AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

Kumar, Surendra; Skjæveland, Åsmund; Orr, Russell J. S.; Enger, Pål; Ruden, Torgeir A.; Mevik, Bjørn-Helge; Burki, Fabien; Botnen, Andreas; Shalchian-Tabrizi, Kamran

doi:10.1186/1471-2105-10-357

Cited by 201 publications

(163 citation statements)

References 35 publications

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“…3 (ref. 15) 36 ). Each data set was run in duplicate using four chains simultaneously (three heated and one cold) for 5×10 6 generations, sampling every 500th cycle from the chain and using default settings in regards to priors.…”

Section: Methodsmentioning

confidence: 99%

Dynamic evolution of venom proteins in squamate reptiles

2012

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Phylogenetic analyses of toxin gene families have revolutionised our understanding of the origin and evolution of reptile venoms, leading to the current hypothesis that venom evolved once in squamate reptiles. However, because of a lack of homologous squamate non-toxin sequences, these conclusions rely on the implicit assumption that recruitments of protein families into venom are both rare and irreversible. Here we use sequences of homologous non-toxin proteins from two snake species to test these assumptions. Phylogenetic and ancestral-state analyses revealed frequent nesting of 'physiological' proteins within venom toxin clades, suggesting early ancestral recruitment into venom followed by reverse recruitment of toxins back to physiological roles. These results provide evidence that protein recruitment into venoms from physiological functions is not a one-way process, but dynamic, with reversal of function and/or co-expression of toxins in different tissues. This requires a major reassessment of our previous understanding of how animal venoms evolve.

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Section: Methodsmentioning

confidence: 99%

Dynamic evolution of venom proteins in squamate reptiles

2012

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“…The most likely number of clusters K in all simulations was assumed to be in the range of K = 1 to K = 10. Ten replicates were conducted for each K with a burn-in period of 1 3 10 6 , followed by 5 3 10 6 MCMC steps using the Bioportal computing resource (http://www.mn.uio.no/ibv/bioportal/index.html; Kumar et al, 2009). These parameters met the requirements for the use of the Structure software proposed by Gilbert et al (2012) to ensure the reproducibility of the results of this study.…”

Section: Estimation Of Population Differentiation and Structurementioning

confidence: 99%

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

Sauvage

Segura

Bauchet³

et al. 2014

Plant Physiology

198

217

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Genome-wide association studies have been successful in identifying genes involved in polygenic traits and are valuable for crop improvement. Tomato (Solanum lycopersicum) is a major crop and is highly appreciated worldwide for its health value. We used a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium to map loci controlling variation in fruit metabolites. Fruits were phenotyped for a broad range of metabolites, including amino acids, sugars, and ascorbate. In parallel, the accessions were genotyped with 5,995 single-nucleotide polymorphism markers spread over the whole genome. Genome-wide association analysis was conducted on a large set of metabolic traits that were stable over 2 years using a multilocus mixed model as a general method for mapping complex traits in structured populations and applied to tomato. We detected a total of 44 loci that were significantly associated with a total of 19 traits, including sucrose, ascorbate, malate, and citrate levels. These results not only provide a list of candidate loci to be functionally validated but also a powerful analytical approach for finding genetic variants that can be directly used for crop improvement and deciphering the genetic architecture of complex traits.

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“…A phylogenetic tree was estimated using maximum likelihood (Felsenstein, 1981) with RAxML version 7.3.2 (Stamatakis, 2006a). Fast bootstrap analyses (Felsenstein, 1985;Stamatakis et al, 2008) over 10,000 rounds were run on the Web-based bioportal facility (Kumar et al, 2009) (http://www.mn.uio.no/ibv/bioportal/) with eight parallel processors, using bootstrap trees as starting trees for heuristic searches, and employing the DAYHOFF model of amino acid substitution as inferred with the ProteinModelSelection perl script (http://www.exelixis-lab.org/), accounting for rate heterogeneity by using the CAT model (Stamatakis, 2006b). The final tree was optimized using the Gamma model of rate heterogeneity (Yang, 1993).…”

Section: Blast Search and Phylogenetic Analysesmentioning

confidence: 99%

VIH2 Regulates the Synthesis of Inositol Pyrophosphate InsP₈ and Jasmonate-Dependent Defenses in Arabidopsis

et al. 2015

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ORCID IDs: 0000-0002-7823-5489 (D.L.); 0000-0002-4512-9508 (P.J.); 0000-0002-1025-9484 (H.J.J.); 0000-0001-9022-4515 (G.S.)Diphosphorylated inositol polyphosphates, also referred to as inositol pyrophosphates, are important signaling molecules that regulate critical cellular activities in many eukaryotic organisms, such as membrane trafficking, telomere maintenance, ribosome biogenesis, and apoptosis. In mammals and fungi, two distinct classes of inositol phosphate kinases mediate biosynthesis of inositol pyrophosphates: Kcs1/IP6K-and Vip1/PPIP5K-like proteins. Here, we report that PPIP5K homologs are widely distributed in plants and that Arabidopsis thaliana VIH1 and VIH2 are functional PPIP5K enzymes. We show a specific induction of inositol pyrophosphate InsP 8 by jasmonate and demonstrate that steady state and jasmonate-induced pools of InsP 8 in Arabidopsis seedlings depend on VIH2. We identify a role of VIH2 in regulating jasmonate perception and plant defenses against herbivorous insects and necrotrophic fungi. In silico docking experiments and radioligand binding-based reconstitution assays show highaffinity binding of inositol pyrophosphates to the F-box protein COI1-JAZ jasmonate coreceptor complex and suggest that coincidence detection of jasmonate and InsP 8 by COI1-JAZ is a critical component in jasmonate-regulated defenses.

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AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

Cited by 201 publications

References 35 publications

Dynamic evolution of venom proteins in squamate reptiles

Dynamic evolution of venom proteins in squamate reptiles

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

VIH2 Regulates the Synthesis of Inositol Pyrophosphate InsP₈ and Jasmonate-Dependent Defenses in Arabidopsis

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AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses

Cited by 201 publications

References 35 publications

Dynamic evolution of venom proteins in squamate reptiles

Dynamic evolution of venom proteins in squamate reptiles

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

VIH2 Regulates the Synthesis of Inositol Pyrophosphate InsP8 and Jasmonate-Dependent Defenses in Arabidopsis

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VIH2 Regulates the Synthesis of Inositol Pyrophosphate InsP₈ and Jasmonate-Dependent Defenses in Arabidopsis