ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

Krishnakumar, Vivek; Contrino, Sergio; Cheng, Chia‐Yi; Belyaeva, Irina; Ferlanti, Erik S.; Miller, Jason R.; Vaughn, Matthew; Micklem, Gos; Town, Christopher D.; Chan, Agnes P.

doi:10.1093/pcp/pcw200

Cited by 34 publications

(41 citation statements)

References 42 publications

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“…To test whether the genes we have uncovered are expressed, and whether they have expression levels similar to validated gene models, we condensed the expression profile of all rice and A. thaliana genes from diverse RNA‐sequencing datasets into density plots of their maximum expression (purple distributions in Fig. ; Table S4) (Kawahara et al , ; Krishnakumar et al , ). As in maize (Walley et al , ), we observed bimodal expression distributions for both A. thaliana and rice genes (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Gene expression profiles were collected for poplar from P op G en IE (Sundell et al , ), for tomato from the Tomato Expression Atlas (Fernandez‐Pozo et al , ), for A. thaliana from Thalemine (Krishnakumar et al , ), for maize from qTeller (Schnable, ), and for rice from the Rice Annotation Project (Kawahara et al , ). Correlation of gene pair expression was analyzed using Pearson's product‐moment correlation (Table S4; Best & Roberts, ).…”

Section: Methodsmentioning

confidence: 99%

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Structural evolution drives diversification of the large LRR‐RLK gene family

2020

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Cells are continuously exposed to chemical signals that they must discriminate between and respond to appropriately. In embryophytes, the leucine-rich repeat receptor-like kinases (LRR-RLKs) are signal receptors critical in development and defense. LRR-RLKs have diversified to hundreds of genes in many plant genomes. Although intensively studied, a well-resolved LRR-RLK gene tree has remained elusive.To resolve the LRR-RLK gene tree, we developed an improved gene discovery method based on iterative hidden Markov model searching and phylogenetic inference. We used this method to infer complete gene trees for each of the LRR-RLK subclades and reconstructed the deepest nodes of the full gene family.We discovered that the LRR-RLK gene family is even larger than previously thought, and that protein domain gains and losses are prevalent. These structural modifications, some of which likely predate embryophyte diversification, led to misclassification of some LRR-RLK variants as members of other gene families. Our work corrects this misclassification.Our results reveal ongoing structural evolution generating novel LRR-RLK genes. These new genes are raw material for the diversification of signaling in development and defense. Our methods also enable phylogenetic reconstruction in any large gene family.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Structural evolution drives diversification of the large LRR‐RLK gene family

2020

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“…Tables of DEGs for each comparison were combined and analyzed through Microsoft Excel, in order to generate lists of Arabidopsis Genome Initiative (AGI) identifiers with their corresponding [Log 2 (Fold Change)] values. Machine annotation of AGI ID lists was carried out using G:Profiler (Raudvere et al, 2019), while the TAIR (Lamesch et al, 2011;Berardini et al, 2015) and Araport ThaleMine (Krishnakumar et al, 2016) databases were used to investigate genes of interest. DEGs of a comparison (e.g., FLT vs. GC) with a greater than twofold change in at least one context of the comparison were retained for analysis (Supplementary File S1).…”

Section: Rna-seq Data Analysismentioning

confidence: 99%

Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

et al. 2020

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The observation that plant roots skew in microgravity recently refuted the long-held conviction that skewing was a gravity-dependent phenomenon. Further, spaceflight root skewing suggests that specific root morphologies and cell wall remodeling systems may be important aspects of spaceflight physiological adaptation. However, connections between skewing, cell wall modification and spaceflight physiology are currently based on inferences rather than direct tests. Therefore, the Advanced Plant Experiments-03-2 (APEX-03-2) spaceflight study was designed to elucidate the contribution of two skewing-and cell wall-associated genes in Arabidopsis to root behavior and gene expression patterns in spaceflight, to assess whether interruptions of different skewing pathways affect the overall spaceflight-associated process. SPIRAL1 is a skewingrelated protein implicated in directional cell expansion, and functions by regulating cortical microtubule dynamics. SKU5 is skewing-related glycosylphosphatidylinositolanchored protein of the plasma membrane and cell wall implicated in stress response signaling. These two genes function in different cellular pathways that affect skewing on the Earth, and enable a test of the relevance of skewing pathways to spaceflight physiological adaptation. In this study, both sku5 and spr1 mutants showed different skewing behavior and markedly different patterns of gene expression in the spaceflight environment. The spr1 mutant showed fewer differentially expressed genes than its Col-0 wild-type, whereas sku5 showed considerably more than its WS wild-type. Developmental age played a substantial role in spaceflight acclimation in all genotypes, but particularly in sku5 plants, where spaceflight 4d seedlings had almost 10-times as many highly differentially expressed genes as the 8d seedlings. These differences demonstrated that the two skewing pathways represented by SKU5 and SPR1 have unique and opposite contributions to physiological adaptation to spaceflight. The spr1 response is less intense than wild type, suggesting that the loss of SPR1 positively impacts spaceflight adaptation. Conversely, the intensity of the sku5 responses suggests that the loss of SKU5 initiates a much more complex, deeper and more stress related response to spaceflight. This suggests that proper SKU5 function is important to spaceflight adaptation.

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“…Cell type-specific localization might also result from alternative mRNA splicing generating multiple protein isoforms. However, the current A. thaliana genome annotation (Krishnakumar et al 2017) only predicts a single FH1 mRNA comprising four exons. Also all empirically obtained cDNA sequences derived from the At3g25500 locus found in the GenBank database match the predicted splicing pattern, or at least are consistent with it (Supplementary data Figure S11).…”

Section: Discussionmentioning

confidence: 99%

Arabidopsis Class I Formin FH1 Relocates Between Membrane Compartments During Root Cell Ontogeny And Associates With Plasmodesmata

Oulehlová

Kollárová

Cifrová

et al. 2018

Preprint

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Formins are evolutionarily conserved eukaryotic proteins engaged in actin nucleation and other aspects of cytoskeletal organization. Angiosperms have two formin clades with multiple paralogs; typical plant Class I formins are integral membrane proteins that can anchor cytoskeletal structures to membranes. For the main Arabidopsis housekeeping Class I formin, FH1 (At3g25500), plasmalemma localization was documented in heterologous expression and overexpression studies. We previously showed that loss of FH1 function increases cotyledon epidermal pavement cell shape complexity via modification of actin and microtubule organization and dynamics. Here we employ transgenic Arabidopsis expressing green fluorescent protein-tagged FH1 (FH1-GFP) from its native promoter to investigate in vivo behaviour of this formin using advanced microscopy techniques. The fusion protein is functional, since its expression complements the fh1 loss-of-function mutant phenotype. Accidental overexpression of FH1-GFP results in a decrease in trichome branch number, while fh1 mutation has the opposite effect, indicating a general role of this formin in controlling cell shape complexity. Consistent with previous reports, FH1-GFP associates with membranes. However, the protein exhibits surprising actin- and secretory pathway-dependent dynamic localization and relocates between cellular endomembranes and the plasmalemma during cell division and differentiation in root tissues, with transient tonoplast localization at the transition/elongation zones border. FH1-GFP also accumulates in actin-rich regions of cortical cytoplasm and associates with plasmodesmata in both the cotyledon epidermis and root tissues. Together with previous reports from metazoan systems, this suggests that formins might have an ancestral role at cell-cell junctions.

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ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

Cited by 34 publications

References 42 publications

Structural evolution drives diversification of the large LRR‐RLK gene family

Structural evolution drives diversification of the large LRR‐RLK gene family

Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

Arabidopsis Class I Formin FH1 Relocates Between Membrane Compartments During Root Cell Ontogeny And Associates With Plasmodesmata

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