Reconstruction of Solanaceae Phylogeny Using the Nuclear Gene SAMT

Martins, Talline R.; Barkman, Todd J.

doi:10.1600/0363644054223675

Cited by 52 publications

(46 citation statements)

References 51 publications

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“…One striking difference is that the COSII phylogeny places tobacco and Petunia as sister taxa vs. Petunia being basal to the Solanaceae (bootstrap value ¼ 100%). This result conflicts with studies based on chloroplast DNA, internal transcribed spacer sequences, and a single nuclear gene, SAMT, in which Nicotiana was closer to Solanum, Capsicum, and Physalis, while Petunia was an outgroup to the above taxa, although the bootstrap values for these studies were generally lower than those obtained with the COSII sequences (Olmstead and Sweere 1994;Olmstead 1999;Santiago-Valentin and Olmstead 2003;Martins and Barkman 2005). The high bootstrap value generated with this study, combined with the fact that 10 unlinked (distributed on different chromosomes) orthologous loci were examined, brings these prior studies into question.…”

Section: Resultscontrasting

confidence: 59%

Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade

et al. 2006

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We report herein the application of a set of algorithms to identify a large number (2869) of single-copy orthologs (COSII), which are shared by most, if not all, euasterid plant species as well as the model species Arabidopsis. Alignments of the orthologous sequences across multiple species enabled the design of ''universal PCR primers,'' which can be used to amplify the corresponding orthologs from a broad range of taxa, including those lacking any sequence databases. Functional annotation revealed that these conserved, single-copy orthologs encode a higher-than-expected frequency of proteins transported and utilized in organelles and a paucity of proteins associated with cell walls, protein kinases, transcription factors, and signal transduction. The enabling power of this new ortholog resource was demonstrated in phylogenetic studies, as well as in comparative mapping across the plant families tomato (family Solanaceae) and coffee (family Rubiaceae). The combined results of these studies provide compelling evidence that (1) the ancestral species that gave rise to the core euasterid families Solanaceae and Rubiaceae had a basic chromosome number of x ¼ 11 or 12.2) No whole-genome duplication event (i.e., polyploidization) occurred immediately prior to or after the radiation of either Solanaceae or Rubiaceae as has been recently suggested.

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Section: Resultscontrasting

confidence: 59%

Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade

et al. 2006

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“…It is not clear what the role of SAMT is in N. alata vegetative tissues because neither MeSA nor MeBA has been detected from its leaves or stems. Like other species, SAMT in N. alata and N. sylvestris appears to experience increased expression in response to SA treatment (Martins and Barkman 2005) making this a conserved, inducible leaf response indicative of a role in pathogen defense. Patterns of BSMT2 gene expression are largely conserved among Nicotiana species with expression highest in leaves and low or absent in roots and it is not induced by any of the treatments administered in this study.…”

Section: Expression Divergence Of Orthologsmentioning

confidence: 94%

“…RNA was isolated from 0.5 to 1 g frozen plant material according to Chang et al (1993) and RNA was stored at -70°C. To isolate SAMT, a leaf disk (1 cm 2 ) was incubated in 5 mM SA (pH 6.5) for 24 h to induce gene expression prior to RNA extraction (Martins and Barkman 2005). For determination of expression levels of Nicotiana SAMT and BSMT genes after induction with SA or BA in leaves, leaf disks (1 cm 2 ) were incubated in 5 mM SA or BA (pH 6.5) for 24 h and RNA was isolated as described above.…”

Section: Rna Isolationmentioning

confidence: 99%

“…The primer sequences and amplification conditions for all reactions are shown in Supplemental Table S2 and S3. All RT-PCR and RACE reactions were performed after DNaseI (Fermentas) digestion of 2 lg total RNA at 37°C for 1 h. 5 0 UTR-regions of all SAMTs were isolated by RT-PCR using a primer derived from the 5 0 UTR of SAMT from N. tabacum (Martins and Barkman 2005). To obtain the 5 0 UTR sequences of the BSMT genes, ThermoScript RT-PCR system (Invitrogen) was used.…”

Section: Sequence Completion Of Samt and Bsmt Sequencesmentioning

confidence: 99%

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Enzymatic, expression and structural divergences among carboxyl O-methyltransferases after gene duplication and speciation in Nicotiana

Hippauf

Michalsky²,

Huang

et al. 2009

Plant Mol Biol

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Methyl salicylate and methyl benzoate have important roles in a variety of processes including pollinator attraction and plant defence. These compounds are synthesized by salicylic acid, benzoic acid and benzoic acid/salicylic acid carboxyl methyltransferases (SAMT, BAMT and BSMT) which are members of the SABATH gene family. Both SAMT and BSMT were isolated from Nicotiana suaveolens, Nicotiana alata, and Nicotiana sylvestris allowing us to discern levels of enzyme divergence resulting from gene duplication in addition to species divergence. Phylogenetic analyses showed that Nicotiana SAMTs and BSMTs evolved in separate clades and the latter can be differentiated into the BSMT1 and the newly established BSMT2 branch. Although SAMT and BSMT orthologs showed minimal change coincident with species divergences, substantial evolutionary change of enzyme activity and expression patterns occurred following gene duplication. After duplication, the BSMT enzymes evolved higher preference for benzoic acid (BA) than salicylic acid (SA) whereas SAMTs maintained ancestral enzymatic preference for SA over BA. Expression patterns are largely complementary in that BSMT transcripts primarily accumulate in flowers, leaves and stems whereas SAMT is expressed mostly in roots. A novel enzyme, nicotinic acid carboxyl methyltransferase (NAMT), which displays a high degree of activity with nicotinic acid was discovered to have evolved in N. gossei from an ancestral BSMT. Furthermore a SAM-dependent synthesis of methyl anthranilate via BSMT2 is reported and contrasts with alternative biosynthetic routes previously proposed. While BSMT in flowers is clearly involved in methyl benzoate synthesis to attract pollinators, its function in other organs and tissues remains obscure.

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“…PICs were calculated using PDAP:PDTREE (48), a module of Mesquite (version 1.1) (49), and Phylomatic (50) was used to generate an initial tree. Most remaining polytomies were resolved using published phylogenies (51)(52)(53)(54)(55)(56)(57)(58), leaving only a few unresolved. Any anatomical trait that had a significant association between the absolute value of its standardized independent contrast versus its standard deviation (59 -61) was log-transformed (FLD and FWT) or arsine-transformed (FLA and FWA).…”

Section: Methodsmentioning

confidence: 99%

Hydraulic integration and shrub growth form linked across continental aridity gradients

Schenk

Espino

Goedhart

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

152

154

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Both engineered hydraulic systems and plant hydraulic systems are protected against failure by resistance, reparability, and redundancy. A basic rule of reliability engineering is that the level of independent redundancy should increase with increasing risk of fatal system failure. Here we show that hydraulic systems of plants function as predicted by this engineering rule. Hydraulic systems of shrubs sampled along two transcontinental aridity gradients changed with increasing aridity from highly integrated to independently redundant modular designs. Shrubs in humid environments tend to be hydraulically integrated, with single, round basal stems, whereas dryland shrubs typically have modular hydraulic systems and multiple, segmented basal stems. Modularity is achieved anatomically at the vessel-network scale or developmentally at the whole-plant scale through asymmetric secondary growth, which results in a semiclonal or clonal shrub growth form that appears to be ubiquitous in global deserts.plant hydraulic systems ͉ wood anatomy ͉ hydraulic redundancy ͉ xylem structure and function I n engineering terms, the hydraulic system of a plant is a negative-pressure flow system. This type of hydraulic system, whether natural or man-made, is prone to fail when air bubbles (emboli) are introduced, because under strong negative pressure a single embolism can lead to breakage of the water column unless the air bubble is isolated in a branch or pipe. Both drought and freezing can cause embolisms in plants (1).Drought-induced embolisms form under negative pressure, when air is pulled into a water-filled conduit from adjacent air-filled spaces or cells, a process known as ''air seeding.'' This common, even daily, event (2-4) can lead to complete failure of the hydraulic system if runaway embolism occurs (5). Two of the three attributes by which plants' negative-pressure flow systems can be protected against failure, resistance and reparability, have been subjects of active research during the last decade (2-4, 6-10). The third attribute, redundancy, has received much less attention as an important drought adaptation but is emerging as a focus of research (11)(12)(13)(14). Attributes of redundancy in hydraulic systems of vessel-bearing angiosperms include the numbers of vessels (14), the vessel network topology (12), the number and sizes of pits between adjacent vessels (13,15,16), and the division of whole plants into independent hydraulic units (17).A basic rule of reliability engineering states that the level of independent redundancy should increase with increasing risk of fatal system failure (18); hydraulic engineers routinely increase the safety of man-made pressure-flow systems by designing them to be redundant (19). Redundancy in hydraulic systems (Fig. 1) can vary from a high degree of inter-connectedness (i.e., integrated redundancy) to complete, independent compartmentation (i.e., modular redundancy). In a negative-pressure flow system, integrated redundancy allows alternate water transport pathways around blockage...

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Reconstruction of Solanaceae Phylogeny Using the Nuclear Gene SAMT

Cited by 52 publications

References 51 publications

Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade

Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade

Enzymatic, expression and structural divergences among carboxyl O-methyltransferases after gene duplication and speciation in Nicotiana

Hydraulic integration and shrub growth form linked across continental aridity gradients

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