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Avvaru AK, Sharma D, Verma A, Mishra RK, Sowpati DT. MSDB: a comprehensive, annotated database of microsatellites. Nucleic Acids Res 2020; 48:D155-D159. [PMID: 31599331 PMCID: PMC6943038 DOI: 10.1093/nar/gkz886] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/28/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022] Open
Abstract
Microsatellites are short tandem repeats of 1–6 nucleotide motifs, studied for their utility as genome markers and in forensics. Recent evidence points to the role of microsatellites in important regulatory functions, and their length polymorphisms at coding regions are linked to various neurodegenerative disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and their evolution remains poorly understood. Though other databases of microsatellites exist, they fall short on several fronts. MSDB (MicroSatellite DataBase) is a collection of >4 billion microsatellites from 37 680 genomes presented in a user-friendly web portal for easy, interactive analysis and visualization. This is by far the most comprehensive, annotated, updated database to access and analyze microsatellite data of multiple species. The features of MSDB enable users to explore the data as tables that can be filtered and exported, and also as interactive charts to view and compare the data of multiple species simultaneously. Its modularity and architecture permit seamless updates with new data, making it a powerful tool and useful resource to researchers working on this important class of DNA elements, particularly in context of their evolution and emerging roles in genome organization and gene regulation.
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Affiliation(s)
- Akshay Kumar Avvaru
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad - 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
| | - Deepak Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad - 500007, India
| | - Archana Verma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad - 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad - 500007, India
| | - Divya Tej Sowpati
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad - 500007, India
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2
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Mokhtar MM, Atia MAM. SSRome: an integrated database and pipelines for exploring microsatellites in all organisms. Nucleic Acids Res 2020; 47:D244-D252. [PMID: 30365025 PMCID: PMC6323889 DOI: 10.1093/nar/gky998] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/14/2018] [Indexed: 11/23/2022] Open
Abstract
Over the past decade, many databases focusing on microsatellite mining on a genomic scale were released online with at least one of the following major deficiencies: (i) lacking the classification of microsatellites as genic or non-genic, (ii) not comparing microsatellite motifs at both genic and non-genic levels in order to identify unique motifs for each class or (iii) missing SSR marker development. In this study, we have developed ‘SSRome’ as a web-based, user-friendly, comprehensive and dynamic database with pipelines for exploring microsatellites in 6533 organisms. In the SSRome database, 158 million microsatellite motifs are identified across all taxa, in addition to all the mitochondrial and chloroplast genomes and expressed sequence tags available from NCBI. Moreover, 45.1 million microsatellite markers were developed and classified as genic or non-genic. All the stored motif and marker datasets can be downloaded freely. In addition, SSRome provides three user-friendly tools to identify, classify and compare motifs on either a genome- or transcriptome-wide scale. With the implementation of PHP, HTML and JavaScript, users can upload their data for analysis via a user-friendly GUI. SSRome represents a powerful database and mega-tool that will assist researchers in developing and dissecting microsatellite markers on a high-throughput scale.
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Affiliation(s)
- Morad M Mokhtar
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, 12619, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, 12619, Egypt
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Chakdar H, Singha A, Satya P. New Generation Markers for Fingerprinting and Structural Analysis of Fungal Community. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Agarwal P, Parida SK, Raghuvanshi S, Kapoor S, Khurana P, Khurana JP, Tyagi AK. Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India. RICE (NEW YORK, N.Y.) 2016; 9:1. [PMID: 26743769 PMCID: PMC4705060 DOI: 10.1186/s12284-015-0073-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/22/2015] [Indexed: 05/05/2023]
Abstract
Rice is one of the main pillars of food security in India. Its improvement for higher yield in sustainable agriculture system is also vital to provide energy and nutritional needs of growing world population, expected to reach more than 9 billion by 2050. The high quality genome sequence of rice has provided a rich resource to mine information about diversity of genes and alleles which can contribute to improvement of useful agronomic traits. Defining the function of each gene and regulatory element of rice remains a challenge for the rice community in the coming years. Subsequent to participation in IRGSP, India has continued to contribute in the areas of diversity analysis, transcriptomics, functional genomics, marker development, QTL mapping and molecular breeding, through national and multi-national research programs. These efforts have helped generate resources for rice improvement, some of which have already been deployed to mitigate loss due to environmental stress and pathogens. With renewed efforts, Indian researchers are making new strides, along with the international scientific community, in both basic research and realization of its translational impact.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
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5
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Yu J, Dossa K, Wang L, Zhang Y, Wei X, Liao B, Zhang X. PMDBase: a database for studying microsatellite DNA and marker development in plants. Nucleic Acids Res 2016; 45:D1046-D1053. [PMID: 27733507 PMCID: PMC5210622 DOI: 10.1093/nar/gkw906] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/11/2016] [Accepted: 10/08/2016] [Indexed: 12/22/2022] Open
Abstract
Microsatellite DNAs (or SSRs) are important genomic components involved in many important biological functions. SSRs have been extensively exploited as molecular markers for diverse applications including genetic diversity, linkage/association mapping of gene/QTL, marker-assisted selection, variety identification and evolution analysis. However, a comprehensive database or web service for studying microsatellite DNAs and marker development in plants is lacking. Here, we developed a database, PMDBase, which integrates large amounts of microsatellite DNAs from genome sequenced plant species and includes a web service for microsatellite DNAs identification. In PMDBase, 26 230 099 microsatellite DNAs were identified spanning 110 plant species. Up to three pairs of primers were supplied for every microsatellite DNA. For 81 species, genomic features of the microsatellite DNAs (genic or non-genic) were supplied with the corresponding genes or transcripts from public databases. Microsatellite DNAs can be explored through browsing and searching modules with a user-friendly web interface and customized software. Furthermore, we developed MISAweb and embedded Primer3web to help users to identify microsatellite DNAs and design corresponding primers in their own genomic sequences online. All datasets of microsatellite DNAs can be downloaded conveniently. PMDBase will be updated regularly with new available genome data and can be accessed freely via the address http://www.sesame-bioinfo.org/PMDBase.
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Affiliation(s)
- Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.,Centre d' Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Sénégal
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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6
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Sablok G, Pérez-Pulido AJ, Do T, Seong TY, Casimiro-Soriguer CS, La Porta N, Ralph PJ, Squartini A, Muñoz-Merida A, Harikrishna JA. PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers. FRONTIERS IN PLANT SCIENCE 2016; 7:878. [PMID: 27446111 PMCID: PMC4922199 DOI: 10.3389/fpls.2016.00878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/03/2016] [Indexed: 05/30/2023]
Abstract
Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intra-generic differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www.bioinfocabd.upo.es/plantssr.
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Affiliation(s)
- Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, SydneyNSW, Australia
| | - Antonio J. Pérez-Pulido
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC), Universidad Pablo de OlavideSevilla, Spain
| | - Thac Do
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, SydneyNSW, Australia
| | - Tan Y. Seong
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
| | | | - Nicola La Porta
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachTrento, Italy
- MountFOR Project Centre, European Forest InstituteTrento, Italy
- Consiglio Nazionale delle Ricerche, Istituto per la Valorizzazione del Legno e delle Specie ArboreeFlorence, Italy
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, SydneyNSW, Australia
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of PadovaPadova, Italy
| | - Antonio Muñoz-Merida
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do PortoVila do Conde, Portugal
| | - Jennifer A. Harikrishna
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
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Daware A, Das S, Srivastava R, Badoni S, Singh AK, Agarwal P, Parida SK, Tyagi AK. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1535. [PMID: 27833617 PMCID: PMC5080349 DOI: 10.3389/fpls.2016.01535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/29/2016] [Indexed: 05/05/2023]
Abstract
Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16-74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7-8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.
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Affiliation(s)
- Anurag Daware
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Sweta Das
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Ashok K. Singh
- Rice Section, Division of Genetics, Indian Agricultural Research Institute (IARI)New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR)New Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
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8
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Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK. Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnol J 2014; 9:1480-92. [PMID: 25349922 DOI: 10.1002/biot.201400063] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/02/2014] [Accepted: 10/01/2014] [Indexed: 12/30/2022]
Abstract
The transcript pool of a plant part, under any given condition, is a collection of mRNAs that will pave the way for a biochemical reaction of the plant to stimuli. Over the past decades, transcriptome study has advanced from Northern blotting to RNA sequencing (RNA-seq), through other techniques, of which real-time quantitative polymerase chain reaction (PCR) and microarray are the most significant ones. The questions being addressed by such studies have also matured from a solitary process to expression atlas and marker-assisted genetic enhancement. Not only genes and their networks involved in various developmental processes of plant parts have been elucidated, but also stress tolerant genes have been highlighted. The transcriptome of a plant with altered expression of a target gene has given information about the downstream genes. Marker information has been used for breeding improved varieties. Fortunately, the data generated by transcriptome analysis has been made freely available for ample utilization and comparison. The review discusses this wide variety of transcriptome data being generated in plants, which includes developmental stages, abiotic and biotic stress, effect of altered gene expression, as well as comparative transcriptomics, with a special emphasis on microarray and RNA-seq. Such data can be used to determine the regulatory gene networks, which can subsequently be utilized for generating improved plant varieties.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Fesenko EE, Heydarov RN, Stepanova EV, Abramov ME, Chudinov AV, Zasedatelev AS, Mikhailovich VM. Microarray with LNA-probes for genotyping of polymorphic variants of Gilbert's syndrome gene UGT1A1(TA)n. Clin Chem Lab Med 2014; 51:1177-84. [PMID: 23241680 DOI: 10.1515/cclm-2012-0656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/09/2012] [Indexed: 11/15/2022]
Abstract
BACKGROUND Gilbert's syndrome is a common metabolic dysfunction characterized by elevated levels of unconjugated bilirubin in the bloodstream. This condition is usually caused by additional (TA) insertions in a promoter region of the uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) gene, which instead of the sequence А(TА)6TАА contains А(TА)7TАА. While the condition itself is benign, it presents elevated risk for patients treated with irinotecan, a common chemotherapy drug. METHODS The technique is based on hybridization analysis of a pre-amplified segment of the UGT1A1 gene promoter performed on a microarray. Specific probes containing locked nucleic acids (LNA) were designed and immobilized on the microarray to provide accurate identification. RESULTS A microarray has been developed to identify both common and rare variants of UGT1A1(TA)n polymorphisms. In total, 108 individuals were genotyped. Out of these, 47 (43.5%) had homozygous wild-type genotypes (TA)6/(TA)6; 41(38%) were heterozygotes (TA)6/(TA)7; and 18 (16.7%)--homozygotes (TA)7/(TA)7. In two cases (1.8%), rare genotypes (TA)5/(TA)7 and (TA)5/(TA)6 were found. The results were in full agreement with the sequencing. In addition, synthetic fragments corresponding to all human allelic variants [(TA)5, (TA)6, (TA)7, (TA)8] were successfully tested. CONCLUSIONS The developed microarray-based approach for identification of polymorphic variants of the UGT1A1 gene is a promising and reliable diagnostic tool that can be successfully implemented in clinical practice.
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Isokpehi RD, Simmons SS, Cohly HHP, Ekunwe SIN, Begonia GB, Ayensu WK. Identification of drought-responsive universal stress proteins in viridiplantae. Bioinform Biol Insights 2011; 5:41-58. [PMID: 21423406 PMCID: PMC3045048 DOI: 10.4137/bbi.s6061] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Genes encoding proteins that contain the universal stress protein (USP) domain are known to provide bacteria, archaea, fungi, protozoa, and plants with the ability to respond to a plethora of environmental stresses. Specifically in plants, drought tolerance is a desirable phenotype. However, limited focused and organized functional genomic datasets exist on drought-responsive plant USP genes to facilitate their characterization. The overall objective of the investigation was to identify diverse plant universal stress proteins and Expressed Sequence Tags (ESTs) responsive to water-deficit stress. We hypothesize that cross-database mining of functional annotations in protein and gene transcript bioinformatics resources would help identify candidate drought-responsive universal stress proteins and transcripts from multiple plant species. Our bioinformatics approach retrieved, mined and integrated comprehensive functional annotation data on 511 protein and 1561 ESTs sequences from 161 viridiplantae taxa. A total of 32 drought-responsive ESTs from 7 plant genera Glycine, Hordeum, Manihot, Medicago, Oryza, Pinus and Triticum were identified. Two Arabidopsis USP genes At3g62550 and At3g53990 that encode ATP-binding motif were up-regulated in a drought microarray dataset. Further, a dataset of 80 simple sequence repeats (SSRs) linked to 20 singletons and 47 transcript assembles was constructed. Integrating the datasets on SSRs and drought-responsive ESTs identified three drought-responsive ESTs from bread wheat (BE604157), soybean (BM887317) and maritime pine (BX682209). The SSR sequence types were CAG, ATA and AT respectively. The datasets from cross-database mining provide organized resources for the characterization of USP genes as useful targets for engineering plant varieties tolerant to unfavorable environmental conditions.
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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12
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Mayer C, Leese F, Tollrian R. Genome-wide analysis of tandem repeats in Daphnia pulex--a comparative approach. BMC Genomics 2010; 11:277. [PMID: 20433735 PMCID: PMC3152781 DOI: 10.1186/1471-2164-11-277] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 04/30/2010] [Indexed: 11/10/2022] Open
Abstract
Background DNA tandem repeats (TRs) are not just popular molecular markers, but are also important genomic elements from an evolutionary and functional perspective. For various genomes, the densities of short TR types were shown to differ strongly among different taxa and genomic regions. In this study we analysed the TR characteristics in the genomes of Daphnia pulex and 11 other eukaryotic species. Characteristics of TRs in different genomic regions and among different strands are compared in details for D. pulex and the two model insects Apis mellifera and Drosophila melanogaster. Results Profound differences in TR characteristics were found among all 12 genomes compared in this study. In D. pulex, the genomic density of TRs was low compared to the arthropod species D. melanogaster and A. mellifera. For these three species, very few common features in repeat type usage, density distribution, and length characteristics were observed in the genomes and in different genomic regions. In introns and coding regions an unexpectedly high strandedness was observed for several repeat motifs. In D. pulex, the density of TRs was highest in introns, a rare feature in animals. In coding regions, the density of TRs with unit sizes 7-50 bp were more than three times as high as for 1-6 bp repeats. Conclusions TRs in the genome of D. pulex show several notable features, which distinguish it from the other genomes. Altogether, the highly non-random distribution of TRs among genomes, genomic regions and even among different DNA-stands raises many questions concerning their functional and evolutionary importance. The high density of TRs with a unit size longer than 6 bp found in non-coding and coding regions underpins the importance to include longer TR units in comparative analyses.
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Affiliation(s)
- Christoph Mayer
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, Bochum, Germany.
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Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T. VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Res 2008; 37:D810-5. [PMID: 18953038 PMCID: PMC2686441 DOI: 10.1093/nar/gkn798] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Creation of a vast variety of proteins is accomplished by genetic variation and a variety of alternative splicing transcripts. Currently, however, the abundant available data on genetic variation and the transcriptome are stored independently and in a dispersed fashion. In order to provide a research resource regarding the effects of human genetic polymorphism on various transcripts, we developed VarySysDB, a genetic polymorphism database based on 187,156 extensively annotated matured mRNA transcripts from 36,073 loci provided by H-InvDB. VarySysDB offers information encompassing published human genetic polymorphisms for each of these transcripts separately. This allows comparisons of effects derived from a polymorphism on different transcripts. The published information we analyzed includes single nucleotide polymorphisms and deletion-insertion polymorphisms from dbSNP, copy number variations from Database of Genomic Variants, short tandem repeats and single amino acid repeats from H-InvDB and linkage disequilibrium regions from D-HaploDB. The information can be searched and retrieved by features, functions and effects of polymorphisms, as well as by keywords. VarySysDB combines two kinds of viewers, GBrowse and Sequence View, to facilitate understanding of the positional relationship among polymorphisms, genome, transcripts, loci and functional domains. We expect that VarySysDB will yield useful information on polymorphisms affecting gene expression and phenotypes. VarySysDB is available at http://h-invitational.jp/varygene/.
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Affiliation(s)
- Makoto K Shimada
- Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Japan Biological Informatics Consortium, Hitachi Software Engineering Co., Ltd., Tokyo, Japan
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14
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Romano P, Manniello A, Aresu O, Armento M, Cesaro M, Parodi B. Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines. Nucleic Acids Res 2008; 37:D925-32. [PMID: 18927105 PMCID: PMC2686526 DOI: 10.1093/nar/gkn730] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.
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Affiliation(s)
- Paolo Romano
- Bioinformatics, Cell Bank, National Cancer Research Institute and IEIIT, National Research Council, Genova, Italy.
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