delhi, India
| | - Alan H Schulman
- Luke/BI Plant Genome Dynamics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Safdar Ali
- Department of Biomedical Sciences, SRCASW, University of Delhi, New Delhi, India.,Department of Biological Sciences, Aliah University, Kolkata, India
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Bhat NN, Mahiya-Farooq, Padder BA, Shah M, Dar M, Nabi A, Bano A, Rasool RS, Sana-Surma. Microsatellite mining in the genus Colletotrichum. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Knight NL, Vaghefi N, Hansen ZR, Kikkert JR, Pethybridge SJ. Temporal Genetic Differentiation of Cercospora beticola Populations in New York Table Beet Fields. PLANT DISEASE 2018; 102:2074-2082. [PMID: 30156961 DOI: 10.1094/pdis-01-18-0175-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Annual epidemics of Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, can result in substantial defoliation in table beet fields in New York. High allelic and genotypic diversity have been described within C. beticola populations; however, information on the temporal stability of populations is lacking. C. beticola isolates were obtained from symptomatic leaves in three table beet fields in successive years. Two of the fields were organic mixed-cropping farms and the third was managed conventionally in a broad-acre cropping system. C. beticola isolates (n = 304) were genotyped using 12 microsatellite markers. Genotypic diversity (Simpson's complement index = 0.178 to 0.990), allele frequencies, and indices of differentiation between years varied. Pairwise index of differentiation values ranged from 0.02 to 0.25 for clone-corrected data, and indicated significant genetic differentiation at Farm 2. No multilocus genotype was shared between years. The shift in multilocus genotypes between years questions the role of clonally reproducing primary inoculum. Collectively, these results suggest that a dominant inoculum source for initiating annual CLS epidemics is external to the field of interest. These findings have implications for CLS disease management in conventional and organic table beet production.
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Affiliation(s)
- Noel L Knight
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Niloofar Vaghefi
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Zachariah R Hansen
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | | | - Sarah J Pethybridge
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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Rao S, Sharda S, Oddi V, Nandineni MR. The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum. Front Microbiol 2018; 9:2367. [PMID: 30337918 PMCID: PMC6180176 DOI: 10.3389/fmicb.2018.02367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Saphy Sharda
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Qi WH, Jiang XM, Yan CC, Zhang WQ, Xiao GS, Yue BS, Zhou CQ. Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes. Sci Rep 2018; 8:14407. [PMID: 30258087 PMCID: PMC6158176 DOI: 10.1038/s41598-018-32286-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/04/2018] [Indexed: 01/23/2023] Open
Abstract
As the first examination of distribution, guanine-cytosine (GC) pattern, and variation analysis of microsatellites (SSRs) in different genomic regions of six bovid species, SSRs displayed nonrandomly distribution in different regions. SSR abundances are much higher in the introns, transposable elements (TEs), and intergenic regions compared to the 3′-untranslated regions (3′UTRs), 5′UTRs and coding regions. Trinucleotide perfect SSRs (P-SSRs) were the most frequent in the coding regions, whereas, mononucleotide P-SSRs were the most in the introns, 3′UTRs, TEs, and intergenic regions. Trifold P-SSRs had more GC-contents in the 5′UTRs and coding regions than that in the introns, 3′UTRs, TEs, and intergenic regions, whereas mononucleotide P-SSRs had the least GC-contents in all genomic regions. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs showed significantly different distributions in different regions (P < 0.01). Except for the coding regions, mononucleotide P-SSRs had the most RCNs, followed by the pattern: di- > tri- > tetra- > penta- > hexanucleotide P-SSRs in the same regions. The analysis of coefficient of variability (CV) of SSRs showed that the CV variations of RCN of the same mono- to hexanucleotide SSRs were relative higher in the intronic and intergenic regions, followed by the CV variation of RCN in the TEs, and the relative lower was in the 5′UTRs, 3′UTRs, and coding regions. Wide SSR analysis of different genomic regions has helped to reveal biological significances of their distributions.
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Affiliation(s)
- Wen-Hua Qi
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404100, P. R. China
| | - Xue-Mei Jiang
- College of Environmental and Chemistry Engineering, Chongqing Three Gorges University, Chongqing, 404100, P. R. China
| | - Chao-Chao Yan
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Wan-Qing Zhang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan Province, 625014, P. R. China
| | - Guo-Sheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404100, P. R. China
| | - Bi-Song Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Cai-Quan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, P. R. China.
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la Bastide PYD, Naumann C, Hintz WE. Assessment of intra-specific variability in Saprolegnia parasitica populations of aquaculture facilities in British Columbia, Canada. DISEASES OF AQUATIC ORGANISMS 2018; 128:235-248. [PMID: 29862981 DOI: 10.3354/dao03224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Among the Saprolegnia species found in aquaculture facilities, S. parasitica is recognized as the primary fish pathogen and remains an ongoing concern in fish health management. Until recently, these pathogens were kept in check by use of malachite green; due to its toxicity, this chemical has now been banned from use in many countries. It is difficult to predict and control S. parasitica outbreaks in freshwater systems and there is a need to understand the population genetic structure of this pathogen. Genetic characterization of this species in aquaculture systems would provide information to track introductions and determine possible sources of inoculum. Degenerate PCR primers containing short sequence repeats were used to create microsatellite-associated genetic markers (random amplified microsatellites) for the comparison of S. parasitica isolates collected primarily from commercial Atlantic salmon aquaculture systems in British Columbia, Canada, over a 15 mo period to describe their spatial and temporal variability. The frequencies of amplified products were compared and the population genetic diversity was measured using Nei's genetic distance and Shannon's information index, while the species population structure was evaluated by phylogenetic analysis. S. parasitica was detected in all facilities sampled. Genetic diversity was low but not clonal, most likely due to repeated introduction events and a low level of sexual recombination over time. A better understanding of pathogen population structure will assist the development of effective preventative measures and targeted treatments for disease outbreaks.
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Affiliation(s)
- Paul Y de la Bastide
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
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Manawasinghe IS, Zhang W, Li X, Zhao W, Chethana K, Xu J, Chen Z, Dissanayaka AJ, Mugnai L, Úrbez-Torres JR, Savocchia S, Hyde KD, Yan J. Novel microsatellite markers reveal multiple origins of Botryosphaeria dothidea causing the Chinese grapevine trunk disease. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Zeng Z, Sun H, Vainio EJ, Raffaello T, Kovalchuk A, Morin E, Duplessis S, Asiegbu FO. Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors. BMC Genomics 2018; 19:220. [PMID: 29580224 PMCID: PMC5870257 DOI: 10.1186/s12864-018-4610-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species. RESULTS To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates. CONCLUSION Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence.
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Affiliation(s)
- Zhen Zeng
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Hui Sun
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Eeva J. Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Emmanuelle Morin
- INRA UMR 1136 Interactions Arbres Micro-organismes, INRA Centre Grand Est Nancy, Champenoux, France
| | - Sébastien Duplessis
- INRA UMR 1136 Interactions Arbres Micro-organismes, INRA Centre Grand Est Nancy, Champenoux, France
- UMR 1136 Interactions Arbres/Microorganismes, Faculté des Sciences et Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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Franco ME, Bitencourt TA, Marins M, Fachin AL. In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866792. [PMID: 29220431 PMCID: PMC5502367 DOI: 10.1093/database/bax035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/28/2017] [Indexed: 01/01/2023]
Abstract
Trichophyton rubrum is the most common etiological agent of dermatophytoses worldwide, which is able to degrade keratinized tissues. The sequencing of the genome of different dermatophyte species has provided a large amount of data, including tandem repeats that may play a role in genetic variability and in the pathogenesis of these fungi. Tandem repeats are adjacent DNA sequences of 2–200 nucleotides in length, which exert regulatory and adaptive functions. These repetitive DNA sequences are found in different classes of fungal proteins, especially those involved in cell adhesion, a determinant factor for the establishment of fungal infection. The objective of this study was to develop a Dermatophyte Tandem Repeat Database (DTRDB) for the storage and identification of tandem repeats in T. rubrum and six other dermatophyte species. The current version of the database contains 35 577 tandem repeats detected in 16 173 coding sequences. The repeats can be searched using entry parameters such as repeat unit length (nt—nucleotide), repeat number, variability score, and repeat sequence motif. These data were used to study the relative frequency and distribution of repeats in the sequences, as well as their possible functions in dermatophytes. A search of the database revealed that these repeats occur in 22–33% of genes transcribed in dermatophytes where they could be involved in the success of adaptation to the host tissue and establishment of infection. The repeats were detected in transcripts that are mainly related to three biological processes: regulation, adhesion, and metabolism. The database developed enables users to identify and analyse tandem repeat regions in target genes related to pathogenicity and fungal–host interactions in dermatophytes and may contribute to the discovery of new targets for the development of antifungal agents. Database URL:http://comp.mch.ifsuldeminas.edu.br/dtrdb/
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Affiliation(s)
- Matheus Eloy Franco
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Federal Institute of Education, Science and Technology of South of Minas Gerais - IFSULDEMINAS, 37750-000, Brazil
| | - Tamires Aparecida Bitencourt
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Departamento de Genetica, 049-900, FMRP-USP, SP, Brazil
| | - Mozart Marins
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Curso de Medicina, Universidade de Ribeirão Preto, SP, Brazil
| | - Ana Lúcia Fachin
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Av: Costabile Romano 2201, 14096-900, Ribeirao Preto SP, Brazil.,Curso de Medicina, Universidade de Ribeirão Preto, SP, Brazil
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Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes. Aging (Albany NY) 2017; 8:2635-2654. [PMID: 27644032 PMCID: PMC5191860 DOI: 10.18632/aging.101025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/22/2016] [Indexed: 01/23/2023]
Abstract
As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5'UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3'UTRs, TEs, and intergenic regions. The GC-contents varied greatly among different intragenic and intergenic regions: 5'UTRs > CDSs > 3'UTRs > TEs > introns > intergenic regions, and high GC-content was frequently distributed in exon-rich regions. Our results also showed that in the same intragenic and intergenic regions, the distribution of GC-contents were great similarity in the different primates. Tri- and hexanucleotide P-SSRs had the most GC-contents in the 5'UTRs and CDSs, whereas mononucleotide P-SSRs had the least GC-contents in the six genomic regions of these primates. The most frequent motifs for different length varied obviously with the different genomic regions.
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Abd Murad NB, Mohamed Nor NMI, Shohaimi S, Mohd Zainudin NAI. Genetic diversity and pathogenicity of Fusarium species associated with fruit rot disease in banana across Peninsular Malaysia. J Appl Microbiol 2017; 123:1533-1546. [PMID: 28891270 DOI: 10.1111/jam.13582] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 08/22/2017] [Accepted: 08/28/2017] [Indexed: 11/26/2022]
Abstract
AIMS The aims of this study were to identify the Fusarium isolates based on translation elongation factor (tef) 1α sequence, to determine the genetic diversity among isolates and species using selected microsatellite markers and to examine the pathogenicity of Fusarium isolates causing fruit rot disease of banana. METHODS AND RESULTS One-hundred and thirteen microfungi isolates were obtained from fruit rot infected banana in Peninsular Malaysia. However, this study was focused on the dominant number of the discovered microfungi that belongs to the genus Fusarium; 48 isolates of the microfungi have been identified belonging to 11 species of Fusarium, namely Fusarium incarnatum, Fusarium equiseti, Fusarium camptoceras, Fusarium solani, Fusarium concolor, Fusarium oxysporum, Fusarium proliferatum, Fusarium verticillioides, Fusarium sacchari, Fusarium concentricum and Fusarium fujikuroi. All Fusarium isolates were grouped into their respective clades indicating their similarities and differences in genetic diversity among isolates. Out of 48 Fusarium isolates tested, 42 isolates caused the fruit rot symptom at different levels of severity based on Disease Severity Index (DSI). The most virulent isolate was F. proliferatum B2433B with DSI of 100%. CONCLUSIONS All the isolated Fusarium species were successfully identified and some of them were confirmed as the causal agents of pre- and postharvest fruit rot in banana across Peninsular Malaysia. SIGNIFICANCE AND IMPACT OF THE STUDY Our results will provide additional information regarding new report of Fusarium species in causing banana fruit rot and in the search of potential biocontrol agent of the disease.
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Affiliation(s)
- N B Abd Murad
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - N M I Mohamed Nor
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Pulau Pinang, Malaysia
| | - S Shohaimi
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - N A I Mohd Zainudin
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Neu E, Featherston J, Rees J, Debener T. A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication. PLoS One 2017; 12:e0185310. [PMID: 28981525 PMCID: PMC5628827 DOI: 10.1371/journal.pone.0185310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus. RESULTS The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs. CONCLUSIONS The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen.
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Affiliation(s)
- Enzo Neu
- Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Jonathan Featherston
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
| | - Jasper Rees
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, South Africa
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz University Hannover, Hannover, Germany
- * E-mail:
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Kang X, Hu L, Shen P, Li R, Liu D. SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis. Front Microbiol 2017; 8:1422. [PMID: 28798740 PMCID: PMC5529405 DOI: 10.3389/fmicb.2017.01422] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/13/2017] [Indexed: 11/24/2022] Open
Abstract
Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis, with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3, 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis, and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.
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Affiliation(s)
- Xincong Kang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural UniversityChangsha, China
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
| | - Liqin Hu
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
| | - Pengyuan Shen
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
| | - Rui Li
- Nextomics BiosciencesWuhan, China
| | - Dongbo Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural UniversityChangsha, China
- Horticulture and Landscape College, Hunan Agricultural UniversityChangsha, China
- State Key Laboratory of Subhealth Intervention TechnologyChangsha, China
- Hunan Co-Innovation Center for Utilization of Botanical Functional IngredientsChangsha, China
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Genetic Variation and Its Reflection on Posttranslational Modifications in Frequency Clock and Mating Type a-1 Proteins in Sordaria fimicola. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1268623. [PMID: 28717646 PMCID: PMC5499255 DOI: 10.1155/2017/1268623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/24/2017] [Accepted: 04/05/2017] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) occur in all essential proteins taking command of their functions. There are many domains inside proteins where modifications take place on side-chains of amino acids through various enzymes to generate different species of proteins. In this manuscript we have, for the first time, predicted posttranslational modifications of frequency clock and mating type a-1 proteins in Sordaria fimicola collected from different sites to see the effect of environment on proteins or various amino acids pickings and their ultimate impact on consensus sequences present in mating type proteins using bioinformatics tools. Furthermore, we have also measured and walked through genomic DNA of various Sordaria strains to determine genetic diversity by genotyping the short sequence repeats (SSRs) of wild strains of S. fimicola collected from contrasting environments of two opposing slopes (harsh and xeric south facing slope and mild north facing slope) of Evolution Canyon (EC), Israel. Based on the whole genome sequence of S. macrospora, we targeted 20 genomic regions in S. fimicola which contain short sequence repeats (SSRs). Our data revealed genetic variations in strains from south facing slope and these findings assist in the hypothesis that genetic variations caused by stressful environments lead to evolution.
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Iquebal MA, Tomar RS, Parakhia MV, Singla D, Jaiswal S, Rathod VM, Padhiyar SM, Kumar N, Rai A, Kumar D. Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence. Sci Rep 2017; 7:5299. [PMID: 28706242 PMCID: PMC5509663 DOI: 10.1038/s41598-017-05478-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/30/2017] [Indexed: 12/24/2022] Open
Abstract
Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25–80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Rukam S Tomar
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - M V Parakhia
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - Deepak Singla
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - V M Rathod
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - S M Padhiyar
- Junagadh Agricultural University, Junagadh, 362 001, Gujarat, India
| | - Neeraj Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India.
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Schizosaccharomyces pombe MutSα and MutLα Maintain Stability of Tetra-Nucleotide Repeats and Msh3 of Hepta-Nucleotide Repeats. G3-GENES GENOMES GENETICS 2017; 7:1463-1473. [PMID: 28341698 PMCID: PMC5427490 DOI: 10.1534/g3.117.040816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Defective mismatch repair (MMR) in humans is associated with colon cancer and instability of microsatellites, that is, DNA sequences with one or several nucleotides repeated. Key factors of eukaryotic MMR are the heterodimers MutSα (Msh2-Msh6), which recognizes base-base mismatches and unpaired nucleotides in DNA, and MutLα (Mlh1-Pms1), which facilitates downstream steps. In addition, MutSβ (Msh2-Msh3) recognizes DNA loops of various sizes, although our previous data and the data presented here suggest that Msh3 of Schizosaccharomyces pombe does not play a role in MMR. To test microsatellite stability in S. pombe and hence DNA loop repair, we have inserted tetra-, penta-, and hepta-nucleotide repeats in the ade6 gene and determined their Ade+ reversion rates and spectra in wild type and various mutants. Our data indicate that loops with four unpaired nucleotides in the nascent and the template strand are the upper limit of MutSα- and MutLα-mediated MMR in S. pombe Stability of hepta-nucleotide repeats requires Msh3 and Exo1 in MMR-independent processes as well as the DNA repair proteins Rad50, Rad51, and Rad2FEN1 Most strikingly, mutation rates in the double mutants msh3 exo1 and msh3 rad51 were decreased when compared to respective single mutants, indicating that Msh3 prevents error prone processes carried out by Exo1 and Rad51. We conclude that Msh3 has no obvious function in MMR in S. pombe, but contributes to DNA repeat stability in MMR-independent processes.
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Duan X, Wang K, Su S, Tian R, Li Y, Chen M. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae). PLoS One 2017; 12:e0172513. [PMID: 28212394 PMCID: PMC5315398 DOI: 10.1371/journal.pone.0172513] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/05/2017] [Indexed: 11/21/2022] Open
Abstract
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.
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Affiliation(s)
- Xinle Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China.,College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Sha Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ruizheng Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yuting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
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50
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Liu S, Hou W, Sun T, Xu Y, Li P, Yue B, Fan Z, Li J. Genome-wide mining and comparative analysis of microsatellites in three macaque species. Mol Genet Genomics 2017; 292:537-550. [PMID: 28160080 DOI: 10.1007/s00438-017-1289-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/09/2017] [Indexed: 12/13/2022]
Abstract
Microsatellites are found in taxonomically different organisms, and such repeats are related with genomic structure, function and certain diseases. To characterize microsatellites for macaques, we searched and compared SSRs with 1-6 bp nucleotide motifs in rhesus, cynomolgus and pigtailed macaque. A total of 1395671, 1284929 and 1266348 perfect SSRs were mined, respectively. The most frequent perfect SSRs were mononucleotide SSRs. The most GC-content was in dinucleotide SSRs and the least was in the mononucleotide SSRs. Chromosome size was positively correlated with SSR number and negatively correlated with the relative frequency and density of SSRs. The GC content of chromosome SSRs were negatively correlated with relative frequency of SSRs and GC content of chromosome sequences. The features of microsatellite distribution in assembled genomes of the three species were greatly similar, which revealed that the distributional pattern of microsatellites is probably conservative in genus Macaca. The degenerated number of repeat motifs was found to be different in pentanucleotide and hexanucleotide repeats. Species-specific motifs for each macaque were significantly underrepresented. Overall, SSR frequencies of each chromosome in rhesus macaque were higher than in cynomolgus macaque. The maximum repeat times of mono- to pentanucleotide repeats in cynomolgus macaque was more than other two macaques. These results emphasize the genetic diversity and phylogenetic relationship of genus Macaca species. Our data will be beneficial for comparative genome mapping, understanding the distribution of SSRs and genome structure between these animal models, and provide a foundation for further development and identification of more macaque-specific SSRs.
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Affiliation(s)
- Sanxu Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Wei Hou
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Tianlin Sun
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yongtao Xu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Peng Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China. .,Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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