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Tang X, Han JY, Pan C, Li CY, Zhao Y, Yi Y, Zhang YS, Zheng BX, Yue XN, Liang AH. Angelicin: A leading culprit involved in fructus Psoraleae liver injury via inhibition of VKORC1. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:117917. [PMID: 38442807 DOI: 10.1016/j.jep.2024.117917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/20/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The adverse effects of Fructus Psoraleae (FP), especially liver injury, have attracted wide attention in recent years. AIM OF THE STUDY To establish a system to explore potential hepatotoxic targets and the chief culprit of liver injury based on clinical experience, network pharmacological method, molecular docking, and in vitro and in vivo experiments. MATERIALS AND METHODS Clinical applications and adverse reactions to FP were obtained from public literatures. Components absorbed in the blood were selected as candidates to search for potential active targets (PATs) of FP. Subsequently, potential pharmacological core targets (PPCTs) were screened through the "drug targets-disease targets" network. Non-drug active targets (NPATs) were obtained by subtracting the PPCTs from the PATs. The potential hepatotoxic targets (PHTs) of FP were the intersection targets obtained from Venn analysis using NPATs, hepatotoxic targets, and adverse drug reaction (ADR) targets provided by the databases. Then, potential hepatotoxic components and targets were obtained using the "NPATS-component" network relationship. Molecular docking and in vitro and in vivo hepatotoxicity experiments were performed to verify the targets and related components. RESULTS Overall, 234 NPATs were acquired from our analysis, and 6 targets were identified as PHTs. Results from molecular docking and in vitro and in vivo experiments showed that angelicin is the leading cause of liver injury in FP, and VKORC1 plays an important role. CONCLUSION The results indicate that six targets, especially VKORC1, are associated with the PHTs of FP, and angelicin is the leading culprit involved in FP liver injury via inhibition of VKORC1.
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Affiliation(s)
- Xuan Tang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Jia-Yin Han
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Engineering Research Center for Pharmaceutics of Chinese Materia Medica and New Drug Development, Ministry of Education, Beijing, 100029, China.
| | - Chen Pan
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Chun-Ying Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Yong Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Yan Yi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Yu-Shi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Bao-Xin Zheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Xing-Nan Yue
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Ai-Hua Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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2
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Tympakianakis S, Trantas E, Avramidou EV, Ververidis F. Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1139647. [PMID: 37180393 PMCID: PMC10169827 DOI: 10.3389/fpls.2023.1139647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.
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Affiliation(s)
- Stylianos Tympakianakis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
| | - Emmanouil Trantas
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organisation “DIMITRA“, Athens, Greece
| | - Filippos Ververidis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
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3
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Hill CB, Angessa TT, McFawn L, Wong D, Tibbits J, Zhang X, Forrest K, Moody D, Telfer P, Westcott S, Diepeveen D, Xu Y, Tan C, Hayden M, Li C. Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:932-944. [PMID: 30407713 PMCID: PMC6587706 DOI: 10.1111/pbi.13029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/14/2018] [Accepted: 10/21/2018] [Indexed: 05/12/2023]
Abstract
Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target-capture method was used to detect genome-wide polymorphisms in a panel of 174 flowering time-related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.
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Affiliation(s)
- Camilla Beate Hill
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
| | - Tefera Tolera Angessa
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
| | - Lee‐Anne McFawn
- Department of Primary Industries and Regional Development, Agriculture and FoodSouth PerthWAAustralia
| | - Debbie Wong
- Agriculture Victoria ResearchAgriBio, Centre for AgriBioscienceBundooraVic.Australia
| | - Josquin Tibbits
- Agriculture Victoria ResearchAgriBio, Centre for AgriBioscienceBundooraVic.Australia
| | - Xiao‐Qi Zhang
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
| | - Kerrie Forrest
- Agriculture Victoria ResearchAgriBio, Centre for AgriBioscienceBundooraVic.Australia
| | | | - Paul Telfer
- Australian Grain Technologies Pty Ltd (AGT)RoseworthySAAustralia
| | - Sharon Westcott
- Department of Primary Industries and Regional Development, Agriculture and FoodSouth PerthWAAustralia
| | - Dean Diepeveen
- Department of Primary Industries and Regional Development, Agriculture and FoodSouth PerthWAAustralia
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouHubeiChina
| | - Cong Tan
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
| | - Matthew Hayden
- Agriculture Victoria ResearchAgriBio, Centre for AgriBioscienceBundooraVic.Australia
- School of Applied Systems BiologyLa Trobe UniversityBundooraVic.Australia
| | - Chengdao Li
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityMurdochWAAustralia
- Department of Primary Industries and Regional Development, Agriculture and FoodSouth PerthWAAustralia
- Hubei Collaborative Innovation Centre for Grain IndustryYangtze UniversityJingzhouHubeiChina
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4
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Fan H, Ives AR, Surget-Groba Y. Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment. Mol Ecol Resour 2018; 18:1482-1491. [PMID: 29939475 DOI: 10.1111/1755-0998.12921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 12/21/2022]
Abstract
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment-free methods are both efficient and accurate for phylogenetic reconstructions with whole genomes and are especially practical for nonmodel organisms; nonetheless, alignment-free methods have not been applied with reduced genome sequencing data. Here, we test a full-genome assembly- and alignment-free method, AAF, in application to RADseq data and propose two procedures for reads selection to remove reads from restriction sites that were not found in taxa being compared. We validate these methods using both simulations and real data sets. Reads selection improved the accuracy of phylogenetic construction in every simulated scenario and the two real data sets, making AAF as good or better than a comparable alignment-based method, even though AAF had much lower computational burdens. We also investigated the sources of missing data in RADseq and their effects on phylogeny reconstruction using AAF. The AAF pipeline modified for RADseq or other reduced-representation sequencing data, phyloRAD, is available on github (https://github.com/fanhuan/phyloRAD).
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Affiliation(s)
- Huan Fan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Anthony R Ives
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Yann Surget-Groba
- Institut des Sciences de la Forêt Tempérée, Université du Québec en Outaouais, Ripon, Quebec, Canada
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5
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Barley Genome Sequencing and Assembly—A First Version Reference Sequence. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-92528-8_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Wu J, Zhao Q, Wu G, Zhang S, Jiang T. Development of Novel SSR Markers for Flax ( Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing. FRONTIERS IN PLANT SCIENCE 2017; 7:2018. [PMID: 28133461 PMCID: PMC5233678 DOI: 10.3389/fpls.2016.02018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/19/2016] [Indexed: 05/29/2023]
Abstract
Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5-8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in this study show potential value for selection of varieties for use in flax breeding programs.
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Affiliation(s)
- Jianzhong Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Qian Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Guangwen Wu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Shuquan Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityHarbin, China
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7
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Kaur P, Gaikwad K. From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:2164. [PMID: 29312405 PMCID: PMC5742236 DOI: 10.3389/fpls.2017.02164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Exome sequencing represents targeted capture and sequencing of 1-2% of 'high-value genomic regions' (subset of the genome) which are enriched for functional variants and harbors low level of repetitive regions. We discuss here an overview of exome sequencing, ways to approach plant exomes, and advantages and applicability of this powerful approach in deciphering functional regions of genomes. Though initially this approach was developed as an alternative to whole genome sequencing (WGS), but the multitude of benefits conferred by sequence capture via hybridization approaches created a niche for itself to solve many of biological riddles, particularly for resolving phylogenetic distances. The technique has also proved to be successful in understanding the basis of natural and induced molecular variation, marker development and developing genomic resources for complex, wild and non-model species, which are still intractable for WGS efforts. Thus, with profound applications of this powerful sequencing strategy, near future is expected to witness a collective expansion of both techniques, i.e., sequence capture via hybridization for evolutionary and ecological research and WGS approaches for its universal accessibility.
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8
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Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH. Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 2016; 17:221. [PMID: 27795210 PMCID: PMC5087116 DOI: 10.1186/s13059-016-1082-1] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/10/2016] [Indexed: 11/18/2022] Open
Abstract
Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Simon G. Krattinger
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
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9
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Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Sci Rep 2016; 6:26632. [PMID: 27226078 PMCID: PMC4880927 DOI: 10.1038/srep26632] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 05/06/2016] [Indexed: 12/26/2022] Open
Abstract
Heritable phenotypic differences between populations, caused by the selective effects of distinct environmental conditions, are of commonplace occurrence in nature. However, the actual genomic targets of this kind of selection are still poorly understood. We conducted a quantitative trait locus (QTL) mapping study to identify genomic regions responsible for morphometric differentiation between genetically and phenotypically divergent marine and freshwater nine-spined stickleback (Pungitius pungitius) populations. Using a dense panel of SNP-markers obtained by restriction site associated DNA sequencing of an F2 recombinant cross, we found 22 QTL that explained 3.5-12.9% of phenotypic variance in the traits under investigation. We detected one fairly large-effect (PVE = 9.6%) QTL for caudal peduncle length-a trait with a well-established adaptive function showing clear differentiation among marine and freshwater populations. We also identified two large-effect QTL for lateral plate numbers, which are different from the lateral plate QTL reported in earlier studies of this and related species. Hence, apart from identifying several large-effect QTL in shape traits showing adaptive differentiation in response to different environmental conditions, the results suggest intra- and interspecific heterogeneity in the genomic basis of lateral plate number variation.
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10
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Upadhyay MR, Patel AB, Subramanian RB, Shah TM, Jakhesara SJ, Bhatt VD, Koringa PG, Rank DN, Joshi CG. Single nucleotide variant detection in Jaffrabadi buffalo (Bubalus bubalis) using high-throughput targeted sequencing. FRONTIERS IN LIFE SCIENCE 2015. [DOI: 10.1080/21553769.2015.1031915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Barba P, Cadle-Davidson L, Harriman J, Glaubitz JC, Brooks S, Hyma K, Reisch B. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:73-84. [PMID: 24072208 DOI: 10.1007/s00122-013-2202-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 09/10/2013] [Indexed: 05/08/2023]
Abstract
Improved efficacy and durability of powdery mildew resistance can be enhanced via knowledge of the genetics of resistance and susceptibility coupled with the development of high-resolution maps to facilitate the stacking of multiple resistance genes and other desirable traits. We studied the inheritance of powdery mildew (Erysiphe necator) resistance and susceptibility of wild Vitis rupestris B38 and cultivated V. vinifera 'Chardonnay', finding evidence for quantitative variation. Molecular markers were identified using genotyping-by-sequencing, resulting in 16,833 single nucleotide polymorphisms (SNPs) based on alignment to the V. vinifera 'PN40024' reference genome sequence. With an average density of 36 SNPs/Mbp and uniform coverage of the genome, this 17K set was used to identify 11 SNPs on chromosome 7 associated with a resistance locus from V. rupestris B38 and ten SNPs on chromosome 9 associated with a locus for susceptibility from 'Chardonnay' using single marker association and linkage disequilibrium analysis. Linkage maps for V. rupestris B38 (1,146 SNPs) and 'Chardonnay' (1,215 SNPs) were constructed and used to corroborate the 'Chardonnay' locus named Sen1 (Susceptibility to Erysiphe necator 1), providing the first insight into the genetics of susceptibility to powdery mildew from V. vinifera. The identification of markers associated with a susceptibility locus in a V. vinifera background can be used for negative selection among breeding progenies. This work improves our understanding of the nature of powdery mildew resistance in V. rupestris B38 and 'Chardonnay', while applying next-generation sequencing tools to advance grapevine genomics and breeding.
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Affiliation(s)
- Paola Barba
- Department of Plant Breeding, Cornell University, Ithaca, NY, 14853, USA
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12
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Carstens BC, Brennan RS, Chua V, Duffie CV, Harvey MG, Koch RA, McMahan CD, Nelson BJ, Newman CE, Satler JD, Seeholzer G, Posbic K, Tank DC, Sullivan J. Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Mol Ecol 2013; 22:4014-28. [PMID: 23848064 DOI: 10.1111/mec.12347] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 12/29/2022]
Abstract
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post-Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate-n and ∂a∂i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
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13
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Neves LG, Davis JM, Barbazuk WB, Kirst M. Whole-exome targeted sequencing of the uncharacterized pine genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:146-156. [PMID: 23551702 DOI: 10.1111/tpj.12193] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/26/2013] [Accepted: 03/26/2013] [Indexed: 05/20/2023]
Abstract
The large genome size of many species hinders the development and application of genomic tools to study them. For instance, loblolly pine (Pinus taeda L.), an ecologically and economically important conifer, has a large and yet uncharacterized genome of 21.7 Gbp. To characterize the pine genome, we performed exome capture and sequencing of 14 729 genes derived from an assembly of expressed sequence tags. Efficiency of sequence capture was evaluated and shown to be similar across samples with increasing levels of complexity, including haploid cDNA, haploid genomic DNA and diploid genomic DNA. However, this efficiency was severely reduced for probes that overlapped multiple exons, presumably because intron sequences hindered probe:exon hybridizations. Such regions could not be entirely avoided during probe design, because of the lack of a reference sequence. To improve the throughput and reduce the cost of sequence capture, a method to multiplex the analysis of up to eight samples was developed. Sequence data showed that multiplexed capture was reproducible among 24 haploid samples, and can be applied for high-throughput analysis of targeted genes in large populations. Captured sequences were de novo assembled, resulting in 11 396 expanded and annotated gene models, significantly improving the knowledge about the pine gene space. Interspecific capture was also evaluated with over 98% of all probes designed from P. taeda that were efficient in sequence capture, were also suitable for analysis of the related species Pinus elliottii Engelm.
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Affiliation(s)
- Leandro G Neves
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
| | - John M Davis
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - William B Barbazuk
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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14
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Lemmon AR, Lemmon EM. High-Throughput Identification of Informative Nuclear Loci for Shallow-Scale Phylogenetics and Phylogeography. Syst Biol 2012; 61:745-61. [DOI: 10.1093/sysbio/sys051] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Alan R. Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA
| | - Emily Moriarty Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306-4102, USA; and 2 Department of Biological Science, Florida State University, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL, 32306-4295, USA
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Zellmer AJ, Hanes MM, Hird SM, Carstens BC. Deep Phylogeographic Structure and Environmental Differentiation in the Carnivorous Plant Sarracenia alata. Syst Biol 2012; 61:763-77. [DOI: 10.1093/sysbio/sys048] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Amanda J. Zellmer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Margaret M. Hanes
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Sarah M. Hird
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Bryan C. Carstens
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
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16
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Tissue-specific temporal exome capture revealed muscle-specific genes and SNPs in Indian buffalo (Bubalus bubalis). GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:107-13. [PMID: 22768984 PMCID: PMC5054198 DOI: 10.1016/j.gpb.2012.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/28/2011] [Indexed: 11/20/2022]
Abstract
Whole genome sequencing of buffalo is yet to be completed, and in the near future it may not be possible to identify an exome (coding region of genome) through bioinformatics for designing probes to capture it. In the present study, we employed in solution hybridization to sequence tissue specific temporal exomes (TST exome) in buffalo. We utilized cDNA prepared from buffalo muscle tissue as a probe to capture TST exomes from the buffalo genome. This resulted in a prominent reduction of repeat sequences (up to 40%) and an enrichment of coding sequences (up to 60%). Enriched targets were sequenced on a 454 pyro-sequencing platform, generating 101,244 reads containing 24,127,779 high quality bases. The data revealed 40,100 variations, of which 403 were indels and 39,218 SNPs containing 195 nonsynonymous candidate SNPs in protein-coding regions. The study has indicated that 80% of the total genes identified from capture data were expressed in muscle tissue. The present study is the first of its kind to sequence TST exomes captured by use of cDNA molecules for SNPs found in the coding region without any prior sequence information of targeted molecules.
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17
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Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences. Mol Phylogenet Evol 2012; 62:397-406. [DOI: 10.1016/j.ympev.2011.10.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 09/20/2011] [Accepted: 10/15/2011] [Indexed: 02/03/2023]
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Abstract
Single nucleotide polymorphisms (SNPs) are single base differences between haplotypes. SNPs are abundant in many species and valuable as markers for genetic map construction, modern molecular breeding programs, and quantitative genetic studies. SNPs are readily mined from genomic DNA or cDNA sequence obtained from individuals having two or more distinct genotypes. While automated Sanger sequencing has become less expensive over time, it is still costly to acquire deep Sanger sequence from several genotypes. "Next-generation" DNA sequencing technologies that utilize new chemistries and massively parallel approaches have enabled DNA sequences to be acquired at extremely high depths of coverage faster and for less cost than traditional sequencing. One such method is represented by the Roche/454 Life Sciences GS-FLX Titanium Series, which currently uses pyrosequencing to produce up to 400-600 million bases of DNA sequence/run (>1 million reads, ~400 bp/read). This chapter discusses the use of high-throughput pyrosequencing for SNP discovery by focusing on 454 sequencing of maize cDNA, the development of a computational pipeline for polymorphism detection, and the subsequent identification of over 7,000 putative SNPs between Mo17 and B73 maize. In addition, alternative alignment and polymorphism detection strategies that implement Illumina short reads, data processing and visualization tools, and reduced representation techniques that reduce the sequencing of repeat DNA, thus enabling efficient analysis of genome sequence, are discussed.
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Affiliation(s)
- W Brad Barbazuk
- Department of Biology and the Genetics Institute, University of Florida, Gainesville, FL, USA.
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19
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Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh CT, Wu W, Swanson-Wagner R, D'Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS. Repeat subtraction-mediated sequence capture from a complex genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:898-909. [PMID: 20230488 DOI: 10.1111/j.1365-313x.2010.04196.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Sequence capture technologies, pioneered in mammalian genomes, enable the resequencing of targeted genomic regions. Most capture protocols require blocking DNA, the production of which in large quantities can prove challenging. A blocker-free, two-stage capture protocol was developed using NimbleGen arrays. The first capture depletes the library of repetitive sequences, while the second enriches for target loci. This strategy was used to resequence non-repetitive portions of an approximately 2.2 Mb chromosomal interval and a set of 43 genes dispersed in the 2.3 Gb maize genome. This approach achieved approximately 1800-3000-fold enrichment and 80-98% coverage of targeted bases. More than 2500 SNPs were identified in target genes. Low rates of false-positive SNP predictions were obtained, even in the presence of captured paralogous sequences. Importantly, it was possible to recover novel sequences from non-reference alleles. The ability to design novel repeat-subtraction and target capture arrays makes this technology accessible in any species.
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Affiliation(s)
- Yan Fu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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20
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Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D. Rapid genomic characterization of the genus vitis. PLoS One 2010; 5:e8219. [PMID: 20084295 PMCID: PMC2805708 DOI: 10.1371/journal.pone.0008219] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 11/16/2009] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Bonnie Hurwitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Charles Simon
- New York State Agricultural Experiment Station, Geneva, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
| | - Gan Yuan Zhong
- New York State Agricultural Experiment Station, Geneva, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
| | - Edward Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
- * E-mail: (EB); (DW)
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
- * E-mail: (EB); (DW)
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21
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Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S, Forrest DK, Wise R, Ware D, Wing RA, Waterman MS, Livny M, Schwartz DC. A single molecule scaffold for the maize genome. PLoS Genet 2009; 5:e1000711. [PMID: 19936062 PMCID: PMC2774507 DOI: 10.1371/journal.pgen.1000711] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/05/2009] [Indexed: 11/18/2022] Open
Abstract
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. The maize genome contains abundant repeats interspersed by low-copy, gene-coding sequences that make it a challenge to sequence; consequently, current BAC sequence assemblies average 11 contigs per clone. The iMap deals with such complexity by the judicious integration of IBM genetic and B73 physical maps, but the B73 genome structure could differ from the IBM population because of genetic recombination and subsequent rearrangements. Accordingly, we report a genome-wide, high-resolution optical map of maize B73 genome that was constructed from the direct analysis of genomic DNA molecules without using genetic markers. The integration of optical and iMap resources with comparisons to FPC maps enabled a uniquely comprehensive and scalable assessment of a given BAC's sequence assembly, its placement within a FPC contig, and the location of this FPC contig within a chromosome-wide pseudomolecule. As such, the overall utility of the maize optical map for the validation of sequence assemblies has been significant and demonstrates the inherent advantages of single molecule platforms. Construction of the maize optical map represents the first physical map of a eukaryotic genome larger than 400 Mb that was created de novo from individual genomic DNA molecules.
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Affiliation(s)
- Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Fusheng Wei
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - John Nguyen
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Mike Bechner
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Konstantinos Potamousis
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Steve Goldstein
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Louise Pape
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael R. Mehan
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Chris Churas
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Dan K. Forrest
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Roger Wise
- Corn Insects and Crop Genetics Research, United States Department of Agriculture–Agricultural Research Service and Department of Plant Pathology, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Plant, Soil, and Nutrition Research, United States Department of Agriculture–Agricultural Research Service, Ithaca, New York, United States of America
| | - Rod A. Wing
- Department of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Michael S. Waterman
- Departments of Mathematics, Biology, and Computer Science, University of Southern California, Los Angeles, California, United States of America
| | - Miron Livny
- Computer Sciences Department, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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22
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Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J. Sequence assembly. Comput Biol Chem 2008; 33:121-36. [PMID: 19152793 DOI: 10.1016/j.compbiolchem.2008.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 11/28/2008] [Accepted: 11/28/2008] [Indexed: 01/20/2023]
Abstract
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.
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Affiliation(s)
- K Scheibye-Alsing
- Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
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23
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Wu Y, Liu L, Close TJ, Lonardi S. Deconvoluting BAC-gene relationships using a physical map. J Bioinform Comput Biol 2008; 6:603-22. [PMID: 18574865 DOI: 10.1142/s0219720008003564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 12/01/2007] [Accepted: 01/03/2008] [Indexed: 11/18/2022]
Abstract
Deconvolution of relationships between bacterial artificial chromosome (BAC) clones and genes is a crucial step in the selective sequencing of regions of interest in a genome. It often includes combinatorial pooling of unique probes obtained from the genes (unigenes), and screening of the BAC library using the pools in a hybridization experiment. Since several probes can hybridize to the same BAC, in order for the deconvolution to be achievable the pooling design has to be able to handle a large number of positives. As a consequence, smaller pools need to be designed, which in turn increases the number of hybridization experiments, possibly making the entire protocol unfeasible. We propose a new algorithm that is capable of producing high-accuracy deconvolution even in the presence of a weak pooling design, i.e. when pools are rather large. The algorithm compensates for the decrease of information in the hybridization data by taking advantage of a physical map of the BAC clones. We show that the right combination of combinatorial pooling and our algorithm not only dramatically reduces the number of pools required, but also successfully deconvolutes the BAC-gene relationships with almost perfect accuracy. Software is available on request from the first author.
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Affiliation(s)
- Yonghui Wu
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92521, USA.
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24
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Affiliation(s)
- Pablo D Rabinowicz
- J. C. Venter Institute, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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25
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Madishetty K, Condamine P, Svensson JT, Rodriguez E, Close TJ. An improved method to identify BAC clones using pooled overgos. Nucleic Acids Res 2006; 35:e5. [PMID: 17151072 PMCID: PMC1761434 DOI: 10.1093/nar/gkl920] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Hybridization using overgo probes is an established approach for screening arrayed bacterial artificial chromosome (BAC) libraries. We have improved the use of overgos by increasing the yield of positive clones using reduced levels of radioisotopes and enzyme. The strategy involves labeling with all four radiolabeled nucleotides in a hot pulse followed by a cold nucleotide chase and then extending the exposure time to compensate for reduced specific activity of the probes. The resulting cost savings and reduced human exposure to radiation make the use of highly pooled overgo probes a more attractive approach for screening of BAC libraries from organisms with large genomes.
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Affiliation(s)
| | | | | | | | - Timothy J. Close
- To whom correspondence should be addressed. Tel: +1 951 827 3318; Fax: +1 951 827 4437; E-mail:
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26
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McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, Luthe DS, Bridges SM, Burgess SC. AgBase: a functional genomics resource for agriculture. BMC Genomics 2006; 7:229. [PMID: 16961921 PMCID: PMC1618847 DOI: 10.1186/1471-2164-7-229] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 09/08/2006] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.
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Affiliation(s)
- Fiona M McCarthy
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
| | - Nan Wang
- Department of Computer Science and Engineering, Bagley College of Engineering, P.O. Box 9637, Mississippi State University, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
| | - G Bryce Magee
- Department of Computer Science and Engineering, Bagley College of Engineering, P.O. Box 9637, Mississippi State University, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA
| | - Evelyn B Camon
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel G Barrell
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David P Hill
- Mouse Genome Informatics, The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mary E Dolan
- Mouse Genome Informatics, The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
| | - W Paul Williams
- USDA ARS Corn Host Plant Resistance Research Unit, Box 5367, Mississippi State University, MS 39762, USA
| | - Dawn S Luthe
- Department of Biochemistry and Molecular Biology, P.O. Box 9650, Mississippi State University, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
| | - Susan M Bridges
- Department of Computer Science and Engineering, Bagley College of Engineering, P.O. Box 9637, Mississippi State University, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
| | - Shane C Burgess
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, P.O. Box 1600, Mississippi State, MS 39762, USA
- Institute for Digital Biology, Mississippi State University, MS 39762, USA
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27
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Wang W, Zheng H, Fan C, Li J, Shi J, Cai Z, Zhang G, Liu D, Zhang J, Vang S, Lu Z, Wong GKS, Long M, Wang J. High rate of chimeric gene origination by retroposition in plant genomes. THE PLANT CELL 2006; 18:1791-802. [PMID: 16829590 PMCID: PMC1533979 DOI: 10.1105/tpc.106.041905] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 04/15/2006] [Accepted: 06/08/2006] [Indexed: 05/10/2023]
Abstract
Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.
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Affiliation(s)
- Wen Wang
- CAS-Max-Plank Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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28
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Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD. The TIGR Maize Database. Nucleic Acids Res 2006; 34:D771-6. [PMID: 16381977 PMCID: PMC1347435 DOI: 10.1093/nar/gkj072] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to accelerate gene discovery and genome analysis in maize: methylation filtration and high C0t selection. These techniques allow the construction of gene-enriched genomic libraries by minimizing repeat sequences due to either their methylation status or their copy number, yielding a 7-fold enrichment in genic sequences relative to a random genomic library. Approximately 900 000 gene-enriched reads from maize were generated and clustered into Assembled Zea mays (AZM) sequences. Here we report the current AZM release, which consists of ∼298 Mb representing 243 807 sequence assemblies and singletons. In order to provide a repository of publicly available maize genomic sequences, we have created the TIGR Maize Database (). In this resource, we have assembled and annotated the AZMs and used available sequenced markers to anchor AZMs to maize chromosomes. We have constructed a maize repeat database and generated draft sequence assemblies of 287 maize bacterial artificial chromosome (BAC) clone sequences, which we annotated along with 172 additional publicly available BAC clones. All sequences, assemblies and annotations are available at the project website via web interfaces and FTP downloads.
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Affiliation(s)
- Agnes P. Chan
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Geo Pertea
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Foo Cheung
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Dan Lee
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Li Zheng
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Cathy Whitelaw
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
| | - Ana C. Pontaroli
- Department of Genetics, University of GeorgiaAthens, GA 30602, USA
| | | | - Yinan Yuan
- Department of Biological Sciences, Purdue UniversityWest Lafayette, IN 47906, USA
| | | | | | - John Quackenbush
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute44 Binney Street, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public HealthBoston, MA 02115, USA
| | - Pablo D. Rabinowicz
- The Institute for Genomic Research9712 Medical Center Drive, Rockville, MD 20850, USA
- To whom correspondence should be addressed. Tel: +1 301 795 7787; Fax: +1 301 838 0208;
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Vij S, Gupta V, Kumar D, Vydianathan R, Raghuvanshi S, Khurana P, Khurana JP, Tyagi AK. Decoding the rice genome. Bioessays 2006; 28:421-32. [PMID: 16547947 DOI: 10.1002/bies.20399] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have been generated by both public and privately funded ventures. The availability of a complete and high-quality map-based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity.
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Affiliation(s)
- Shubha Vij
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110 021, India
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