FLAGdb++: a database for the functional analysis of the Arabidopsis genome

Samson, Franck; Brunaud, Véronique; Duchêne, Sylvain; Oliveira, Yannick de; Caboche, Michel; Lecharny, Alain; Aubourg, Santiago P.

doi:10.1093/nar/gkh134

Cited by 52 publications

(58 citation statements)

References 17 publications

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“…Among the 210,388 cDNA and EST sequences (including many sequences from normalized and subtracted libraries) available from FLAGdb þþ (Samson et al, 2004), only 843 transcripts are from PPR genes, corresponding to only 215 out of the 441 genes (48.7%) described here (Table 3; see Supplemental Table S5 online). Using the same database, 69.1% of all predicted Arabidopsis genes have proof of expression from EST or cDNA data.…”

Section: Analysis Of Ppr Gene Expressionmentioning

confidence: 99%

“…A modified version of the FLAGdb þþ database and interface (Samson et al, 2004) was used for much of the visualization needed for manual annotation, including display of PPR motifs, AGI ORF models, known mRNAs, and predicted mitochondrial and plastid targeting sequences. Predotar version 1.03 (Small et al, 2004) and TargetP version 1.01 (Emanuelsson et al, 2000) were used for prediction of organelle targeting from protein sequences.…”

Section: Bioinformaticsmentioning

confidence: 99%

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Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W]

et al. 2004

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The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.

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Section: Analysis Of Ppr Gene Expressionmentioning

confidence: 99%

Section: Bioinformaticsmentioning

confidence: 99%

Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W]

et al. 2004

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“…We obtained the T-DNA insertion mutants from either the ABRC or from Institut National de la Recherche Agronomique (INRA) (Samson et al, 2004). The mutants were genotyped according to the published protocols (Alonso et al, 2003;Samson et al, 2004).…”

Section: Plant Materialsmentioning

confidence: 99%

“…The mutants were genotyped according to the published protocols (Alonso et al, 2003;Samson et al, 2004). Genotyping primers for yuc1, yuc2, yuc4, and yuc6 were described previously (Cheng et al, 2006).…”

Section: Plant Materialsmentioning

confidence: 99%

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Auxin Synthesized by the YUCCA Flavin Monooxygenases Is Essential for Embryogenesis and Leaf Formation inArabidopsis

2007

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Auxin plays a key role in embryogenesis and seedling development, but the auxin sources for the two processes are not defined. Here, we demonstrate that auxin synthesized by the YUCCA (YUC) flavin monooxygenases is essential for the establishment of the basal body region during embryogenesis and the formation of embryonic and postembryonic organs. Both YUC1 and YUC4 are expressed in discrete groups of cells throughout embryogenesis, and their expression patterns overlap with those of YUC10 and YUC11 during embryogenesis. The quadruple mutants of yuc1 yuc4 yuc10 yuc11 fail to develop a hypocotyl and a root meristem, a phenotype similar to those of mp and tir1 afb1 afb2 afb3 auxin signaling mutants. We further show that YUC genes play an essential role in the formation of rosette leaves by analyzing combinations of yuc mutants and the polar auxin transport mutants pin1 and aux1. Disruption of YUC1, YUC4, or PIN1 alone does not abolish leaf formation, but the triple mutant yuc1 yuc4 pin1 fails to form leaves and flowers. Furthermore, disruption of auxin influx carrier AUX1 in the quadruple mutant yuc1 yuc2 yuc4 yuc6, but not in wild-type background, phenocopies yuc1 yuc4 pin1, demonstrating that auxin influx is required for plant leaf and flower development. Our data demonstrate that auxin synthesized by the YUC flavin monooxygenases is an essential auxin source for Arabidopsis thaliana embryogenesis and postembryonic organ formation.

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A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections

O’Malley

Barragan

Ecker

2015

Methods in Molecular Biology

115

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The T-DNA sequence-indexed mutant collections contain insertional mutants for most Arabidopsis thaliana genes and have played an important role in plant biology research for almost two decades. By providing a large source of mutant alleles for in vivo characterization of gene function, this resource has been leveraged thousands of times to study a wide range of problems in plant biology. Our primary goal in this chapter is to provide a general guide to strategies for the effective use of the data and materials in these collections. To do this, we provide a general introduction to the T-DNA insertional sequence-indexed mutant collections with a focus on how best to use the available data sources for good line selection. As isolation of a homozygous line is a common next step once a potential disruption line has been identified, the second half of the chapter provides a step-by-step guide for the design and implementation of a T-DNA genotyping pipeline. Finally, we describe interpretation of genotyping results and include a troubleshooting section for common types of segregation distortions that we have observed. In this chapter we introduce both basic concepts and specific applications to both new and more experienced users of the collections for the design and implementation of small- to large-scale genotyping pipelines.

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FLAGdb++: a database for the functional analysis of the Arabidopsis genome

Cited by 52 publications

References 17 publications

Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W]

Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W]

Auxin Synthesized by the YUCCA Flavin Monooxygenases Is Essential for Embryogenesis and Leaf Formation inArabidopsis

A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections

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