共查询到20条相似文献，搜索用时 28 毫秒
1.
Background
The creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest') showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to create MTP sub-libraries from the soybean cv. Forrest physical map builds 2 to 4. 相似文献2.
Berendzen K Searle I Ravenscroft D Koncz C Batschauer A Coupland G Somssich IE Ulker B 《Plant methods》2005,1(1):4
Background
Many established PCR-based approaches in plant molecular biology rely on lengthy and expensive methods for isolation of nucleic acids. Although several rapid DNA isolation protocols are available, they have not been tested for simultaneous RNA isolation for RT-PCR applications. In addition, traditional map-based cloning technologies often use ill-proportioned marker regions even when working with the model plant Arabidopsis thaliana, where the availability of the full genome sequence can now be exploited for the creation of a high-density marker systems. 相似文献3.
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Background
Suppression subtractive hybridization is a popular technique for gene discovery from non-model organisms without an annotated genome sequence, such as cowpea (Vigna unguiculata (L.) Walp). We aimed to use this method to enrich for genes expressed during drought stress in a drought tolerant cowpea line. However, current methods were inefficient in screening libraries and management of the sequence data, and thus there was a need to develop software tools to facilitate the process. 相似文献6.
Andrzej Pacak Katrin Geisler Bodil Jørgensen Maria Barciszewska-Pacak Lena Nilsson Tom Hamborg Nielsen Elisabeth Johansen Mette Grønlund Iver Jakobsen Merete Albrechtsen 《Plant methods》2010,6(1):26
Background
Gene silencing vectors based on Barley stripe mosaic virus (BSMV) are used extensively in cereals to study gene function, but nearly all studies have been limited to genes expressed in leaves of barley and wheat. However since many important aspects of plant biology are based on root-expressed genes we wanted to explore the potential of BSMV for silencing genes in root tissues. Furthermore, the newly completed genome sequence of the emerging cereal model species Brachypodium distachyon as well as the increasing amount of EST sequence information available for oat (Avena species) have created a need for tools to study gene function in these species. 相似文献7.
Background
Plant genome sequencing has resulted in the identification of a large number of uncharacterized genes. To investigate these unknown gene functions, several transient transformation systems have been developed as quick and convenient alternatives to the lengthy transgenic assay. These transient assays include biolistic bombardment, protoplast transfection and Agrobacterium-mediated transient transformation, each having advantages and disadvantages depending on the research purposes. 相似文献8.
Yong-Li Xiao Julia C Redman Erin L Monaghan Jun Zhuang Beverly A Underwood William A Moskal Wei Wang Hank C Wu Christopher D Town 《Plant methods》2010,6(1):18
Background
Although the complete genome sequence and annotation of Arabidopsis were released at the end of year 2000, it is still a great challenge to understand the function of each gene in the Arabidopsis genome. One way to understand the function of genes on a genome-wide scale is expression profiling by microarrays. However, the expression level of many genes in Arabidopsis genome cannot be detected by microarray experiments. In addition, there are many more novel genes that have been discovered by experiments or predicted by new gene prediction programs. Another way to understand the function of individual genes is to investigate their in vivo expression patterns by reporter constructs in transgenic plants which can provide basic information on the patterns of gene expression. 相似文献9.
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Yingzhen Yang Alex Costa Nathalie Leonhardt Robert S Siegel Julian I Schroeder 《Plant methods》2008,4(1):6
Background
A common limitation in guard cell signaling research is that it is difficult to obtain consistent high expression of transgenes of interest in Arabidopsis guard cells using known guard cell promoters or the constitutive 35S cauliflower mosaic virus promoter. An additional drawback of the 35S promoter is that ectopically expressing a gene throughout the organism could cause pleiotropic effects. To improve available methods for targeted gene expression in guard cells, we isolated strong guard cell promoter candidates based on new guard cell-specific microarray analyses of 23,000 genes that are made available together with this report. 相似文献11.
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Robin A Atherton Bennet J McComish Lara D Shepherd Lorraine A Berry Nick W Albert Peter J Lockhart 《Plant methods》2010,6(1):22
Background
Complete chloroplast genome sequences provide a valuable source of molecular markers for studies in molecular ecology and evolution of plants. To obtain complete genome sequences, recent studies have made use of the polymerase chain reaction to amplify overlapping fragments from conserved gene loci. However, this approach is time consuming and can be more difficult to implement where gene organisation differs among plants. An alternative approach is to first isolate chloroplasts and then use the capacity of high-throughput sequencing to obtain complete genome sequences. We report our findings from studies of the latter approach, which used a simple chloroplast isolation procedure, multiply-primed rolling circle amplification of chloroplast DNA, Illumina Genome Analyzer II sequencing, and de novo assembly of paired-end sequence reads. 相似文献13.
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Joanne G Bartlett Sílvia C Alves Mark Smedley John W Snape Wendy A Harwood 《Plant methods》2008,4(1):22
Background
Plant transformation is an invaluable tool for basic plant research, as well as a useful technique for the direct improvement of commercial crops. Barley (Hordeum vulgare) is the fourth most abundant cereal crop in the world. It also provides a useful model for the study of wheat, which has a larger and more complex genome. Most existing barley transformation methodologies are either complex or have low (<10%) transformation efficiencies. 相似文献15.
Miao Wang AnQun Tan LingYun Zhang JiaWei Yang ZhaoXin Wei ChunZhen Cheng ZhiQin Zhou GuangYan Zhong 《Scientia Horticulturae》2010
A deep-coverage bacterial artificial chromosome (BAC) library of Yanxiwanlu Ponkan, a late maturing cultivar, was constructed and evaluated. Results showed that the library contained a total of 61,000 clones. Restriction analysis indicated that the DNA insert sizes ranged from 30 to 170 kb with an average of ∼82 kb. No empty clone was found. Therefore, the library should cover ∼13.6-fold of the citrus genome. Continuous sub-cultivation of 5 randomly chosen clones for up to 100 generations showed no detectable change in their restriction profiles. To demonstrate the application of the library in discovery of genes, 7 ethylene-regulated genes were screened by PCR amplification from hierarchically pooled library clones with gene-specific primers. Five positive clones, each representing a different gene, were thus identified from 3840 clones. Sequencing of the clones showed that all of them matched the expected genes, indicating that the library was highly representative. 相似文献
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Background
We have developed a functional genomics approach based on expression cloning in Xenopus oocytes to identify plant transporter function. We utilized the full-length cDNA databases to generate a normalized library consisting of 239 full-length Arabidopsis thaliana transporter cDNAs. The genes were arranged into a 96-well format and optimized for expression in Xenopus oocytes by cloning each coding sequence into a Xenopus expression vector. 相似文献17.
Background
CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas.Results
A single construct was assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37 nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate.Conclusions
CRISPR-Cas can precisely and efficiently edit the genome of T. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species.18.
Daniel J Marshall Alice Hayward Dominic Eales Michael Imelfort Jiri Stiller Paul J Berkman Terry Clark Megan McKenzie Kaitao Lai Chris Duran Jacqueline Batley David Edwards 《Plant methods》2010,6(1):1-6
Background
The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes.Results
We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome.Conclusions
The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly. 相似文献19.
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Isolation of intact sub-dermal secretory cavities from <Emphasis Type="Italic">Eucalyptus</Emphasis>
Jason QD Goodger Allison M Heskes Madeline C Mitchell Drew J King Elizabeth H Neilson Ian E Woodrow 《Plant methods》2010,6(1):20