Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

Doherty, Colleen J.; Friesner, Joanna; Loraine, Ann E.; Megraw, Molly; Meyers, Blake C.; Provart, Nicholas J.; Slotkin, R. Keith; Town, Chris; Assmann, Sarah M.; Axtell, Michael J.; Berardini, Tanya Z.; Chen, Sixue; Gehan, Malia; Huala, Eva; Jaiswal, Pankaj; Larson, Stephen; Li, Song; May, Sean; Todd, M. J.; Pires, Chris J; Topp, Chris; Walley, Justin W.; Wurtele, Eve Syrkin

doi:10.1002/pld3.109

Cited by 15 publications

(2 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fortunately, the genome project of resequencing A. thaliana with Illumina technology provided a gene model of 18 A. thaliana genomes [52]. In addition, reinvestigation of A. thaliana GATA TFs is also needed because the previous research of genome-wide GATA TF identification was conducted in 2004 [73], when the version gene model of A. thaliana was older than the current version (TAIR 10.1) [88]. Taken together, we investigated GATA TFs from 19 A. thaliana genomes including reference genome (A. thaliana Col0) and analyzed them in the aspects of intraspecific variations of chromosomal distribution, amino acid sequences, and phylogenetic relationships.…”

Section: Plos Onementioning

confidence: 99%

See 1 more Smart Citation

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Kim¹,

Xi²,

Park³

2021

PLoS ONE

View full text Add to dashboard Cite

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

show abstract

Section: Plos Onementioning

confidence: 99%

“…thaliana GATA TFs is also needed because the previous research of genome-wide GATA TF identification was conducted in 2004 [ 73 ], when the version gene model of A . thaliana was older than the current version (TAIR 10.1) [ 88 ]. Taken together, we investigated GATA TFs from 19 A .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Kim¹,

Xi²,

Park³

2021

PLoS ONE

View full text Add to dashboard Cite

show abstract

Arabidopsis Thaliana: From Weed to Model Organism

Diaz¹

2019

CP Essential Lab Tech

View full text Add to dashboard Cite

Arabidopsis thaliana is a small plant of significant economic and agronomic importance. While Arabidopsis is not a crop plant, it is not so different in its fundamental properties. Arabidopsis is a member of the Brassicaceae family, which constitutes one of the world's most economically important plant groups. According to the United Nations, globally Brassicaceae crops are worth $31 billion, and the number is likely to increase since a number of related species within this family are underutilized edible varieties. Its small size is an advantage to researchers with limited space and funding; simply put, a smaller plant requires fewer resources. Arabidopsis has been studied most intensely for the last 40 years and officially became a model plant in the late 1990s. Since then, the community has developed genetic and genomic resources so numerous that the barrier to entry to studying Arabidopsis is relatively low. This article provides a primer to how Arabidopsis came to be a model organism and highlights essential techniques every Arabidopsis researcher should be aware of to advance the pace of discovery. © 2019 by John Wiley & Sons, Inc.

show abstract

Directions for research and training in plant omics: Big Questions and Big Data

et al. 2019

Self Cite

View full text Add to dashboard Cite

A key remit of the NSF ‐funded “Arabidopsis Research and Training for the 21 st Century” ( ART ‐21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology , 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART ‐21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post‐doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.

show abstract

Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

Cited by 15 publications

References 5 publications

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

Arabidopsis Thaliana: From Weed to Model Organism

Directions for research and training in plant omics: Big Questions and Big Data

Contact Info

Product

Resources

About