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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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Flinn B, Dale S, Disharoon A, Kresovich S. Comparative Analysis of In Vitro Responses and Regeneration between Diverse Bioenergy Sorghum Genotypes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E248. [PMID: 32075100 PMCID: PMC7076383 DOI: 10.3390/plants9020248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 01/09/2023]
Abstract
Sorghum has been considered a recalcitrant plant in vitro and suffers from a lack of regeneration protocols that function broadly and efficiently across a range of genotypes. This study was initiated to identify differential genotype-in vitro protocol responses across a range of bioenergy sorghum parental lines and the common grain sorghum genotype Tx430 in order to characterize response profiles for use in future genetic studies. Two different in vitro protocols, LG and WU, were used for comparisons. Distinct genotype-protocol responses were observed, and the WU protocol performed significantly better for plantlet regeneration. Most bioenergy genotypes performed as well, if not better than Tx430, with Rio and PI329311 as the top regenerating lines. Genotypes displayed protocol-dependent, differential phenolic exudation responses, as indicated by medium browning. During the callus induction phase, genotypes prone to medium browning exhibited a response on WU medium which was either equal or greater than on LG medium. Genotype- and protocol-dependent albino plantlet regeneration was also noted, with three of the bioenergy genotypes showing albino plantlet regeneration. Grassl, Rio and Pink Kafir were susceptible to albino plantlet regeneration, with the response strongly associated with the WU protocol. These bioenergy parental genotypes, and their differential responses under two in vitro protocols, provide tools to further explore and assess the role of genetic loci, candidate genes, and allelic variants in the regulation of in vitro responsiveness in sorghum.
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Affiliation(s)
- Barry Flinn
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA;
| | - Savanah Dale
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA; (S.D.); (A.D.)
| | - Andrew Disharoon
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA; (S.D.); (A.D.)
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA;
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA; (S.D.); (A.D.)
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Tang X, Wang H, Shao C, Shao H. Global Gene Expression of Kosteletzkya virginica Seedlings Responding to Salt Stress. PLoS One 2015; 10:e0124421. [PMID: 25901608 PMCID: PMC4406580 DOI: 10.1371/journal.pone.0124421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/13/2015] [Indexed: 11/19/2022] Open
Abstract
Soil salinization is becoming a serious threat to crop yield all over the world. Nowadays, acquainting the specific molecular mechanisms underlying various abiotic stresses especially to salt stress should be of great importance. While the development of the high-throughout sequencing technology promoted the progress powerfully. The intricate perception, transduction and regulation mechanisms underlying salt stress are being illustrated more and more clearly. As a perennial halophytic plant, Kosteletzkya virginica is able to help us to understand the mechanisms more directly and effectively. We carried out the whole transcriptome analysis on young seedlings with or without salt treatment through high-throughout sequencing technology. The results revealed that the numbers of different expressed transcripts between control and different treatments are 4145 and 9134, respectively. The ORF prediction suggested that there were 94308 ORF out of the 103489 (91.10%) total transcripts. We also carried out further differential expression analysis through gene ontology (GO) classification, cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In a word, our transcriptome study on Kosteletzkya virginica would provide direct and effective references for researches on molecular mechanisms of salt-tolerance, extending our view of salt tolerance in plant further. Above all, the related report in this paper is the first about Kosteletzkya virginica.
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Affiliation(s)
- Xiaoli Tang
- Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongyan Wang
- Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, China
- Yantai Academy of China Agriculture University, Yantai, 264670, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuyang Shao
- Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Hongbo Shao
- Key Laboratory of Coastal Biology & Bioresources Utilization, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, 264003, China
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- * E-mail:
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Grativol C, Regulski M, Bertalan M, McCombie WR, da Silva FR, Neto AZ, Vicentini R, Farinelli L, Hemerly AS, Martienssen RA, Ferreira PCG. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:162-72. [PMID: 24773339 PMCID: PMC4458261 DOI: 10.1111/tpj.12539] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 05/21/2023]
Abstract
Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.
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Affiliation(s)
- Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
| | - Michael Regulski
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Marcelo Bertalan
- Institute of Biological Psychiatry Mental Health Center, Sct. Hans MHS - Capital Region of Denmark Boserupvej, DK-4000 Roskilde, Denmark
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Felipe Rodrigues da Silva
- Embrapa Informática Agropecuária, Av. Andre Tosello, 209, Barão Geraldo 13.083-886, Campinas, SP, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Av. Andre Tosello, 209, Barão Geraldo 13.083-886, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724, USA
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
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Low ETL, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R. Analyses of hypomethylated oil palm gene space. PLoS One 2014; 9:e86728. [PMID: 24497974 PMCID: PMC3907425 DOI: 10.1371/journal.pone.0086728] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 12/15/2013] [Indexed: 12/21/2022] Open
Abstract
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
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Affiliation(s)
- Eng-Ti L. Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Ab Halim Mohd-Amin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Paul Maclean
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Rudi Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Alan McCulloch
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Roger Moraga
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
- * E-mail:
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Rai KM, Singh SK, Bhardwaj A, Kumar V, Lakhwani D, Srivastava A, Jena SN, Yadav HK, Bag SK, Sawant SV. Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:953-963. [PMID: 23782852 DOI: 10.1111/pbi.12088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/19/2013] [Accepted: 05/04/2013] [Indexed: 06/02/2023]
Abstract
The sequence information has been proved to be an essential genomic resource in case of crop plants for their genetic improvement and better utilization by humans. To dissect the Gossypium hirsutum genome for large-scale development of genomic resources, we adopted hypomethylated restriction-based genomic enrichment strategy to sequence six diverse genotypes. Approximately 5.2-Gb data (more than 18.36 million reads) was generated which, after assembly, represents nearly 1.27-Gb genomic sequences. We predicted a total of 93,363 gene models (21,399 full length) and identified 35,923 gene models which were validated against already sequenced plant genomes. A total of 1,093 transcription factor-encoding genes, 3,135 promoter sequences and 78 miRNA (including 17 newly identified in Gossypium) were predicted. We identified significant no. of molecular markers including 47,093 novel simple sequence repeats and 66,364 novel single nucleotide polymorphisms. In addition, we developed NBRI-Comprehensive Cotton Genomics database, a web resource to provide access of cotton-related genomic resources developed at NBRI. This study contributes considerable amount of genomic resources and suggests a potential role of genic-enriched sequencing in genomic resource development for orphan crop plants.
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Affiliation(s)
- Krishan Mohan Rai
- Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
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Singh R, Ong-Abdullah M, Low ETL, Manaf MAA, Rosli R, Nookiah R, Ooi LCL, Ooi SE, Chan KL, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway JM, Martienssen RA, Sambanthamurthi R. Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 2013; 500:335-9. [PMID: 23883927 PMCID: PMC3929164 DOI: 10.1038/nature12309] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 05/16/2013] [Indexed: 11/09/2022]
Abstract
Oil palm is the most productive oil-bearing crop. Planted on only 5% of the total vegetable oil acreage, palm oil accounts for 33% of vegetable oil, and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8 gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators1, which are highly expressed in the kernel. We also report the draft sequence of the S. American oil palm Elaeis oleifera, which has the same number of chromosomes (2n=32) and produces fertile interspecific hybrids with E. guineensis2, but appears to have diverged in the new world. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations which restrict the use of clones in commercial plantings3, and thus helps achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
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Affiliation(s)
- Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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Morishige DT, Klein PE, Hilley JL, Sahraeian SME, Sharma A, Mullet JE. Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome. BMC Genomics 2013; 14:448. [PMID: 23829350 PMCID: PMC3716661 DOI: 10.1186/1471-2164-14-448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 06/28/2013] [Indexed: 11/18/2022] Open
Abstract
Background Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome sequences for the purpose of genotyping is still relatively inefficient and too expensive to be carried out on a high-throughput basis. Sorghum bicolor is a C4 grass with a sequenced genome size of ~730 Mb, of which ~80% is highly repetitive. We have developed a restriction enzyme targeted genome resequencing method for genetic analysis, termed Digital Genotyping (DG), to be applied to sorghum and other grass species with large repeat-rich genomes. Results DG templates are generated using one of three methylation sensitive restriction enzymes that recognize a nested set of 4, 6 or 8 bp GC-rich sequences, enabling varying depth of analysis and integration of results among assays. Variation in sequencing efficiency among DG markers was correlated with template GC-content and length. The expected DG allele sequence was obtained 97.3% of the time with a ratio of expected to alternative allele sequence acquisition of >20:1. A genetic map aligned to the sorghum genome sequence with an average resolution of 1.47 cM was constructed using 1,772 DG markers from 137 recombinant inbred lines. The DG map enhanced the detection of QTL for variation in plant height and precisely aligned QTL such as Dw3 to underlying genes/alleles. Higher-resolution NgoMIV-based DG haplotypes were used to trace the origin of DNA on SBI-06, spanning Ma1 and Dw2 from progenitors to BTx623 and IS3620C. DG marker analysis identified the correct location of two miss-assembled regions and located seven super contigs in the sorghum reference genome sequence. Conclusion DG technology provides a cost-effective approach to rapidly generate accurate genotyping data in sorghum. Currently, data derived from DG are used for many marker-based analyses, including marker-assisted breeding, pedigree and QTL analysis, genetic map construction, map-based gene cloning and association studies. DG in combination with whole genome resequencing is dramatically accelerating all aspects of genetic analysis of sorghum, an important genetic reference for C4 grass species.
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Griffiths AG, Barrett BA, Simon D, Khan AK, Bickerstaff P, Anderson CB, Franzmayr BK, Hancock KR, Jones CS. An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago. BMC Genomics 2013; 14:388. [PMID: 23758831 PMCID: PMC3693905 DOI: 10.1186/1471-2164-14-388] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND White clover (Trifolium repens L.) is a temperate forage legume with an allotetraploid genome (2n=4×=32) estimated at 1093 Mb. Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linkage analysis among unrelated mapping populations. Such integrative analysis requires tools for homoeologue matching among populations. Development of these tools provides for a consistent framework map of the white clover genome, and facilitates in silico alignment with the model forage legume, Medicago truncatula. RESULTS This is the first report of integration of independent linkage maps in white clover, and adds to the literature on methyl filtered GeneThresher®-derived microsatellite (simple sequence repeat; SSR) markers for linkage mapping. Gene-targeted SSR markers were discovered in a GeneThresher® (TrGT) methyl-filtered database of 364,539 sequences, which yielded 15,647 SSR arrays. Primers were designed for 4,038 arrays and of these, 465 TrGT-SSR markers were used for parental consensus genetic linkage analysis in an F1 mapping population (MP2). This was merged with an EST-SSR consensus genetic map of an independent population (MP1), using markers to match homoeologues and develop a multi-population integrated map of the white clover genome. This integrated map (IM) includes 1109 loci based on 804 SSRs over 1274 cM, covering 97% of the genome at a moderate density of one locus per 1.2 cM. Eighteen candidate genes and one morphological marker were also placed on the IM. Despite being derived from disparate populations and marker sources, the component maps and the derived IM had consistent representations of the white clover genome for marker order and genetic length. In silico analysis at an E-value threshold of 1e-20 revealed substantial co-linearity with the Medicago truncatula genome, and indicates a translocation between T. repens groups 2 and 6 relative to M. truncatula. CONCLUSIONS This integrated genetic linkage analysis provides a consistent and comprehensive linkage analysis of the white clover genome, with alignment to a model forage legume. Associated marker locus information, particularly the homoeologue-specific markers, offers a new resource for forage legume research to enable genetic analysis and improvement of this forage and grassland species.
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Affiliation(s)
- Andrew G Griffiths
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
- Pastoral Genomics, ℅ AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Brent A Barrett
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Deborah Simon
- Landcorp Farming Limited, PO Box 5349, Wellington, 6145, New Zealand
| | - Anar K Khan
- AgResearch Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | | | - Craig B Anderson
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
- Pastoral Genomics, ℅ AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Benjamin K Franzmayr
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
- Pastoral Genomics, ℅ AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Kerry R Hancock
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
- Pastoral Genomics, ℅ AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Chris S Jones
- AgResearch Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand
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Regulski M, Lu Z, Kendall J, Donoghue MTA, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen RA. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res 2013; 23:1651-62. [PMID: 23739895 PMCID: PMC3787262 DOI: 10.1101/gr.153510.112] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.
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Affiliation(s)
- Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Jiang SY, Ma Z, Vanitha J, Ramachandran S. Genetic variation and expression diversity between grain and sweet sorghum lines. BMC Genomics 2013; 14:18. [PMID: 23324212 PMCID: PMC3616923 DOI: 10.1186/1471-2164-14-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 01/09/2013] [Indexed: 01/20/2023] Open
Abstract
Background Biological scientists have long sought after understanding how genes and their structural/functional changes contribute to morphological diversity. Though both grain (BT×623) and sweet (Keller) sorghum lines originated from the same species Sorghum bicolor L., they exhibit obvious phenotypic variations. However, the genome re-sequencing data revealed that they exhibited limited functional diversity in their encoding genes in a genome-wide level. The result raises the question how the obvious morphological variations between grain and sweet sorghum occurred in a relatively short evolutionary or domesticated period. Results We implemented an integrative approach by using computational and experimental analyses to provide a detail insight into phenotypic, genetic variation and expression diversity between BT×623 and Keller lines. We have investigated genome-wide expression divergence between BT×623 and Keller under normal and sucrose treatment. Through the data analysis, we detected more than 3,000 differentially expressed genes between these two varieties. Such expression divergence was partially contributed by differential cis-regulatory elements or DNA methylation, which was genetically determined by functionally divergent genes between these two varieties. Both tandem and segmental duplication played important roles in the genome evolution and expression divergence. Conclusion Substantial differences in gene expression patterns between these two varieties have been observed. Such an expression divergence is genetically determined by the divergence in genome level.
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Affiliation(s)
- Shu-Ye Jiang
- Temasek Life Sciences Laboratory, 1 Research Link, the National University of Singapore, Singapore, 117604, Singapore
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13
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Higuchi M, Kondou Y, Mori M, Ichikawa T, Matsui M. Characterization of rice genes using a heterologous full-length cDNA expression system. Methods Mol Biol 2012; 847:75-90. [PMID: 22351001 DOI: 10.1007/978-1-61779-558-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
As a result of the progress in sequencing technology, many plant genomes have now been determined. Functional genomics is required to clarify gene function in many of these species. To identify useful genes easily and quickly, we have developed a FOX (full-length cDNA overexpressor) hunting system in which full-length cDNAs are overexpressed in Arabidopsis plants. This system was applied to high-throughput analysis of rice genes through heterologous expression in Arabidopsis (rice FOX Arabidopsis lines). We demonstrated that it is possible to carry out high-throughput analysis of gene function by utilizing rice FOX Arabidopsis lines. In this protocol, we describe how to isolate candidate rice FOX Arabidopsis lines and to determine the rice fl-cDNA that is responsible for the observed phenotype.
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Affiliation(s)
- Mieko Higuchi
- RIKEN Plant Science Center, Tsurumi-ku, Yokohama, Kanagawa, Japan
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14
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Gao D, Chen J, Chen M, Meyers BC, Jackson S. A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One 2012; 7:e32010. [PMID: 22359654 PMCID: PMC3281118 DOI: 10.1371/journal.pone.0032010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/18/2012] [Indexed: 12/31/2022] Open
Abstract
LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (>4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to date, only 292 bp. The element is found in rice, maize, sorghum and other grass genomes, which indicates that it was present in the ancestor of grass species, at least 50-80 MYA. Estimated insertion times, comparisons between sequenced rice lines, and mRNA data indicate that this element may still be active in some genomes. Unlike other LTR retrotransposons, the small LTR retrotransposons (SMARTs) are distributed throughout the genomes and are often located within or near genes with insertion patterns similar to MITEs (miniature inverted repeat transposable elements). Our data suggests that insertions of SMARTs into or near genes can, in a few instances, alter both gene structures and gene expression. Further evidence for a role in regulating gene expression, SMART-specific small RNAs (sRNAs) were identified that may be involved in gene regulation. Thus, SMARTs may have played an important role in genome evolution and genic innovation and may provide a valuable tool for gene tagging systems in grass.
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Affiliation(s)
- Dongying Gao
- Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Blake C. Meyers
- Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Scott Jackson
- Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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15
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Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. ANNALS OF BOTANY 2011; 108:1453-62. [PMID: 21224269 PMCID: PMC3219487 DOI: 10.1093/aob/mcq266] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/19/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.
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Affiliation(s)
- Estelle Jaligot
- UMR DIADE (IRD, UM2), IRD/CIRAD Palm Development Group, 911 avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
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16
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Guleria P, Mahajan M, Bhardwaj J, Yadav SK. Plant small RNAs: biogenesis, mode of action and their roles in abiotic stresses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2011; 9:183-99. [PMID: 22289475 PMCID: PMC5054152 DOI: 10.1016/s1672-0229(11)60022-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 10/21/2011] [Indexed: 01/01/2023]
Abstract
Small RNAs (sRNAs) are 18-30 nt non-coding regulatory elements found in diverse organisms, which were initially identified as small double-stranded RNAs in Caenorhabditis elegans. With the development of new and improved technologies, sRNAs have also been identified and characterized in plant systems. Among them, micro RNAs (miRNAs) and small interfering RNAs (siRNAs) are found to be very important riboregulators in plants. Various types of sRNAs differ in their mode of biogenesis and in their function of gene regulation. sRNAs are involved in gene regulation at both transcriptional and post-transcriptional levels. They are known to regulate growth and development of plants. Furthermore, sRNAs especially plant miRNAs have been found to be involved in various stress responses, such as oxidative, mineral nutrient deficiency, dehydration, and even mechanical stimulus. Therefore, in the present review, we focus on the current understanding of biogenesis and regulatory mechanisms of plant sRNAs and their responses to various abiotic stresses.
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Affiliation(s)
- Praveen Guleria
- Plant Metabolic Engineering, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, CSIR, Palampur 176061 (HP), India
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17
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Uthup TK, Ravindran M, Bini K, Thakurdas S. Divergent DNA methylation patterns associated with abiotic stress in Hevea brasiliensis. MOLECULAR PLANT 2011; 4:996-1013. [PMID: 21705581 DOI: 10.1093/mp/ssr039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cytosine methylation is a fundamental epigenetic mechanism for gene-expression regulation and development in plants. Here, we report for the first time the identification of DNA methylation patterns and their putative relationship with abiotic stress in the tree crop Hevea brasiliensis (source of 99% of natural rubber in the world). Regulatory sequences of four major genes involved in the mevalonate pathway (rubber biosynthesis pathway) and one general defense-related gene of three high-yielding popular rubber clones grown at two different agroclimatic conditions were analyzed for the presence of methylation. We found several significant variations in the methylation pattern at core DNA binding motifs within all the five genes. Several consistent clone-specific and location-specific methylation patterns were identified. The differences in methylation pattern observed at certain pivotal cis-regulatory sites indicate the direct impact of stress on the genome and support the hypothesis of site-specific stress-induced DNA methylation. It is assumed that some of the methylation patterns observed may be involved in the stress-responsive mechanism in plants by which they adapt to extreme conditions. The study also provide clues towards the existence of highly divergent phenotypic characters among Hevea clones despite their very similar genetic make-up. Altogether, the observations from this study prove beyond doubt that there exist epigenetic variations in Hevea and environmental factors play a significant role in the induction of site-specific epigenetic mutations in its genome.
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Affiliation(s)
- Thomas K Uthup
- Genome Analysis Lab, Rubber Research Institute of India, Rubber Board PO, Kottayam, Kerala, 686009, India.
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18
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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Zhang L, Zheng Y, Jagadeeswaran G, Li Y, Gowdu K, Sunkar R. Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 2011; 98:460-8. [PMID: 21907786 DOI: 10.1016/j.ygeno.2011.08.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 07/12/2011] [Accepted: 08/17/2011] [Indexed: 11/26/2022]
Abstract
Sweet Sorghum is largely grown for grain production but also recently emerged as one of the model feedstock plants for biofuel production. In plants, microRNA (miRNA)-guided gene regulation plays a key role in diverse biological processes, thus, their identification in different plant species is essential to understand post-transcriptional gene regulation. To identify miRNAs in Sorghum, we sequenced a small RNA library. Sequence analysis revealed the identity of 29 conserved miRNA families. Importantly, 13 novel miRNAs are identified, seven of which are conserved in closely related monocots. Temporal expression analysis of conserved and novel miRNAs indicated differential expression of several miRNAs. Approximately 125 genes that play diverse roles have been predicted as targets and a few targets were experimentally validated. These results provided insights into miRNA-controlled processes in Sorghum and also laid the foundation for manipulating miRNAs or their targets for improving biomass production and stress tolerance in Sorghum.
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Affiliation(s)
- Li Zhang
- Department of Biochemistry and Molecular Biology Oklahoma State University, Stillwater, OK 74078, USA
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20
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Bandopadhyay R, Rustgi S, Chaudhuri RK, Khurana P, Khurana JP, Tyagi AK, Balyan HS, Houben A, Gupta PK. Use of methylation filtration and C(0)t fractionation for analysis of genome composition and comparative genomics in bread wheat. J Genet Genomics 2011; 38:315-25. [PMID: 21777856 DOI: 10.1016/j.jgg.2011.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 06/08/2011] [Accepted: 06/13/2011] [Indexed: 11/16/2022]
Abstract
We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C(0)t fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences (e.g., transposable elements and simple sequence repeats), protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/exclusion in methylation-filtered (MF) library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags (ESTs) available in the public domain. Only a limited overlap among MF, high C(0)t (HC), and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space.
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Affiliation(s)
- Rajib Bandopadhyay
- Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut, India
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21
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Nelson JC, Wang S, Wu Y, Li X, Antony G, White FF, Yu J. Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum. BMC Genomics 2011; 12:352. [PMID: 21736744 PMCID: PMC3146956 DOI: 10.1186/1471-2164-12-352] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 07/07/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated. RESULTS Alignment of eight genome equivalents (6 Gb) to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage. CONCLUSIONS A sequence quantity of 3 million 50-base reads per accession using a BsrFI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.
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Affiliation(s)
- James C Nelson
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA.
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22
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Rivarola M, Foster JT, Chan AP, Williams AL, Rice DW, Liu X, Melake-Berhan A, Huot Creasy H, Puiu D, Rosovitz MJ, Khouri HM, Beckstrom-Sternberg SM, Allan GJ, Keim P, Ravel J, Rabinowicz PD. Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One 2011; 6:e21743. [PMID: 21750729 PMCID: PMC3131294 DOI: 10.1371/journal.pone.0021743] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 06/10/2011] [Indexed: 11/26/2022] Open
Abstract
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
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MESH Headings
- Base Sequence
- Ricinus communis/classification
- Ricinus communis/genetics
- Ricinus communis/growth & development
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Genetic Variation
- Genome, Chloroplast/genetics
- Genome, Mitochondrial/genetics
- Genome, Plant/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Maximo Rivarola
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Amber L. Williams
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Danny W. Rice
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Xinyue Liu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Heather Huot Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Daniela Puiu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - M. J. Rosovitz
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Hoda M. Khouri
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen M. Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Gerard J. Allan
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Pablo D. Rabinowicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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Abstract
In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as “evolutionary transients”, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.
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24
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Agrawal GK, Rakwal R. Rice proteomics: A move toward expanded proteome coverage to comparative and functional proteomics uncovers the mysteries of rice and plant biology. Proteomics 2011; 11:1630-49. [DOI: 10.1002/pmic.201000696] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/05/2011] [Accepted: 01/24/2011] [Indexed: 12/13/2022]
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25
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Agrawal GK, Job D, Zivy M, Agrawal VP, Bradshaw RA, Dunn MJ, Haynes PA, van Wijk KJ, Kikuchi S, Renaut J, Weckwerth W, Rakwal R. Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics 2011; 11:1559-68. [DOI: 10.1002/pmic.201000608] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/23/2010] [Accepted: 12/27/2010] [Indexed: 01/11/2023]
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26
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Wang J, Zhou J, Zhang B, Vanitha J, Ramachandran S, Jiang SY. Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:212-31. [PMID: 21205183 DOI: 10.1111/j.1744-7909.2010.01017.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plant bZIP transcription factors play crucial roles in multiple biological processes. However, little is known about the sorghum bZIP gene family although the sorghum genome has been completely sequenced. In this study, we have carried out a genome-wide identification and characterization of this gene family in sorghum. Our data show that the genome encodes at least 92 bZIP transcription factors. These bZIP genes have been expanded mainly by segmental duplication. Such an expansion mechanism has also been observed in rice, arabidopsis and many other plant organisms, suggesting a common expansion mode of this gene family in plants. Further investigation shows that most of the bZIP members have been present in the most recent common ancestor of sorghum and rice and the major expansion would occur before the sorghum-rice split era. Although these bZIP genes have been duplicated with a long history, they exhibited limited functional divergence as shown by nonsynonymous substitutions (Ka)/synonymous substitutions (Ks) analyses. Their retention was mainly due to the high percentages of expression divergence. Our data also showed that this gene family might play a role in multiple developmental stages and tissues and might be regarded as important regulators of various abiotic stresses and sugar signaling.
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Affiliation(s)
- Jizhou Wang
- Institute of Botany and Temasek Life Sciences Laboratory Joint Research & Development Laboratory, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
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27
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Bibikova M, Fan JB. Genome-wide DNA methylation profiling. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:210-223. [PMID: 20836023 DOI: 10.1002/wsbm.35] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA methylation plays a critical role in the regulation of gene expression. The ability to access the methylation status for a large number of genes or the entire genome should greatly facilitate the understanding of the nature of gene regulation in cells, and epigenetic mechanism of interactions between cells and environment. Microarray and sequencing-based DNA methylation profiling technologies have been developed to meet this goal. These methods can be categorized into three main classes based on how the methylation status is interrogated: discrimination of bisulfite induced C to T transition; cleavage of genomic DNA by methylation-sensitive restriction enzymes; and immunoprecipitation with methyl-binding protein or antibodies against methylated cytosines. With the development of next-generation sequencing technologies, genome-wide bisulfite sequencing has become a reality. Either whole- or reduced-genome approaches have been used to get the most comprehensive DNA methylation profiles in organisms of various genome sizes.
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Affiliation(s)
- Marina Bibikova
- Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121, USA
| | - Jian-Bing Fan
- Illumina, Inc., 9885 Towne Centre Drive, San Diego, CA 92121, USA
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28
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Abstract
The rich collection of known genetic information and the recent completion of rice genome sequencing project provided the cereal plant researchers a useful tool to investigate the roles of genes and genomic organization that contribute to numerous agronomic traits. Gramene ( http://www.gramene.org ) is a unique database where users are allowed to query and explore the power of genomic colinearity and comparative genomics for genetic and genomic studies on plant genomes. Gramene presents a wholesome perspective by assimilating data from a broad range of publicly available data sources for cereals like rice, sorghum, maize, wild rice, wheat, oats, barley, and other agronomically important crop plants such as poplar and grape, and the model plant Arabidopsis. As part of the process, it preserves the original data, but also reanalyzes for integration into several knowledge domains of maps, markers, genes, proteins, pathways, phenotypes, including Quantitative Trait Loci (QTL) and genetic diversity/natural variation. This allows researchers to use this information resource to decipher the known and predicted interactions between the components of biological systems, and how these interactions regulate plant development. Using examples from rice, this article describes how the database can be helpful to researchers representing an array of knowledge domains ranging from plant biology, plant breeding, molecular biology, genomics, biochemistry, genetics, bioinformatics, and phylogenomics.
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Affiliation(s)
- Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
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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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Chi Y, Cheng Y, Vanitha J, Kumar N, Ramamoorthy R, Ramachandran S, Jiang SY. Expansion mechanisms and functional divergence of the glutathione s-transferase family in sorghum and other higher plants. DNA Res 2010; 18:1-16. [PMID: 21169340 PMCID: PMC3041506 DOI: 10.1093/dnares/dsq031] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Glutathione S-transferases (GSTs) exist in various eukaryotes and function in detoxification of xenobiotics and in response to abiotic and biotic stresses. We have carried out a genome-wide survey of this gene family in 10 plant genomes. Our data show that tandem duplication has been regarded as the major expansion mechanism and both monocot and dicot plants may have practiced different expansion and evolutionary history. Non-synonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analyses showed that N- and C-terminal functional domains of GSTs (GST_N and GST_C) seem to have evolved under a strong purifying selection (Ka/Ks < 1) under different selective pressures. Differential evolutionary rates between GST_N and GST_C and high degree of expression divergence have been regarded as the major drivers for the retention of duplicated genes and the adaptability to various stresses. Expression profiling also indicated that the gene family plays a role not only in stress-related biological processes but also in the sugar-signalling pathway. Our survey provides additional annotation of the plant GST gene family and advance the understanding of plant GSTs in lineage-specific expansion and species diversification.
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Affiliation(s)
- Yunhua Chi
- IOB-TLL Joint R&D Laboratory, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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[Construction of a methylation filtration library in Hevea brasiliensis.]. YI CHUAN = HEREDITAS 2010; 32:1071-6. [PMID: 20943496 DOI: 10.3724/sp.j.1005.2010.01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In order to enrich gene encoding region of Hevea brasiliensis, a methylation filtration library was constructed using Escherichia coli McrBC restriction-modification system. The titers of the non-amplified library and the amplified library were 2.6×106 pfu/ml and 9.0×109, respectively. The rate of positive clones was 86.4%. The lengths of inserted DNA sequence ranged from 1 kb to 2.5 kb and the average size of inserts was 1.2 kb. One hundred clones were selected randomly for sequencing, resulting in splicing out of 81 non-redundant sequences, including 6 contigs and 75 singlets. The redundancy was 17.35%. Blast analysis showed that 39.5% of non-redundant sequences were homologous with the Nr database, 14.81% with the EST database, and 32.1% were unknown sequences. Some sequences were related genes for flowering, insect and disease resistance. Therefore, the rubber tree methylation library is helpful for discovery and cloning of functional genes.
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Agrawal GK, Jwa NS, Lebrun MH, Job D, Rakwal R. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 2010; 10:799-827. [PMID: 19953550 DOI: 10.1002/pmic.200900514] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Plant secretomics is a newly emerging area of the plant proteomics field. It basically describes the global study of secreted proteins into the extracellular space of plant cell or tissue at any given time and under certain conditions through various secretory mechanisms. A combination of biochemical, proteomics and bioinformatics approaches has been developed to isolate, identify and profile secreted proteins using complementary in vitro suspension-cultured cells and in planta systems. Developed inventories of secreted proteins under normal, biotic and abiotic conditions revealed several different types of novel secreted proteins, including the leaderless secretory proteins (LSPs). On average, LSPs can account for more than 50% of the total identified secretome, supporting, as in other eukaryotes, the existence of novel secretory mechanisms independent of the classical endoplasmic reticulum-Golgi secretory pathway, and suggesting that this non-classical mechanism of protein expression is, for as yet unknown reasons, more massively used than in other eukaryotic systems. Plants LSPs, which seem to be potentially involved in the defense/stress responses, might have dual (extracellular and/or intracellular) roles as most of them have established intracellular functions, yet presently unknown extracellular functions. Evidence is emerging on the role of glycosylation in the apical sorting and trafficking of secretory proteins. These initial secretome studies in plants have considerably advanced our understanding on secretion of different types of proteins and their underlying mechanisms, and opened a door for comparative analyses of plant secretomes with those of other organisms. In this first review on plant secretomics, we summarize and discuss the secretome definition, the applied approaches for unlocking secrets of the secreted proteins in the extracellular fluid, the possible functional significance and secretory mechanisms of LSPs, as well as glycosylation of secreted proteins and challenges involved ahead. Further improvements in existing and developing strategies and techniques will continue to drive forward plant secretomics research to building comprehensive and confident data sets of secreted proteins. This will lead to an increased understanding on how cells couple the concerted action of secreted protein networks to their internal and external environments.
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Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC, Moose SP, Hudson ME. Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol 2010; 11:R12. [PMID: 20128909 PMCID: PMC2872872 DOI: 10.1186/gb-2010-11-2-r12] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 10/04/2009] [Accepted: 02/03/2010] [Indexed: 01/26/2023] Open
Abstract
Genomic data together with sequencing of tissue specific small RNA libraries reveals insights into the genome content, small RNA repertoire and evolutionary origins of the grass Miscanthus × giganteus. Background Miscanthus × giganteus (Mxg) is a perennial grass that produces superior biomass yields in temperate environments. The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid. Results A survey of the complex Mxg genome was conducted using 454 pyrosequencing of genomic DNA and Illumina sequencing-by-synthesis of small RNA. We found that the coding fraction of the Mxg genome has a high level of sequence identity to that of other grasses. Highly repetitive sequences representing the great majority of the Mxg genome were predicted using non-cognate assembly for de novo repeat detection. Twelve abundant families of repeat were observed, with those related to either transposons or centromeric repeats likely to comprise over 95% of the genome. Comparisons of abundant repeat sequences to a small RNA survey of three Mxg organs (leaf, rhizome, inflorescence) revealed that the majority of observed 24-nucleotide small RNAs are derived from these repetitive sequences. We show that high-copy-number repeats match more of the small RNA, even when the amount of the repeat sequence in the genome is accounted for. Conclusions We show that major repeats are present within the triploid Mxg genome and are actively producing small RNAs. We also confirm the hypothesized origins of Mxg, and suggest that while the repeat content of Mxg differs from sorghum, the sorghum genome is likely to be of utility in the assembly of a gene-space sequence of Mxg.
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Affiliation(s)
- Kankshita Swaminathan
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Li Q, Yang X, Bai G, Warburton ML, Mahuku G, Gore M, Dai J, Li J, Yan J. Cloning and characterization of a putative GS3 ortholog involved in maize kernel development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:753-63. [PMID: 19898828 DOI: 10.1007/s00122-009-1196-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Accepted: 10/17/2009] [Indexed: 05/04/2023]
Abstract
The GS3 gene was the first identified gene controlling the grain size in rice. It has been proven to be involved in the evolution of grain size during domestication. We isolated the maize ortholog, ZmGS3 and investigated its role in the evolution of maize grain size. ZmGS3 has five exons encoding a protein with 198 amino acids, and has domains in common with the rice GS3 protein. Compared with teosinte, maize has reduced nucleotide diversity at ZmGS3, and the reduction is comparable to that found in neutrally evolving maize genes. No positive selection was detected along the length of the gene using either the Hudson-Kreitman-Aguadé or Tajima's D tests. Phylogenetic analysis reveals a distribution of maize sequences among two different clades, with one clade including related teosinte sequences. The nucleotide polymorphism analysis, selection test and phylogenetic analysis reveal that ZmGS3 has not been subjected to selection, and appears to be a neutrally evolving gene. In maize, ZmGS3 is primarily expressed in immature ears and kernels, implying a role in maize kernel development. Association mapping analysis revealed one polymorphism in the fifth exon that is significantly associated with kernel length in two environments. Also one polymorphism in the promoter region was found to affect hundred kernel weight in both environments. Collectively, these results imply that ZmGS3 is involved in maize kernel development but with different functional polymorphisms and thus, possibly different mechanisms from that of the rice GS3 gene.
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Affiliation(s)
- Qing Li
- National Maize Improvement Center of China, Key Laboratory of Crop Genomics and Genetic Improvement (Ministry of Agriculture), China Agricultural University, Yuanmingyuan West Road, Haidian, Beijing, China
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Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, Sommanas W, Tragoonrung S, Srinives P. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC PLANT BIOLOGY 2009; 9:137. [PMID: 19930676 PMCID: PMC2788553 DOI: 10.1186/1471-2229-9-137] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 11/24/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean. RESULT We have generated and characterized a total of 470,024 genome shotgun sequences covering 100.5 Mb of the mungbean (Vigna radiata (L.) Wilczek) genome using 454 sequencing technology. We identified 1,493 SSR motifs that could be used as potential molecular markers. Among 192 tested primer pairs in 17 mungbean accessions, 60 loci revealed polymorphism with polymorphic information content (PIC) values ranging from 0.0555 to 0.6907 with an average of 0.2594. Majority of microsatellite markers were transferable in Vigna species, whereas transferability rates were only 22.90% and 24.43% in Phaseolus vulgaris and Glycine max, respectively. We also used 16 SSR loci to evaluate phylogenetic relationship of 35 genotypes of the Asian Vigna group. The genome survey sequences were further analyzed to search for gene content. The evidence suggested 1,542 gene fragments have been sequence tagged, that fell within intersected existing gene models and shared sequence homology with other proteins in the database. Furthermore, potential microRNAs that could regulate developmental stages and environmental responses were discovered from this dataset. CONCLUSION In this report, we provided evidence of generating remarkable levels of diverse microsatellite markers and gene content from high throughput genome shotgun sequencing of the mungbean genomic DNA. The markers could be used in germplasm analysis, accessing genetic diversity and linkage mapping of mungbean.
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Affiliation(s)
- Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Pichahpuk Uthaipaisanwong
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Juntima Chanprasert
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Worapa Seehalak
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Warunee Sommanas
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Peerasak Srinives
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
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Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database. Nucleic Acids Res 2009; 38:D806-13. [PMID: 19808935 PMCID: PMC2808885 DOI: 10.1093/nar/gkp818] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNA) are approximately 21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.
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Affiliation(s)
- Zhenhai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry and State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Gupta V, Mathur S, Solanke AU, Sharma MK, Kumar R, Vyas S, Khurana P, Khurana JP, Tyagi AK, Sharma AK. Genome analysis and genetic enhancement of tomato. Crit Rev Biotechnol 2009; 29:152-81. [PMID: 19319709 DOI: 10.1080/07388550802688870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.
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Affiliation(s)
- Vikrant Gupta
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Varshney RK, Nayak SN, May GD, Jackson SA. Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 2009; 27:522-30. [PMID: 19679362 DOI: 10.1016/j.tibtech.2009.05.006] [Citation(s) in RCA: 396] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/21/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
Using next-generation sequencing technologies it is possible to resequence entire plant genomes or sample entire transcriptomes more efficiently and economically and in greater depth than ever before. Rather than sequencing individual genomes, we envision the sequencing of hundreds or even thousands of related genomes to sample genetic diversity within and between germplasm pools. Identification and tracking of genetic variation are now so efficient and precise that thousands of variants can be tracked within large populations. In this review, we outline some important areas such as the large-scale development of molecular markers for linkage mapping, association mapping, wide crosses and alien introgression, epigenetic modifications, transcript profiling, population genetics and de novo genome/organellar genome assembly for which these technologies are expected to advance crop genetics and breeding, leading to crop improvement.
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Affiliation(s)
- Rajeev K Varshney
- Centre of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, A.P., India.
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Zeller G, Henz SR, Widmer CK, Sachsenberg T, Rätsch G, Weigel D, Laubinger S. Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:1068-82. [PMID: 19222804 DOI: 10.1111/j.1365-313x.2009.03835.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.
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Affiliation(s)
- Georg Zeller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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40
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Yonemaru JI, Ando T, Mizubayashi T, Kasuga S, Matsumoto T, Yano M. Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of sorghum (Sorghum bicolor (L.) Moench). DNA Res 2009; 16:187-93. [PMID: 19363056 PMCID: PMC2695772 DOI: 10.1093/dnares/dsp005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Simple sequence repeat (SSR) markers with a high degree of polymorphism contribute to the molecular dissection of agriculturally important traits in sorghum (Sorghum bicolor (L.) Moench). We designed 5599 non-redundant SSR markers, including regions flanking the SSRs, in whole-genome shotgun sequences of sorghum line ATx623. (AT/TA)n repeats constituted 26.1% of all SSRs, followed by (AG/TC)n at 20.5%, (AC/TG)n at 13.7% and (CG/GC)n at 11.8%. The chromosomal locations of 5012 SSR markers were determined by comparing the locations identified by means of electronic PCR with the predicted positions of 34 008 gene loci. Most SSR markers had a similar distribution to the gene loci. Among 970 markers validated by fragment analysis, 67.8% (658 of 970) markers successfully provided PCR amplification in sorghum line BTx623, with a mean polymorphism rate of 45.1% (297 of 658) for all SSR loci in combinations of 11 sorghum lines and one sudangrass (Sorghum sudanense (Piper) Stapf) line. The product of 5012 and 0.678 suggests that ∼3400 SSR markers could be used to detect SSR polymorphisms and that more than 1500 (45.1% of 3400) markers could reveal SSR polymorphisms in combinations of Sorghum lines.
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Affiliation(s)
- Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
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Kondou Y, Higuchi M, Takahashi S, Sakurai T, Ichikawa T, Kuroda H, Yoshizumi T, Tsumoto Y, Horii Y, Kawashima M, Hasegawa Y, Kuriyama T, Matsui K, Kusano M, Albinsky D, Takahashi H, Nakamura Y, Suzuki M, Sakakibara H, Kojima M, Akiyama K, Kurotani A, Seki M, Fujita M, Enju A, Yokotani N, Saitou T, Ashidate K, Fujimoto N, Ishikawa Y, Mori Y, Nanba R, Takata K, Uno K, Sugano S, Natsuki J, Dubouzet JG, Maeda S, Ohtake M, Mori M, Oda K, Takatsuji H, Hirochika H, Matsui M. Systematic approaches to using the FOX hunting system to identify useful rice genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 57:883-94. [PMID: 18980645 DOI: 10.1111/j.1365-313x.2008.03733.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ectopic gene expression, or the gain-of-function approach, has the advantage that once the function of a gene is known the gene can be transferred to many different plants by transformation. We previously reported a method, called FOX hunting, that involves ectopic expression of Arabidopsis full-length cDNAs in Arabidopsis to systematically generate gain-of-function mutants. This technology is most beneficial for generating a heterologous gene resource for analysis of useful plant gene functions. As an initial model we generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt tolerance, UV signaling, high light tolerance, and heat stress tolerance. Some of the mutant phenotypes displayed by rice FOX Arabidopsis lines resulted from the expression of rice genes that had no homologs in Arabidopsis. This result demonstrated that rice fl-cDNAs could be used to introduce new gene functions in Arabidopsis. Furthermore, these findings showed that rice gene function could be analyzed by employing Arabidopsis as a heterologous host. This technology provides a framework for the analysis of plant gene function in a heterologous host and of plant improvement by using heterologous gene resources.
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Buell CR. Poaceae genomes: going from unattainable to becoming a model clade for comparative plant genomics. PLANT PHYSIOLOGY 2009; 149:111-6. [PMID: 19005087 PMCID: PMC2613712 DOI: 10.1104/pp.108.128926] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 11/05/2008] [Indexed: 05/21/2023]
Affiliation(s)
- C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.
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Messing J. Synergy of two reference genomes for the grass family. PLANT PHYSIOLOGY 2009; 149:117-24. [PMID: 19126702 PMCID: PMC2613724 DOI: 10.1104/pp.108.128520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 10/10/2008] [Indexed: 05/19/2023]
Affiliation(s)
- Joachim Messing
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020, USA.
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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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45
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Lu YD, Gan QH, Chi XY, Qin S. Roles of microRNA in plant defense and virus offense interaction. PLANT CELL REPORTS 2008; 27:1571-9. [PMID: 18626646 DOI: 10.1007/s00299-008-0584-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 06/24/2008] [Accepted: 06/25/2008] [Indexed: 05/22/2023]
Abstract
MicroRNAs (miRNA) that are around 22 nucleotides long non-protein-coding RNAs, play key regulatory roles in plants. Recent research findings show that miRNAs are involved in plant defense and viral offense systems. Advances in understanding the mechanism of miRNA biogenesis and evolution are useful for elucidating the complicated roles they play in viral infection networks. In this paper a brief summary of evolution of plant anti-virus defense is given and the function of miRNAs involved in plant-virus competition is highlighted. It is believed that miRNAs have several advantages over homology-dependent and siRNA-mediated gene silencing when they are applied biotechnologically to promote plant anti-virus defense. miRNA-mediated anti-virus pathway is an ancient mechanism with a promising future. However, using miRNAs as a powerful anti-virus tool will be better realized only if miRNA genomics and functions in plant viral infection are fully understood.
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Affiliation(s)
- Yan-du Lu
- YanTai Institute of Coastal Zone Research for Sustainable Development, Chinese Academy of Science, 264003, Yantai, China.
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Chan AP, Melake-Berhan A, O'Brien K, Buckley S, Quan H, Chen D, Lewis M, Banks JA, Rabinowicz PD. The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii. BMC Genomics 2008; 9:282. [PMID: 18549478 PMCID: PMC2442089 DOI: 10.1186/1471-2164-9-282] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 06/12/2008] [Indexed: 11/28/2022] Open
Abstract
Background The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be produced, little is known about basic aspects of its molecular biology. In order to provide the first glimpse to the epigenetic landscape of this early divergent vascular plant, we used the methylation filtration technique. Methylation filtration genomic libraries select unmethylated DNA clones due to the presence of the methylation-dependent restriction endonuclease McrBC in the bacterial host. Results We conducted a characterization of the DNA methylation patterns of the S. moellendorffii genome by sequencing a set of S. moellendorffii shotgun genomic clones, along with a set of methylation filtered clones. Chloroplast DNA, which is typically unmethylated, was enriched in the filtered library relative to the shotgun library, showing that there is DNA methylation in the extremely small S. moellendorffii genome. The filtered library also showed enrichment in expressed and gene-like sequences, while the highest-copy repeats were largely under-represented in this library. These results show that genes and repeats are differentially methylated in the S. moellendorffii genome, as occurs in other plants studied. Conclusion Our results shed light on the genome methylation pattern in a member of a relatively unexplored plant lineage. The DNA methylation data reported here will help understanding the involvement of this epigenetic mark in fundamental biological processes, as well as the evolutionary aspects of epigenetics in land plants.
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Affiliation(s)
- Agnes P Chan
- J. Craig Venter Institute, Rockville, MD 20850, USA.
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Rushton PJ, Bokowiec MT, Han S, Zhang H, Brannock JF, Chen X, Laudeman TW, Timko MP. Tobacco transcription factors: novel insights into transcriptional regulation in the Solanaceae. PLANT PHYSIOLOGY 2008; 147:280-95. [PMID: 18337489 PMCID: PMC2330323 DOI: 10.1104/pp.107.114041] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 03/04/2008] [Indexed: 05/18/2023]
Abstract
Tobacco (Nicotiana tabacum) is a member of the Solanaceae, one of the agronomically most important groups of flowering plants. We have performed an in silico analysis of 1.15 million gene-space sequence reads from the tobacco nuclear genome and report the detailed analysis of more than 2,500 tobacco transcription factors (TFs). The tobacco genome contains at least one member of each of the 64 well-characterized TF families identified in sequenced vascular plant genomes, indicating that evolution of the Solanaceae was not associated with the gain or loss of TF families. However, we found notable differences between tobacco and non-Solanaceae species in TF family size and evidence for both tobacco- and Solanaceae-specific subfamily expansions. Compared with TF families from sequenced plant genomes, tobacco has a higher proportion of ERF/AP2, C2H2 zinc finger, homeodomain, GRF, TCP, zinc finger homeodomain, BES, and STERILE APETALA (SAP) genes and novel subfamilies of BES, C2H2 zinc finger, SAP, and NAC genes. The novel NAC subfamily, termed TNACS, appears restricted to the Solanaceae, as they are absent from currently sequenced plant genomes but present in tomato (Solanum lycopersicum), pepper (Capsicum annuum), and potato (Solanum tuberosum). They constitute approximately 25% of NAC genes in tobacco. Based on our phylogenetic studies, we predict that many of the more than 50 tobacco group IX ERF genes are involved in jasmonate responses. Consistent with this, over two-thirds of group IX ERF genes tested showed increased mRNA levels following jasmonate treatment. Our data are a major resource for the Solanaceae and fill a void in studies of TF families across the plant kingdom.
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Affiliation(s)
- Paul J Rushton
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X. Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 2008; 9:103. [PMID: 18304330 PMCID: PMC2279124 DOI: 10.1186/1471-2164-9-103] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 02/27/2008] [Indexed: 11/16/2022] Open
Abstract
Background Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly by poor subsistence farmers. Despite its economic and social importance in the developing world, cowpea remains to a large extent an underexploited crop. Among the major goals of cowpea breeding and improvement programs is the stacking of desirable agronomic traits, such as disease and pest resistance and response to abiotic stresses. Implementation of marker-assisted selection and breeding programs is severely limited by a paucity of trait-linked markers and a general lack of information on gene structure and organization. With a nuclear genome size estimated at ~620 Mb, the cowpea genome is an ideal target for reduced representation sequencing. Results We report here the sequencing and analysis of the gene-rich, hypomethylated portion of the cowpea genome selectively cloned by methylation filtration (MF) technology. Over 250,000 gene-space sequence reads (GSRs) with an average length of 610 bp were generated, yielding ~160 Mb of sequence information. The GSRs were assembled, annotated by BLAST homology searches of four public protein annotation databases and four plant proteomes (A. thaliana, M. truncatula, O. sativa, and P. trichocarpa), and analyzed using various domain and gene modeling tools. A total of 41,260 GSR assemblies and singletons were annotated, of which 19,786 have unique GenBank accession numbers. Within the GSR dataset, 29% of the sequences were annotated using the Arabidopsis Gene Ontology (GO) with the largest categories of assigned function being catalytic activity and metabolic processes, groups that include the majority of cellular enzymes and components of amino acid, carbohydrate and lipid metabolism. A total of 5,888 GSRs had homology to genes encoding transcription factors (TFs) and transcription associated factors (TAFs) representing about 5% of the total annotated sequences in the dataset. Sixty-two (62) of the 64 well-characterized plant transcription factor (TF) gene families are represented in the cowpea GSRs, and these families are of similar size and phylogenetic organization to those characterized in other plants. The cowpea GSRs also provides a rich source of genes involved in photoperiodic control, symbiosis, and defense-related responses. Comparisons to available databases revealed that about 74% of cowpea ESTs and 70% of all legume ESTs were represented in the GSR dataset. As approximately 12% of all GSRs contain an identifiable simple-sequence repeat, the dataset is a powerful resource for the design of microsatellite markers. Conclusion The availability of extensive publicly available genomic data for cowpea, a non-model legume with significant importance in the developing world, represents a significant step forward in legume research. Not only does the gene space sequence enable the detailed analysis of gene structure, gene family organization and phylogenetic relationships within cowpea, but it also facilitates the characterization of syntenic relationships with other cultivated and model legumes, and will contribute to determining patterns of chromosomal evolution in the Leguminosae. The micro and macrosyntenic relationships detected between cowpea and other cultivated and model legumes should simplify the identification of informative markers for marker-assisted trait selection and map-based gene isolation necessary for cowpea improvement.
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Affiliation(s)
- Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA.
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Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP. TOBFAC: the database of tobacco transcription factors. BMC Bioinformatics 2008; 9:53. [PMID: 18221524 PMCID: PMC2246155 DOI: 10.1186/1471-2105-9-53] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 01/25/2008] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Regulation of gene expression at the level of transcription is a major control point in many biological processes. Transcription factors (TFs) can activate and/or repress the transcriptional rate of target genes and vascular plant genomes devote approximately 7% of their coding capacity to TFs. Global analysis of TFs has only been performed for three complete higher plant genomes - Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa) and rice (Oryza sativa). Presently, no large-scale analysis of TFs has been made from a member of the Solanaceae, one of the most important families of vascular plants. To fill this void, we have analysed tobacco (Nicotiana tabacum) TFs using a dataset of 1,159,022 gene-space sequence reads (GSRs) obtained by methylation filtering of the tobacco genome. An analytical pipeline was developed to isolate TF sequences from the GSR data set. This involved multiple (typically 10-15) independent searches with different versions of the TF family-defining domain(s) (normally the DNA-binding domain) followed by assembly into contigs and verification. Our analysis revealed that tobacco contains a minimum of 2,513 TFs representing all of the 64 well-characterised plant TF families. The number of TFs in tobacco is higher than previously reported for Arabidopsis and rice. RESULTS TOBFAC: the database of tobacco transcription factors, is an integrative database that provides a portal to sequence and phylogeny data for the identified TFs, together with a large quantity of other data concerning TFs in tobacco. The database contains an individual page dedicated to each of the 64 TF families. These contain background information, domain architecture via Pfam links, a list of all sequences and an assessment of the minimum number of TFs in this family in tobacco. Downloadable phylogenetic trees of the major families are provided along with detailed information on the bioinformatic pipeline that was used to find all family members. TOBFAC also contains EST data, a list of published tobacco TFs and a list of papers concerning tobacco TFs. The sequences and annotation data are stored in relational tables using a PostgrelSQL relational database management system. The data processing and analysis pipelines used the Perl programming language. The web interface was implemented in JavaScript and Perl CGI running on an Apache web server. The computationally intensive data processing and analysis pipelines were run on an Apple XServe cluster with more than 20 nodes. CONCLUSION TOBFAC is an expandable knowledgebase of tobacco TFs with data currently available for over 2,513 TFs from 64 gene families. TOBFAC integrates available sequence information, phylogenetic analysis, and EST data with published reports on tobacco TF function. The database provides a major resource for the study of gene expression in tobacco and the Solanaceae and helps to fill a current gap in studies of TF families across the plant kingdom. TOBFAC is publicly accessible at http://compsysbio.achs.virginia.edu/tobfac/.
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Affiliation(s)
- Paul J Rushton
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marta T Bokowiec
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Thomas W Laudeman
- Academic Computing Health Sciences, Information Technology and Communication, University of Virginia, Charlottesville, VA 22908, USA
| | - Jennifer F Brannock
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Xianfeng Chen
- Department of Microbiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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Gui Y, Wang S, Quan L, Zhou C, Long S, Zheng H, Jin L, Zhang X, Ma N, Fan L. Genome size and sequence composition of moso bamboo: a comparative study. ACTA ACUST UNITED AC 2008; 50:700-5. [PMID: 17879070 DOI: 10.1007/s11427-007-0081-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 07/04/2007] [Indexed: 11/27/2022]
Abstract
Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo--over two-thirds of the total bamboo forest area--and the highest economic value in China. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize genome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotransposons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to confirm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos.
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Affiliation(s)
- YiJie Gui
- Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China
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