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Du J, Zhang Z, Zhang H, Junhong T. EST–SSR marker development and transcriptome sequencing analysis of different tissues of Korean pine ( Pinus koraiensis Sieb. et Zucc.). BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1331755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Jia Du
- Department of Environmental Engineering and Science, Hangzhou Dianzi University, Hangzhou, P. R. China
| | - Zhen Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, P. R. China
| | - Hanguo Zhang
- School of Forestry, Northeast Forestry University, Harbin, P. R. China
| | - Tang Junhong
- Department of Environmental Engineering and Science, Hangzhou Dianzi University, Hangzhou, P. R. China
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Carvalho A, Paiva J, Louzada J, Lima-Brito J. The transcriptomics of secondary growth and wood formation in conifers. Mol Biol Int 2013; 2013:974324. [PMID: 24288610 PMCID: PMC3830773 DOI: 10.1155/2013/974324] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/22/2013] [Accepted: 09/09/2013] [Indexed: 11/17/2022] Open
Abstract
In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality.
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Affiliation(s)
- Ana Carvalho
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology (IBB/CGB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - Jorge Paiva
- Instituto de Investigação Científica Tropical (IICT), Centro de Florestas e Produtos Florestais (FLOR), Tapada da Ajuda, 1349-018 Lisboa, Portugal
| | - José Louzada
- Department of Forestry Sciences and Landscape (CIFAP), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - José Lima-Brito
- Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology (IBB/CGB), University of Tras-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
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Mann IK, Wegrzyn JL, Rajora OP. Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource. BMC Genomics 2013; 14:702. [PMID: 24119028 PMCID: PMC4007752 DOI: 10.1186/1471-2164-14-702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/08/2013] [Indexed: 12/01/2022] Open
Abstract
Background EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change. Results We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified. Conclusions We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and ecological traits. We have also identified full-length genes and microsatellite-containing ESTs. Based on EST sequence similarities, black spruce showed close evolutionary relationships with congeneric Picea glauca and Picea sitchensis compared to other Pinaceae members and angiosperms. The EST sequences reported here provide an important resource for genome annotation, functional and comparative genomics, molecular breeding, conservation and management studies and applications in black spruce and related conifer species.
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Affiliation(s)
- Ishminder K Mann
- Forest Genetics and Biotechnology Group, Department of Biology, Life Sciences Centre, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4J1, Canada.
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Niu SH, Li ZX, Yuan HW, Chen XY, Li Y, Li W. Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny. BMC Genomics 2013; 14:263. [PMID: 23597112 PMCID: PMC3640921 DOI: 10.1186/1471-2164-14-263] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 04/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of P. tabuliformis genomic information. RESULTS The increasing amount of transcriptome data on Pinus provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first P. tabuliformis transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the Pinus lineage. CONCLUSIONS A large collection of high-quality ESTs was obtained, de novo assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of P. tabuliformis and which will gradually be applied in breeding programs of P. tabuliformis. Furthermore, these data will facilitate future studies of the comparative genomics of P. tabuliformis and other related species.
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Affiliation(s)
- Shi-Hui Niu
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People's Republic of China
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Pavy N, Pelgas B, Laroche J, Rigault P, Isabel N, Bousquet J. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers. BMC Biol 2012; 10:84. [PMID: 23102090 PMCID: PMC3519789 DOI: 10.1186/1741-7007-10-84] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. RESULTS To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. CONCLUSIONS Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec G1V 0A6, Canada.
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Raherison E, Rigault P, Caron S, Poulin PL, Boyle B, Verta JP, Giguère I, Bomal C, Bohlmann J, MacKay J. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression. BMC Genomics 2012; 13:434. [PMID: 22931377 PMCID: PMC3534630 DOI: 10.1186/1471-2164-13-434] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/11/2012] [Indexed: 12/22/2022] Open
Abstract
Background Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. This report presents a global overview of transcriptome variation in a conifer tree and documents conservation and diversity of gene expression patterns among major vegetative tissues. Results An oligonucleotide microarray was developed from Picea glauca and P. sitchensis cDNA datasets. It represents 23,853 unique genes and was shown to be suitable for transcriptome profiling in several species. A comparison of secondary xylem and phelloderm tissues showed that preferential expression in these vascular tissues was highly conserved among Picea spp. RNA-Sequencing strongly confirmed tissue preferential expression and provided a robust validation of the microarray design. A small database of transcription profiles called PiceaGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PiceaGenExpress. In conifer trees, dehydrins and late embryogenesis abundant (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. Conclusion Together, the oligonucleotide microarray and the PiceaGenExpress database represent the first resource of this kind for gymnosperm plants. The spruce transcriptome analysis reported here is expected to accelerate genetic studies in the large and important group comprised of conifer trees.
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Affiliation(s)
- Elie Raherison
- Center for Forest Research and Institute for Integrative and Systems Biology, Université Laval, Québec, QC, Canada, G1V 0A6
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Villalobos DP, Díaz-Moreno SM, Said ESS, Cañas RA, Osuna D, Van Kerckhoven SHE, Bautista R, Claros MG, Cánovas FM, Cantón FR. Reprogramming of gene expression during compression wood formation in pine: coordinated modulation of S-adenosylmethionine, lignin and lignan related genes. BMC PLANT BIOLOGY 2012; 12:100. [PMID: 22747794 PMCID: PMC3406974 DOI: 10.1186/1471-2229-12-100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 06/29/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Transcript profiling of differentiating secondary xylem has allowed us to draw a general picture of the genes involved in wood formation. However, our knowledge is still limited about the regulatory mechanisms that coordinate and modulate the different pathways providing substrates during xylogenesis. The development of compression wood in conifers constitutes an exceptional model for these studies. Although differential expression of a few genes in differentiating compression wood compared to normal or opposite wood has been reported, the broad range of features that distinguish this reaction wood suggest that the expression of a larger set of genes would be modified. RESULTS By combining the construction of different cDNA libraries with microarray analyses we have identified a total of 496 genes in maritime pine (Pinus pinaster, Ait.) that change in expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Samples from different provenances collected in different years and geographic locations were integrated into the analyses to mitigate the effects of multiple sources of variability. This strategy allowed us to define a group of genes that are consistently associated with compression wood formation. Correlating with the deposition of a thicker secondary cell wall that characterizes compression wood development, the expression of a number of genes involved in synthesis of cellulose, hemicellulose, lignin and lignans was up-regulated. Further analysis of a set of these genes involved in S-adenosylmethionine metabolism, ammonium recycling, and lignin and lignans biosynthesis showed changes in expression levels in parallel to the levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. CONCLUSIONS The comparative transcriptomic analysis reported here have revealed a broad spectrum of coordinated transcriptional modulation of genes involved in biosynthesis of different cell wall polymers associated with within-tree variations in pine wood structure and composition. In particular, we demonstrate the coordinated modulation at transcriptional level of a gene set involved in S-adenosylmethionine synthesis and ammonium assimilation with increased demand for coniferyl alcohol for lignin and lignan synthesis, enabling a better understanding of the metabolic requirements in cells undergoing lignification.
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Affiliation(s)
- David P Villalobos
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
- Department of Plant Molecular Biology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Sara M Díaz-Moreno
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, SE-10691, Stockholm, Sweden
| | - El-Sayed S Said
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Rafael A Cañas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Daniel Osuna
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
- Departamento de Fisiología Vegetal, Centro Hispano-Luso de Investigaciones Agrarias, Facultad de Biología, Universidad de Salamanca, C/Río Duero 12, 37185, Salamanca, Spain
| | - Sonia H E Van Kerckhoven
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Rocío Bautista
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Manuel Gonzalo Claros
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Francisco M Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
| | - Francisco R Cantón
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus Universitario de Teatinos, 29071, Málaga, Spain
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Zhou S, Ji G, Liu X, Li P, Moler J, Karro JE, Liang C. Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data. BMC Biotechnol 2012; 12:16. [PMID: 22554190 PMCID: PMC3424822 DOI: 10.1186/1472-6750-12-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 03/15/2012] [Indexed: 11/12/2022] Open
Abstract
Background Expressed Sequence Tag (EST) sequences are widely used in applications such as genome annotation, gene discovery and gene expression studies. However, some of GenBank dbEST sequences have proven to be “unclean”. Identification of cDNA termini/ends and their structures in raw ESTs not only facilitates data quality control and accurate delineation of transcription ends, but also furthers our understanding of the potential sources of data abnormalities/errors present in the wet-lab procedures for cDNA library construction. Results After analyzing a total of 309,976 raw Pinus taeda ESTs, we uncovered many distinct variations of cDNA termini, some of which prove to be good indicators of wet-lab artifacts, and characterized each raw EST by its cDNA terminus structure patterns. In contrast to the expected patterns, many ESTs displayed complex and/or abnormal patterns that represent potential wet-lab errors such as: a failure of one or both of the restriction enzymes to cut the plasmid vector; a failure of the restriction enzymes to cut the vector at the correct positions; the insertion of two cDNA inserts into a single vector; the insertion of multiple and/or concatenated adapters/linkers; the presence of 3′-end terminal structures in designated 5′-end sequences or vice versa; and so on. With a close examination of these artifacts, many problematic ESTs that have been deposited into public databases by conventional bioinformatics pipelines or tools could be cleaned or filtered by our methodology. We developed a software tool for Abnormality Filtering and Sequence Trimming for ESTs (AFST, http://code.google.com/p/afst/) using a pattern analysis approach. To compare AFST with other pipelines that submitted ESTs into dbEST, we reprocessed 230,783 Pinus taeda and 38,709 Arachis hypogaea GenBank ESTs. We found 7.4% of Pinus taeda and 29.2% of Arachis hypogaea GenBank ESTs are “unclean” or abnormal, all of which could be cleaned or filtered by AFST. Conclusions cDNA terminal pattern analysis, as implemented in the AFST software tool, can be utilized to reveal wet-lab errors such as restriction enzyme cutting abnormities and chimeric EST sequences, detect various data abnormalities embedded in existing Sanger EST datasets, improve the accuracy of identifying and extracting bona fide cDNA inserts from raw ESTs, and therefore greatly benefit downstream EST-based applications.
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Affiliation(s)
- Sun Zhou
- Department of Automation, Xiamen University, Fujian, China.
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Emiliani G, Traversi ML, Anichini M, Giachi G, Giovannelli A. Transcript Accumulation Dynamics of Phenylpropanoid Pathway Genes in the Maturing Xylem and Phloem of Picea abies during Latewood Formation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2011; 53:783-799. [PMID: 21767344 DOI: 10.1111/j.1744-7909.2011.01069.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In temperate regions, latewood is produced when cambial activity declines with the approach of autumnal dormancy. The understanding of the temporal (cambium activity vs dormancy) and spatial (phloem, cambial region, maturing xylem) regulation of key genes involved in the phenylpropanoid pathway during latewood formation represents a crucial step towards providing new insights into the molecular basis of xylogenesis. In this study, the temporal pattern of transcript accumulation of 12 phenylpropanoid genes (PAL1, C4H3/5, C4H4, 4CL3, 4CL4, HCT1, C3H3, CCoAOMT1, COMT2, COMT5, CCR2) was analyzed in maturing xylem and phloem of Picea abies during latewood formation. Quantitative reverse transcription-polymerase chain reaction analyses revealed a well-defined RNA accumulation pattern of genes involved in the phenylpropanoid pathway during latewood formation. Differences in the RNA accumulation patterns were detected between the different tissue types analyzed. The results obtained here demonstrated that the molecular processes involved in monolignol biosynthesis are not restricted to the cambial activity timeframe but continued after the end of cambium cell proliferation. Furthermore, since it has been shown that lignification of maturing xylem takes place in late autumn, we argue on the basis of our data that phloem could play a key role in the monolignol biosynthesis process.
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Affiliation(s)
- Giovanni Emiliani
- Trees and Timber Institute-National Research Council, I-50019 Sesto Fiorentino, ItalyDepartment of Chemistry "U. Schiff", University of Florence, I-50019 Sesto Fiorentino, Italy
| | - Maria Laura Traversi
- Trees and Timber Institute-National Research Council, I-50019 Sesto Fiorentino, ItalyDepartment of Chemistry "U. Schiff", University of Florence, I-50019 Sesto Fiorentino, Italy
| | - Monica Anichini
- Trees and Timber Institute-National Research Council, I-50019 Sesto Fiorentino, ItalyDepartment of Chemistry "U. Schiff", University of Florence, I-50019 Sesto Fiorentino, Italy
| | - Guido Giachi
- Trees and Timber Institute-National Research Council, I-50019 Sesto Fiorentino, ItalyDepartment of Chemistry "U. Schiff", University of Florence, I-50019 Sesto Fiorentino, Italy
| | - Alessio Giovannelli
- Trees and Timber Institute-National Research Council, I-50019 Sesto Fiorentino, ItalyDepartment of Chemistry "U. Schiff", University of Florence, I-50019 Sesto Fiorentino, Italy
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Beaulieu J, Doerksen T, Boyle B, Clément S, Deslauriers M, Beauseigle S, Blais S, Poulin PL, Lenz P, Caron S, Rigault P, Bicho P, Bousquet J, Mackay J. Association genetics of wood physical traits in the conifer white spruce and relationships with gene expression. Genetics 2011; 188:197-214. [PMID: 21385726 PMCID: PMC3120141 DOI: 10.1534/genetics.110.125781] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/22/2011] [Indexed: 01/01/2023] Open
Abstract
Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker-trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P ≤ 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q ≤ 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P ≤ 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a β-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.
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Affiliation(s)
- Jean Beaulieu
- Natural Resources Canada, Canadian Wood Fibre Centre, Québec City, Québec, Canada.
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Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 2010; 11:681. [PMID: 21122097 PMCID: PMC3053591 DOI: 10.1186/1471-2164-11-681] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 12/01/2010] [Indexed: 12/03/2022] Open
Abstract
Background De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a Eucalyptus tree species (E. grandis) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs. Results We present an extensive expressed gene catalog for a commercially grown E. grandis × E. urophylla hybrid clone constructed using only Illumina mRNA-Seq technology and de novo assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any Eucalyptus tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions. Conclusions De novo assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in Eucalyptus and other non-model organisms. The transcriptome resource (Eucspresso, http://eucspresso.bi.up.ac.za/) generated by this study will be of value for genomic analysis of woody biomass production in Eucalyptus and for comparative genomic analysis of growth and development in woody and herbaceous plants.
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Affiliation(s)
- Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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Pitre FE, Lafarguette F, Boyle B, Pavy N, Caron S, Dallaire N, Poulin PL, Ouellet M, Morency MJ, Wiebe N, Ly Lim E, Urbain A, Mouille G, Cooke JEK, Mackay JJ. High nitrogen fertilization and stem leaning have overlapping effects on wood formation in poplar but invoke largely distinct molecular pathways. TREE PHYSIOLOGY 2010; 30:1273-89. [PMID: 20739427 DOI: 10.1093/treephys/tpq073] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Previous studies indicated that high nitrogen fertilization may impact secondary xylem development and alter fibre anatomy and composition. The resulting wood shares some resemblance with tension wood, which has much thicker cell walls than normal wood due to the deposition of an additional layer known as the G-layer. This report compares the short-term effects of high nitrogen fertilization and tree leaning to induce tension wood, either alone or in combination, upon wood formation in young trees of Populus trichocarpa (Torr. & Gray) × P. deltoides Bartr. ex Marsh. Fibre anatomy, chemical composition and transcript profiles were examined in newly formed secondary xylem. Each of the treatments resulted in thicker cell walls relative to the controls. High nitrogen and tree leaning had overlapping effects on chemical composition based on Fourier transform infrared analysis, specifically indicating that secondary cell wall composition was shifted in favour of cellulose and hemicelluloses relative to lignin content. In contrast, the high-nitrogen trees had shorter fibres, whilst the leaning trees had longer fibres that the controls. Microarray transcript profiling carried out after 28 days of treatment identified 180 transcripts that accumulated differentially in one or more treatments. Only 10% of differentially expressed transcripts were affected in all treatments relative to the controls. Several of the affected transcripts were related to carbohydrate metabolism, secondary cell wall formation, nitrogen metabolism and osmotic stress. RT-qPCR analyses at 1, 7 and 28 days showed that several transcripts followed very different accumulation profiles in terms of rate and level of accumulation, depending on the treatment. Our findings suggest that high nitrogen fertilization and tension wood induction elicit largely distinct and molecular pathways with partial overlap. When combined, the two types of environmental cue yielded additive effects.
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Affiliation(s)
- Frederic E Pitre
- ARBOREA, Centre for Forest Research, Universite Laval, Quebec QC, Canada G1K 7P4
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13
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Bedon F, Bomal C, Caron S, Levasseur C, Boyle B, Mansfield SD, Schmidt A, Gershenzon J, Grima-Pettenati J, Séguin A, MacKay J. Subgroup 4 R2R3-MYBs in conifer trees: gene family expansion and contribution to the isoprenoid- and flavonoid-oriented responses. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3847-64. [PMID: 20732878 PMCID: PMC2935864 DOI: 10.1093/jxb/erq196] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 06/09/2010] [Accepted: 06/10/2010] [Indexed: 05/18/2023]
Abstract
Transcription factors play a fundamental role in plants by orchestrating temporal and spatial gene expression in response to environmental stimuli. Several R2R3-MYB genes of the Arabidopsis subgroup 4 (Sg4) share a C-terminal EAR motif signature recently linked to stress response in angiosperm plants. It is reported here that nearly all Sg4 MYB genes in the conifer trees Picea glauca (white spruce) and Pinus taeda (loblolly pine) form a monophyletic clade (Sg4C) that expanded following the split of gymnosperm and angiosperm lineages. Deeper sequencing in P. glauca identified 10 distinct Sg4C sequences, indicating over-representation of Sg4 sequences compared with angiosperms such as Arabidopsis, Oryza, Vitis, and Populus. The Sg4C MYBs share the EAR motif core. Many of them had stress-responsive transcript profiles after wounding, jasmonic acid (JA) treatment, or exposure to cold in P. glauca and P. taeda, with MYB14 transcripts accumulating most strongly and rapidly. Functional characterization was initiated by expressing the P. taeda MYB14 (PtMYB14) gene in transgenic P. glauca plantlets with a tissue-preferential promoter (cinnamyl alcohol dehydrogenase) and a ubiquitous gene promoter (ubiquitin). Histological, metabolite, and transcript (microarray and targeted quantitative real-time PCR) analyses of PtMYB14 transgenics, coupled with mechanical wounding and JA application experiments on wild-type plantlets, allowed identification of PtMYB14 as a putative regulator of an isoprenoid-oriented response that leads to the accumulation of sesquiterpene in conifers. Data further suggested that PtMYB14 may contribute to a broad defence response implicating flavonoids. This study also addresses the potential involvement of closely related Sg4C sequences in stress responses and plant evolution.
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Affiliation(s)
- Frank Bedon
- Centre d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada
- UMR UPS/CNRS 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville Tolosane, 31326 Castanet Tolosan, France
| | - Claude Bomal
- Centre d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada
| | - Sébastien Caron
- Centre d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada
| | - Caroline Levasseur
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec (QC), G1V A06, Canada
| | - Brian Boyle
- Centre d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada
| | - Shawn D. Mansfield
- Canada Research Chair in Wood and Fibre Quality, Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver (BC), V6T 1Z4, Canada
| | - Axel Schmidt
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str.8, Beutenberg-Campus, D-07745 Jena, Germany
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str.8, Beutenberg-Campus, D-07745 Jena, Germany
| | - Jacqueline Grima-Pettenati
- UMR UPS/CNRS 5546, Pôle de Biotechnologies Végétales, 24 chemin de Borde Rouge, BP42617, Auzeville Tolosane, 31326 Castanet Tolosan, France
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec (QC), G1V A06, Canada
| | - John MacKay
- Centre d’Étude de la Forêt, Université Laval, Québec (QC), G1V A06, Canada
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Barros E, van Staden CA, Lezar S. A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis. BMC Biotechnol 2009; 9:51. [PMID: 19473481 PMCID: PMC2698882 DOI: 10.1186/1472-6750-9-51] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 05/27/2009] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. The most serious problem affecting the quality and yield of solid wood products is the occurrence of end splitting in logs. Selection of E. grandis planting stock that exhibit preferred wood qualities is thus a priority of the South African forestry industry. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven different E. grandis trees. RESULTS A 1578-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP clones and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. CONCLUSION A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.
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Affiliation(s)
- Eugenia Barros
- CSIR – Biosciences, Meiring Naude Road, Brummeria, Pretoria, 0001, South Africa
| | | | - Sabine Lezar
- CSIR – Biosciences, Meiring Naude Road, Brummeria, Pretoria, 0001, South Africa
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15
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Lindlöf A, Bräutigam M, Chawade A, Olsson O, Olsson B. Evaluation of combining several statistical methods with a flexible cutoff for identifying differentially expressed genes in pairwise comparison of EST sets. Bioinform Biol Insights 2008; 2:215-37. [PMID: 19812778 PMCID: PMC2735943 DOI: 10.4137/bbi.s431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The detection of differentially expressed genes from EST data is of importance for the discovery of potential biological or pharmaceutical targets, especially when studying biological processes in less characterized organisms and where large-scale microarrays are not an option. We present a comparison of five different statistical methods for identifying up-regulated genes through pairwise comparison of EST sets, where one of the sets is generated from a treatment and the other one serves as a control. In addition, we specifically address situations where the sets are relatively small (~2,000–10,000 ESTs) and may differ in size. The methods were tested on both simulated and experimentally derived data, and compared to a collection of cold stress induced genes identified by microarrays. We found that combining the method proposed by Audic and Claverie with Fisher’s exact test and a method based on calculating the difference in relative frequency was the best combination for maximizing the detection of up-regulated genes. We also introduced the use of a flexible cutoff, which takes the size of the EST sets into consideration. This could be considered as an alternative to a static cutoff. Finally, the detected genes showed a low overlap with those identified by microarrays, which indicates, as in previous studies, low overall concordance between the two platforms.
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Affiliation(s)
- Angelica Lindlöf
- School of Humanities and Informatics, University of Skövde, Box 408, 541 28 Skövde, Sweden.
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Oh TJ, Wartell RM, Cairney J, Pullman GS. Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA processing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda). THE NEW PHYTOLOGIST 2008; 179:67-80. [PMID: 18433430 DOI: 10.1111/j.1469-8137.2008.02448.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are known to regulate plant development, but have not been studied in gymnosperm seed tissues. The presence and characteristics of several miRNAs were examined in zygotic embryos (ZEs) and female gametophytes (FGs) of Pinus taeda (loblolly pine). Evidence for miRNAs was obtained using northern analyses and quantitative reverse transcription polymerase chain reaction (qRT-PCR) mediated with poly(A) polymerase. Partial sequences of two miRNAs were verified. Three regions of putative mRNA targets were analyzed by qRT-PCR to monitor the occurrence of stage-dependent miRNA-mediated cleavage. Five miRNAs were identified in ZEs and FGs along with partial sequences of Pta-miR166 and Pta-miR167. Both miRNAs showed differing degrees of tissue-specific and stage-specific modulation. Analysis of HB15L mRNA (a potential Pta-miR166 target) suggested miRNA-guided cleavage in ZEs and FGs. Analysis of ARF8L mRNA (a potential Pta-miR167 target) implied cleavage in ZEs but not in FGs. Argonaute9-like mRNA (ptAGO9L) showed stage-specific modulation of expression in ZEs that appeared to be inverted in the corresponding FGs. MicroRNAs and argonaute genes varied spatiotemporally during seed development. The peak levels of Pta-miR166 in FGs and ptAGO9L in embryos occurred at stage 9.1, a critical transition point during embryo development and a point where somatic embryo maturation often stops. MicroRNAs identified in FG tissue may play a role in embryogenesis.
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Affiliation(s)
- Thomas J Oh
- Forest Biology, Institute of Paper Science and Technology (IPST)
| | - Roger M Wartell
- School of Biology and
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0620, USA
| | - John Cairney
- Forest Biology, Institute of Paper Science and Technology (IPST)
- School of Biology and
| | - Gerald S Pullman
- Forest Biology, Institute of Paper Science and Technology (IPST)
- School of Biology and
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Pavy N, Boyle B, Nelson C, Paule C, Giguère I, Caron S, Parsons LS, Dallaire N, Bedon F, Bérubé H, Cooke J, Mackay J. Identification of conserved core xylem gene sets: conifer cDNA microarray development, transcript profiling and computational analyses. THE NEW PHYTOLOGIST 2008; 180:766-86. [PMID: 18811621 DOI: 10.1111/j.1469-8137.2008.02615.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
One approach for investigating the molecular basis of wood formation is to integrate microarray profiling data sets and sequence analyses, comparing tree species with model plants such as Arabidopsis. Conifers may be included in comparative studies thanks to large-scale expressed sequence tag (EST) analyses, which enable the development of cDNA microarrays with very significant genome coverage. A microarray of 10,400 low-redundancy sequences was designed starting from white spruce (Picea glauca (Moench.) Voss) cDNAs. Computational procedures that were developed to ensure broad transcriptome coverage and efficient PCR amplification were used to select cDNA clones, which were re-sequenced in the microarray manufacture process. White spruce transcript profiling experiments that compared secondary xylem to phloem and needles identified 360 xylem-preferential gene sequences. The functional annotations of all differentially expressed sequences were highly consistent with the results of similar analyses carried out in angiosperm trees and herbaceous plants. Computational analyses comparing the spruce microarray sequences and core xylem gene sets from Arabidopsis identified 31 transcripts that were highly conserved in angiosperms and gymnosperms, in terms of both sequence and xylem expression. Several other spruce sequences have not previously been linked to xylem differentiation (including genes encoding TUBBY-like domain proteins (TLPs) and a gibberellin insensitive (gai) gene sequence) or were shown to encode proteins of unknown function encompassing diverse conserved domains of unknown function.
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Affiliation(s)
- Nathalie Pavy
- Centre d'Etude de la Forêt, 1030 rue de la Médecine, Université Laval, Québec, Québec, Canada, G1K 7P4
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18
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Liang C, Wang G, Liu L, Ji G, Fang L, Liu Y, Carter K, Webb JS, Dean JFD. ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics 2007; 8:134. [PMID: 17535431 PMCID: PMC1894976 DOI: 10.1186/1471-2164-8-134] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 05/29/2007] [Indexed: 11/30/2022] Open
Abstract
Background With the advent of low-cost, high-throughput sequencing, the amount of public domain Expressed Sequence Tag (EST) sequence data available for both model and non-model organism is growing exponentially. While these data are widely used for characterizing various genomes, they also present a serious challenge for data quality control and validation due to their inherent deficiencies, particularly for species without genome sequences. Description ConiferEST is an integrated system for data reprocessing, visualization and mining of conifer ESTs. In its current release, Build 1.0, it houses 172,229 loblolly pine EST sequence reads, which were obtained from reprocessing raw DNA sequencer traces using our software – WebTraceMiner. The trace files were downloaded from NCBI Trace Archive. ConiferEST provides biologists unique, easy-to-use data visualization and mining tools for a variety of putative sequence features including cloning vector segments, adapter sequences, restriction endonuclease recognition sites, polyA and polyT runs, and their corresponding Phred quality values. Based on these putative features, verified sequence features such as 3' and/or 5' termini of cDNA inserts in either sense or non-sense strand have been identified in-silico. Interestingly, only 30.03% of the designated 3' ESTs were found to have an authenticated 5' terminus in the non-sense strand (i.e., polyT tails), while fewer than 5.34% of the designated 5' ESTs had a verified 5' terminus in the sense strand. Such previously ignored features provide valuable insight for data quality control and validation of error-prone ESTs, as well as the ability to identify novel functional motifs embedded in large EST datasets. We found that "double-termini adapters" were effective indicators of potential EST chimeras. For all sequences with in-silico verified termini/terminus, we used InterProScan to assign protein domain signatures, results of which are available for in-depth exploration using our biologist-friendly web interfaces. Conclusion ConiferEST represents a unique and complementary public resource for EST data integration and mining in conifers by reprocessing raw DNA traces, identifying putative sequence features and determining and annotating in-silico verified features. Seamlessly integrated with other public resources, ConiferEST provides biologists powerful tools to verify data, visualize abnormalities, including EST chimeras, and explore large EST datasets.
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Affiliation(s)
- Chun Liang
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Gang Wang
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Lin Liu
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Lin Fang
- Beijing Genomics Institute, Beijing 101300, China
| | - Yuansheng Liu
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Kikia Carter
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Jason S Webb
- Department of Botany, Miami University, Oxford, Ohio 45056, USA
| | - Jeffrey FD Dean
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA
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Bedon F, Grima-Pettenati J, Mackay J. Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca). BMC PLANT BIOLOGY 2007; 7:17. [PMID: 17397551 PMCID: PMC1851958 DOI: 10.1186/1471-2229-7-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 03/30/2007] [Indexed: 05/14/2023]
Abstract
BACKGROUND Several members of the R2R3-MYB family of transcription factors act as regulators of lignin and phenylpropanoid metabolism during wood formation in angiosperm and gymnosperm plants. The angiosperm Arabidopsis has over one hundred R2R3-MYBs genes; however, only a few members of this family have been discovered in gymnosperms. RESULTS We isolated and characterised full-length cDNAs encoding R2R3-MYB genes from the gymnosperms white spruce, Picea glauca (13 sequences), and loblolly pine, Pinus taeda L. (five sequences). Sequence similarities and phylogenetic analyses placed the spruce and pine sequences in diverse subgroups of the large R2R3-MYB family, although several of the sequences clustered closely together. We searched the highly variable C-terminal region of diverse plant MYBs for conserved amino acid sequences and identified 20 motifs in the spruce MYBs, nine of which have not previously been reported and three of which are specific to conifers. The number and length of the introns in spruce MYB genes varied significantly, but their positions were well conserved relative to angiosperm MYB genes. Quantitative RTPCR of MYB genes transcript abundance in root and stem tissues revealed diverse expression patterns; three MYB genes were preferentially expressed in secondary xylem, whereas others were preferentially expressed in phloem or were ubiquitous. The MYB genes expressed in xylem, and three others, were up-regulated in the compression wood of leaning trees within 76 hours of induction. CONCLUSION Our survey of 18 conifer R2R3-MYB genes clearly showed a gene family structure similar to that of Arabidopsis. Three of the sequences are likely to play a role in lignin metabolism and/or wood formation in gymnosperm trees, including a close homolog of the loblolly pine PtMYB4, shown to regulate lignin biosynthesis in transgenic tobacco.
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Affiliation(s)
- Frank Bedon
- Centre d'étude de la Forêt, Université Laval, Pavillon Charles-Eugène Marchand, Sainte Foy G1K7P4, Québec, Canada
- UMR CNRS/UPS 5546 Surfaces Cellulaires et Signalisation chez les Végétaux, Pôle de Biotechnologie Végétale, BP426 17 – Auzeville 31226, Castanet Tolosan, France
| | - Jacqueline Grima-Pettenati
- UMR CNRS/UPS 5546 Surfaces Cellulaires et Signalisation chez les Végétaux, Pôle de Biotechnologie Végétale, BP426 17 – Auzeville 31226, Castanet Tolosan, France
| | - John Mackay
- Centre d'étude de la Forêt, Université Laval, Pavillon Charles-Eugène Marchand, Sainte Foy G1K7P4, Québec, Canada
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Demura T, Fukuda H. Transcriptional regulation in wood formation. TRENDS IN PLANT SCIENCE 2007; 12:64-70. [PMID: 17224301 DOI: 10.1016/j.tplants.2006.12.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 11/06/2006] [Accepted: 12/20/2006] [Indexed: 05/13/2023]
Abstract
Wood (i.e. xylem tissue) in trees is mainly composed of two types of cells, fibres and tracheary elements. Recent molecular studies of various trees, as well as the non-tree species Arabidopsis thaliana and Zinnia elegans, have revealed coordinated gene expression during differentiation of these cells in wood and the presence of several transcription factors that might govern the complex networks of transcriptional regulation. This article reviews recent findings concerning the regulation of genes by transcription factors involved in wood formation such as AUXIN RESPONSE FACTOR (ARF), CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII), KANADI (KAN), MYB and NAM/ATAF/CUC (NAC).
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Affiliation(s)
- Taku Demura
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.
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21
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Guillaumie S, San-Clemente H, Deswarte C, Martinez Y, Lapierre C, Murigneux A, Barrière Y, Pichon M, Goffner D. MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. PLANT PHYSIOLOGY 2007; 143:339-63. [PMID: 17098859 PMCID: PMC1761967 DOI: 10.1104/pp.106.086405] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Accepted: 11/03/2006] [Indexed: 05/12/2023]
Abstract
An extensive search for maize (Zea mays) genes involved in cell wall biosynthesis and assembly has been performed and 735 sequences have been centralized in a database, MAIZEWALL (http://www.polebio.scsv.ups-tlse.fr/MAIZEWALL). MAIZEWALL contains a bioinformatic analysis for each entry and gene expression data that are accessible via a user-friendly interface. A maize cell wall macroarray composed of a gene-specific tag for each entry was also constructed to monitor global cell wall-related gene expression in different organs and during internode development. By using this macroarray, we identified sets of genes that exhibit organ and internode-stage preferential expression profiles. These data provide a comprehensive fingerprint of cell wall-related gene expression throughout the maize plant. Moreover, an in-depth examination of genes involved in lignin biosynthesis coupled to biochemical and cytological data from different organs and stages of internode development has also been undertaken. These results allow us to trace spatially and developmentally regulated, putative preferential routes of monolignol biosynthesis involving specific gene family members and suggest that, although all of the gene families of the currently accepted monolignol biosynthetic pathway are conserved in maize, there are subtle differences in family size and a high degree of complexity in spatial expression patterns. These differences are in keeping with the diversity of lignified cell types throughout the maize plant.
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Affiliation(s)
- Sabine Guillaumie
- Université Paul Sabatier, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5546, 31326 Castanet-Tolosan, France
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22
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Cairney J, Zheng L, Cowels A, Hsiao J, Zismann V, Liu J, Ouyang S, Thibaud-Nissen F, Hamilton J, Childs K, Pullman GS, Zhang Y, Oh T, Buell CR. Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis. PLANT MOLECULAR BIOLOGY 2006; 62:485-501. [PMID: 17001497 DOI: 10.1007/s11103-006-9035-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 06/15/2006] [Indexed: 05/06/2023]
Abstract
The process of embryogenesis in gymnosperms differs in significant ways from the more widely studied process in angiosperms. To further our understanding of embryogenesis in gymnosperms, we have generated Expressed Sequence Tags (ESTs) from four cDNA libraries constructed from un-normalized, normalized, and subtracted RNA populations of zygotic and somatic embryos of loblolly pine (Pinus taeda L.). A total of 68,721 ESTs were generated from 68,131 cDNA clones. Following clustering and assembly, these sequences collapsed into 5,274 contigs and 6,880 singleton sequences for a total of 12,154 non-redundant sequences. Searches of a non-identical amino acid database revealed a putative homolog for 9,189 sequences, leaving 2,965 sequences with no known function. More extensive searches of additional plant sequence data sets revealed a putative homolog for all but 1,388 (11.4%) of the sequences. Using gene ontologies, a known function could be assigned for 5,495 of the 12,154 total non-redundant sequences with 13,633 associations in total assigned. When compared to approximately 72,000 sequences in a collated P. taeda transcript assembly derived from >245,000 ESTs derived from root, xylem, stem, needles, pollen cone, and shoot ESTs, 3,458 (28.5%) of the non-redundant embryo sequences were unique and thereby provide a valuable addition to development of a complete loblolly pine transcriptome. To assess similarities between angiosperm and gymnosperm embryo development, we examined our EST collection for putative homologs of angiosperm genes implicated in embryogenesis. Out of 108 angiosperm embryogenesis-related genes, homologs were present for 83 of these genes suggesting that pine contains similar genes for embryogenesis and that our RNA sampling methods were successful. We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development.
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Affiliation(s)
- John Cairney
- School of Biology and Institute of Paper Science and Technology, Georgia Institute of Technology, 500, 10th Street, NW, Atlanta, GA 30332-0620, USA
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Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, Taliercio E, Turley R, McFadden H, Payton P, Klueva N, Allen R, Zhang D, Haigler C, Wilkerson C, Suo J, Schulze SR, Pierce ML, Essenberg M, Kim H, Llewellyn DJ, Dennis ES, Kudrna D, Wing R, Paterson AH, Soderlund C, Wendel JF. A global assembly of cotton ESTs. Genome Res 2006; 16:441-50. [PMID: 16478941 PMCID: PMC1415220 DOI: 10.1101/gr.4602906] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D(T) genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.
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Affiliation(s)
- Joshua A Udall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
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Kawaura K, Mochida K, Ogihara Y. Expression profile of two storage-protein gene families in hexaploid wheat revealed by large-scale analysis of expressed sequence tags. PLANT PHYSIOLOGY 2005; 139:1870-80. [PMID: 16306141 PMCID: PMC1310565 DOI: 10.1104/pp.105.070722] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To discern expression patterns of individual storage-protein genes in hexaploid wheat (Triticum aestivum cv Chinese Spring), we analyzed comprehensive expressed sequence tags (ESTs) of common wheat using a bioinformatics technique. The gene families for alpha/beta-gliadins and low molecular-weight glutenin subunit were selected from the EST database. The alignment of these genes enabled us to trace the single nucleotide polymorphism sites among both genes. The combinations of single nucleotide polymorphisms allowed us to assign haplotypes into their homoeologous chromosomes by allele-specific PCR. Phylogenetic analysis of these genes showed that both storage-protein gene families rapidly diverged after differentiation of the three genomes (A, B, and D). Expression patterns of these genes were estimated based on the frequencies of ESTs. The storage-protein genes were expressed only during seed development stages. The alpha/beta-gliadin genes exhibited two distinct expression patterns during the course of seed maturation: early expression and late expression. Although the early expression genes among the alpha/beta-gliadin and low molecular-weight glutenin subunit genes showed similar expression patterns, and both genes from the D genome were preferentially expressed rather than those from the A or B genome, substantial expression of two early expression genes from the A genome was observed. The phylogenetic relationships of the genes and their expression patterns were not correlated. These lines of evidence suggest that expression of the two storage-protein genes is independently regulated, and that the alpha/beta-gliadin genes possess novel regulation systems in addition to the prolamin box.
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Affiliation(s)
- Kanako Kawaura
- Laboratory of Genetic Engineering, Kyoto Prefectural University and Kyoto Prefectural Institute of Agricultural Biotechnology, Shimogamo, Kyoto 606-8522, Japan
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Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 2005; 6:144. [PMID: 16236172 PMCID: PMC1277824 DOI: 10.1186/1471-2164-6-144] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Accepted: 10/19/2005] [Indexed: 12/02/2022] Open
Abstract
Background The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). Results We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. Conclusion This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics.
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Affiliation(s)
- Nathalie Pavy
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
| | - Charles Paule
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - Lee Parsons
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - John A Crow
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - Marie-Josee Morency
- Laurentian Forestry Center (Canadian Forestry Service), Natural Resources Canada, 1055 rue du PEPS, Québec, Québec, G1V 4C7, Canada
| | - Janice Cooke
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - James E Johnson
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - Etienne Noumen
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
| | - Carine Guillet-Claude
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
| | - Yaron Butterfield
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Sarah Barber
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - George Yang
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jerry Liu
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Jeff Stott
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Robert Kirkpatrick
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Asim Siddiqui
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Robert Holt
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Marco Marra
- Genome Sciences Center, BC Cancer Agency, 675 West 10 th Avenue, Vancouver, BC, V5Z 1L3, Canada
| | - Armand Seguin
- Laurentian Forestry Center (Canadian Forestry Service), Natural Resources Canada, 1055 rue du PEPS, Québec, Québec, G1V 4C7, Canada
| | - Ernest Retzel
- Center for Computational Genomics and Bioinformatics, University of Minnesota, 420 Delaware St. S.E., MMC 43, Minneapolis, MN 55455, USA
| | - Jean Bousquet
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
| | - John MacKay
- ARBOREA and Canada Research Chair in Forest Genomics, Pavillon Charles-Eugène-Marchand, Université Laval, Ste.Foy, Québec G1K 7P4, Canada
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Plomion C, Richardson T, MacKay J. Advances in forest tree genomics. Forest Trees Workshop, Plant and Animal Genome XIII Conference, San Diego, CA, USA, January 2005. THE NEW PHYTOLOGIST 2005; 166:713-7. [PMID: 15869635 DOI: 10.1111/j.1469-8137.2005.01446.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Christophe Plomion
- UMR BioGeco, INRA Equipe de Génétique, 69 Route d'Arcachon, 33612 Cestas Cédex, France.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447491 DOI: 10.1002/cfg.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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