ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae

Goertzen, Leslie R.; Cannone, Jamie J.; Gutell, Robin R.; Jansen, Robert K.

doi:10.1016/s1055-7903(03)00094-0

Cited by 141 publications

(114 citation statements)

References 54 publications

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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.

156

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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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.

156

154

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“…MatK sequences were translated into proteins with GeneJockey (Biosoft, Carnbridge, U. K.) to verify the absence of internal stop codons. Dueto the high leve1 of variability of the ITS sequences, our alignment was checked with the ITS alignment for the whole Compositae by Goertzen et al (2003) and adjusted manually. In order to conserve the phylogenetic information of insertions-deletions which constitute the main part of the variation of the irnL-trnF region and at the same time avoiding over-estimation of lengthy indels, they where coded as presence-absence characters and added to the end of matrices in al1 the cases.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

THE CARDUEAE (COMPOSITAE) REVISITED: INSIGHTS FROM ITS,trnL-trnF, ANDmatK NUCLEAR AND CHLOROPLAST DNA ANALYSIS^1,²

Susanna¹,

Garcia‐Jacas²,

Hidalgo³

et al. 2006

Annals of the Missouri Botanical Garden

124

128

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“…Because of the assumed conservation in secondary structure, it is also referred to as a double-edged tool for eukaryote evolutionary comparison (Mai and Coleman 1997;Morgan and Blair 1998;Joseph et al 1999;Michot et al 1999;Suh and Kim 2002;Alvarez and Wendel 2003;Coleman 2003;Goertzen et al 2003;Young and Coleman 2004). Although the biological role of the ITS spacers is not well understood, the utilization of yeast models has definitely shown their importance for production of the mature rRNA.…”

Section: Introductionmentioning

confidence: 99%

ITS2 secondary structure and phylogeny of cyst-forming nematodes of the genus Heterodera (Tylenchida: Heteroderidae)

Overstreet

Subbotin

2008

Organisms Diversity & Evolution

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The internal transcribed spacer 2 (ITS2) of the ribosomal RNA gene is a double-edged tool for eukaryote evolutionary comparison. In this paper, we re-evaluate the putative ITS2 secondary structures proposed for 29 species of cyst-forming nematodes in the genus Heterodera and present optimized variants. The models are organized in four main helices emerging from a central core. Helix III is always the longest and has two branches exhibited as a Y-shaped structure near the apex. In most species, helices III and IV have merged to form a segment of the central core. Two conservative motifs, GAUCR and UURC, were found in helices II and III, respectively. Using the MARNA program taking into consideration both the primary sequence and the secondary structure, we generated an optimal alignment for Heterodera sequences. The alignment was analyzed by Bayesian inference under a general-time-reversible model and the complex models, and by a maximum parsimony approach using original data and sequence data converted according to secondary-structure information. The consensus ITS2 secondary structure model for Heteroderidae can serve as a useful guide for reconstruction of optimal alignment and can be used as an additional source of data incorporating structural parameters of molecules for the study of nematode phylogeny. Application of the secondary ITS2 structure data allows a more resolved and realistic picture of relationships within Heteroderidae.

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ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae

Cited by 141 publications

References 54 publications

Hydraulic integration and shrub growth form linked across continental aridity gradients

Hydraulic integration and shrub growth form linked across continental aridity gradients

THE CARDUEAE (COMPOSITAE) REVISITED: INSIGHTS FROM ITS,trnL-trnF, ANDmatK NUCLEAR AND CHLOROPLAST DNA ANALYSIS^1,²

ITS2 secondary structure and phylogeny of cyst-forming nematodes of the genus Heterodera (Tylenchida: Heteroderidae)

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ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae

Cited by 141 publications

References 54 publications

Hydraulic integration and shrub growth form linked across continental aridity gradients

Hydraulic integration and shrub growth form linked across continental aridity gradients

THE CARDUEAE (COMPOSITAE) REVISITED: INSIGHTS FROM ITS,trnL-trnF, ANDmatK NUCLEAR AND CHLOROPLAST DNA ANALYSIS1,2

ITS2 secondary structure and phylogeny of cyst-forming nematodes of the genus Heterodera (Tylenchida: Heteroderidae)

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Product

Resources

About

THE CARDUEAE (COMPOSITAE) REVISITED: INSIGHTS FROM ITS,trnL-trnF, ANDmatK NUCLEAR AND CHLOROPLAST DNA ANALYSIS^1,²