A plant-transformation-competent BIBAC library from the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics

2003 ◽  
Vol 106 (2) ◽  
pp. 269-276 ◽  
Author(s):  
Y.-L. Chang ◽  
X. Henriquez ◽  
D. Preuss ◽  
G. Copenhaver ◽  
H.-B. Zhang
Keyword(s):  
Arabidopsis Thaliana ◽  
Comparative Genomics ◽  
Plant Transformation ◽  
Bibac Library

Construction and characterization of a plant transformation-competent BIBAC library of the black Sigatoka-resistant banana Musa acuminata cv. Tuu Gia (AA)

2005 ◽  
Vol 110 (4) ◽  
pp. 706-713 ◽  
Author(s):  
E. Ortiz-Vázquez ◽  
D. Kaemmer ◽  
H-B. Zhang ◽  
J. Muth ◽  
M. Rodríguez-Mendiola ◽  
...  
Keyword(s):  
Plant Transformation ◽  
Musa Acuminata ◽  
Black Sigatoka ◽  
Bibac Library

Characterization of a plant-transformation-ready large-insert BIBAC library of Arabidopsis and bombardment transformation of a large-insert BIBAC of the library into tobacco

Genome ◽  
2011 ◽  
Vol 54 (6) ◽  
pp. 437-447 ◽  
Author(s):  
Yueh-Long Chang ◽  
Huey-Wen Chuang ◽  
Khalid Meksem ◽  
Fang-Chun Wu ◽  
Chang-Yee Chang ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Plant Transformation ◽  
Large Scale ◽  
Nuclear Dna ◽  
Gene Clusters ◽  
Arabidopsis Genome ◽  
Insert Size ◽  
Biolistic Bombardment ◽  
Bibac Library

Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.

An Integrated Map of Arabidopsis thaliana for Functional Analysis of Its Genome Sequence

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1231-1242
Author(s):  
Yueh-Long Chang ◽  
Quanzhou Tao ◽  
Chantel Scheuring ◽  
Kejiao Ding ◽  
Khalid Meksem ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Arabidopsis Thaliana ◽  
Genome Sequence ◽  
Rapid Development ◽  
Whole Genome ◽  
Genome Research ◽  
Integrated Map ◽  
Physical Maps ◽  
Gap Closure ◽  
Bibac Library

Abstract The genome of the model plant species Arabidopsis thaliana has recently been sequenced. To accelerate its current genome research, we developed a whole-genome, BAC/BIBAC-based, integrated physical, genetic, and sequence map of the A. thaliana ecotype Columbia. This new map was constructed from the clones of a new plant-transformation-competent BIBAC library and is integrated with the existing sequence map. The clones were restriction fingerprinted by DNA sequencing gel-based electrophoresis, assembled into contigs, and anchored to an existing genetic map. The map consists of 194 BAC/BIBAC contigs, spanning 126 Mb of the 130-Mb Arabidopsis genome. A total of 120 contigs, spanning 114 Mb, were anchored to the chromosomes of Arabidopsis. Accuracy of the integrated map was verified using the existing physical and sequence maps and numerous DNA markers. Integration of the new map with the sequence map has enabled gap closure of the sequence map and will facilitate functional analysis of the genome sequence. The method used here has been demonstrated to be sufficient for whole-genome physical mapping from large-insert random bacterial clones and thus is applicable to rapid development of whole-genome physical maps for other species.

scholarly journals Comparative genomics approaches accurately predict deleterious variants in plants

2017 ◽  
Author(s):  
Thomas J. Y. Kono ◽  
Li Lei ◽  
Ching-Hua Shih ◽  
Paul J. Hoffman ◽  
Peter L. Morrell ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Comparative Genomics ◽  
Plant Species ◽  
Phenotypic Variation ◽  
Genetic Variants ◽  
Comparative Genomic ◽  
Deleterious Mutations ◽  
Genome Resequencing ◽  
Functional Consequences ◽  
Nonhuman Species

AbstractRecent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.

scholarly journals An Expanded Role for WRINKLED1 Metabolic Control Based on Combined Phylogenetic and Biochemical Analyses

2020 ◽  
Author(s):  
Cathleen Kuczynski ◽  
Sean McCorkle ◽  
Jantana Keereetaweep ◽  
John Shanklin ◽  
Jorg Schwender
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Fatty Acid ◽  
Comparative Genomics ◽  
Dna Binding ◽  
Binding Affinity ◽  
Fatty Acid Biosynthesis ◽  
Binding Motif ◽  
Central Metabolism ◽  
Brassicaceae Species

AbstractDuring triacylglycerol biosynthesis in developing oilseeds of Arabidopsis thaliana, fatty acid production is regulated by the seed-specific transcription factor WRINKLED1 (WRI1). WRI1 is known to directly stimulate the expression of fatty acid biosynthetic enzymes and a few targets in glycolysis. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors in seeds is controlled by WRI1. Based on a previously reported DNA binding motif for WRI1, the ASML1/WRI1 (AW)- box, we developed a comparative genomics approach to search for conserved binding motifs in upstream regions of Arabidopsis thaliana protein-encoding genes and orthologous regions of 11 other Brassicaceae species. The AW-box was over-represented across orthologs for 915 Arabidopsis thaliana genes. Among these, 73 genes with functions in the biosynthesis of fatty acids and triacylglycerols and in glycolysis were enriched. For 90 AW-box sequences associated with these target genes, binding affinity to heterologously expressed Arabidopsis thaliana WRI1 protein was determined using Microscale Thermophoresis. Sites with low dissociation constants are preferentially located close to the transcriptional start site and are highly conserved between the 12 Brassicaceae species. Most of the associated genes were found to be co-expressed with WRI1 during seed development. When 46 automatically and manually curated genes containing conserved AW-sites with high binding affinity are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in fatty acid biosynthesis and glycolysis. Among unexpectedly identified putative targets of WRI1 are plastidic fructokinase, phosphoglucose isomerase and several transcription factors.One sentence summaryA combined comparative genomics and in-vitro DNA binding assay approach was used to identify conserved binding sites for the WRINKLED1 transcription factor in central metabolism and lipid biosynthesis.

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