Simulating DNA coding sequence evolution with EvolveAGene 3

Phylogenetic reconstruction based upon multiple alignments ofmolecular sequences is important to most branches of modernbiology and is central to molecular evolution. Understandingthe historical relationships among macromolecules depends uponcomputer programs that implement a variety of analytical methods.Because it is impossible to know those historical relationshipswith certainty, assessment of the accuracy of methods and theprograms that implement them requires the use of programs thatrealistically simulate the evolution of DNA sequences. EvolveAGene3 is a realistic coding sequence simulation program that separatesmutation from selection and allows the user to set selectionconditions, including variable regions of selection intensitywithin the sequence and variation in intensity of selectionover branches. Variation includes base substitutions, insertions,and deletions. To the best of my knowledge, it is the only programavailable that simulates the evolution of intact coding sequences.Output includes the true tree and true alignments of the resultingcoding sequence and corresponding protein sequences. A log filereports the frequencies of each kind of base substitution, theratio of transition to transversion substitutions, the ratioof indel to base substitution mutations, and the numbers ofsilent and amino acid replacement mutations. The realism ofthe data sets has been assessed by comparing the d_N/d_S ratio,the ratio of transition to transversion substitutions, and theratio of indel to base substitution mutations of the simulateddata sets with those parameters of real data sets from the "goldstandard" BaliBase collection of structural alignments. Resultsshow that the data sets produced by EvolveAGene 3 are very similarto real data sets, and EvolveAGene 3 is therefore a realisticsimulation program that can be used to evaluate a variety ofprograms and methods in molecular evolution.     

Expression of the nuclear gene TaF(A)d is under mitochondrial retrograde regulation in anthers of male sterile wheat plants with timopheevii cytoplasm

Alterations of mitochondrial-encoded subunits of the F_oF₁-ATPsynthase are frequently associated with cytoplasmic male sterility(CMS) in plants; however, little is known about the relationshipof the nuclear encoded subunits of this enzyme with CMS. Inthe present study, the full cDNA of the gene TaF_Ad that encodesthe putative F_Ad subunit of the F_oF₁-ATP synthase was isolatedfrom the wheat (Triticum aestivum) fertility restorer ‘2114’for timopheevii cytoplasm-based CMS. The deduced 238 amino acidpolypeptide is highly similar to its counterparts in dicotsand other monocots but has low homology to its mammalian equivalents.TaF_Ad is a single copy gene in wheat and maps to the short armof the group 6 chromosomes. Transient expression of the TaF_Ad–GFPfusion in onion epidermal cells demonstrated TaF_Ad's mitochondriallocation. TaF_Ad was expressed abundantly in stem, leaf, anther,and ovary tissues of 2114. Nevertheless, its expression wasrepressed in anthers of CMS plants with timopheevii cytoplasm.Genic male sterility did not affect its expression in anthers.The expression of the nuclear gene encoding the 20 kDa subunitof F_o was down-regulated in a manner similar to TaF_Ad in theT-CMS anthers while that of genes encoding the 6 kDa subunitof F_o and the subunit of F₁ was unaffected. These observationsimplied that TaF_Ad is under mitochondrial retrograde regulationin the anthers of CMS plants with timopheevii cytoplasm. Key words: CMS, F_Ad subunit, F_oF₁-ATP synthase, retrograde regulation, wheat Received 8 October 2007; Revised 9 January 2008 Accepted 28 January 2008     

Internode Length in Pisum. A New Allele at the le Locus

In Pisum sativum L. a third, more severe, allele at the internodelength locus le is identified and named le^d. Plants homozygousfor le^d possess shorter internodes and appear relatively lessresponsive to GA₂₀ than comparable le (dwarf) plants. Gene le^dmay act by reducing the 3ß-hydroxylation of GA₂₀ tothe highly active GA₁ more effectively than does gene le. Theresults indicate that le is a leaky mutant and therefore thatendogenous GA₁ influences internode elongation in dwarf (le)plants. Pisum sativum, peas, internode length, genetics, gibberellin, dwarf elongation     

Canopy Photosynthesis of Tomato, Cucumber and Sweet Pepper in Greenhouses: Measurements Compared to Models

Two models for canopy photosynthesis (modified versions of thoseof Acock et al. , 1978 and of Thornley, 1976) were examinedby comparison with experimental photosynthesis data of cucumber(Cucumis sativus L.), sweet pepper (Capsicum annuum L.) andtomato (Lycopersicon esculentum Mill.). The data were obtainedin six large-scale, long-term, semi-commercial cultivationsin greenhouses (Nederhoff and Vegter, 1994). Measured environmentalconditions and measured LAI were input to the model. The emphasiswas on the models' sensitivity to the prevailing CO₂ concentration. The (modified) Acock model with 'standard' (originally published)parameters underestimated the photosynthesis rate. This modeltuned to one of our experimental data sets did not fit verywell to the other data sets. As expected, if the model was tunedto each particular data set, it was fairly in agreement withthe measurements, but the fitted parameter values were sometimesquestionable. With the (modified) Thornley model it was obligatoryto estimate or tune the light extinction. The model performedreasonably if all parameters were tuned and also if only thelight extinction was tuned. The modified models were considered usable for practical applications,after parameter tuning. As the sensitivity to CO₂ was not alwaysequal among the models and the measurements, care should betaken when applying the models for CO₂ supply control.Copyright1994, 1999 Academic Press Canopy photosynthesis, Capsicum annuum L., carbon dioxide, cucumber, CO₂, Cucumis sativus L., glasshouse, greenhouse, Lycopersicon esculentum Mill., measurements, model, sweet pepper, tomato     

Comparative Potency of Nine Gibberellins

Gibberellins A₁ to A₉ have been compared, each at several doselevels, in bioassays based on extension of stems of dwarf gardenpea (Pisum sativum), dwarf bean (Phaseolus vulgaris) and Lunariaannua, of hypocotyls of cucumber (Cucumis sativus) and lettuce(Lactuca sativa), and of leaf sheaths of three dwarf mutants(d–1, d–3, d–5) of maize (Zea mays). GibberellinsA₃ (gibberellic acid) and A₇ are of high potency in most bioassays.A₈ is of negligible potency in all and is probably not a functionalhormone. The other gibberellins show a more or less marked tendencyto specificity. The plants used as bioassay material also differin the specificity of their response. Some, for example, maizedwarfs d–3 and d–5 and lettuce, respond well tomost gibberellins; others, for example, cucumber, respond onlyto a few; extreme specificity is shown by Lunaria annua which,in the unvernalized condition, responds by stem elongation onlyto gibberellin A₇. Dose/response curves of the various gibberellinsare usually parallel, but certain exceptions to this have beenfound. Possible explanations of specificity are discussed inrelation to the results obtained, and it is concluded that insufficientevidence is available to make it possible to draw any validconclusions. Current definitions of gibberellins, whether basedon chemical structure or biological activity, are unsatisfactory.     

Alteration of Soybean Seedling Development in Darkness and Light by the Stay-green Mutation cytG and Gd1d2

The stay-green mutations cytG and Gd₁d₂ prevent the normal yellowingduring senescence of soybean (Glycine max) leaves and cotyledons.Because light plays such an important role in regulating morphogenesisand it promotes the formation of chlorophyll (Chl), we determinedthe effect of cytG and Gd₁d₂ (in a cv. Clark background) onthe development and some light responses of seedlings. AlthoughcytG and Gd₁d₂ seeds, particularly the cotyledons, are greenwhen mature, 44 and 71 % respectively of this Chl broke downwhen the seeds were germinated in darkness. Chlorophyllidesand phaeophytins were not present in the seeds in significantamounts. cytG and Gd₁d₂ as well as wild type (cv. Clark) seedlingsdeveloped a full etiolation syndrome (morphology and lack ofChl) in darkness. Light induced rapid Chl accumulation in thedark-grown seedlings with no apparent difference among the threeisolines. A short (8 h) exposure to light induced some Chl inthe cotyledons of dark-grown plants, and 22 h of light producedfour times more. Following return to darkness, the 8-h groupshowed very little breakdown over the next 12 d. After the 22-hgroup was returned to darkness, the wild-type lost Chl steadily,but Gd₁d₂ and eventually also cytG inhibited this breakdown.In the 22-h group, the Chl a/b ratio decreased in wild typeand cytG indicating preferential breakdown of Chl a relativeto Chl b; however, Gd₁d₂ prevented this change. cytG and Gd₁d₂seem to act preferentially on Chl breakdown rather than synthesis.Copyright1995, 1999 Academic Press Glycine max, soybean, chlorophyll, chlorophyll a/b ratio, cotyledons, etiolation, cytG, Gd₁d₂, mutations, senescence     

Nitrogen Utilization in N-limited Barley during Vegetative and Generative Growth: I. GROWTH AND NITRATE UPTAKE KINETICS IN VEGETATIVE CULTURES GROWN AT DIFFERENT RELATIVE ADDITION RATES OF NITRATE-N

Growth and nitrate uptake kinetics in vegetatively growing barley(Hordeum vulgare L., cvs Laevigatum, Golf, and Mette) were investigatedin solution culture under long-term limitations of externalnitrogen availability. Nitrate was fed to the cultures at relativeaddition rates (RA) ranging from 0.02 to 0.2 d^–1. Therelative growth rate (RG, calculated for total plant dry weight)correlated well with RA in the range 0.02 to 0.07 d^–1.In the RA range from 0.07 to 0.2 d^–1 RG continued to increase,but an increasing fraction of nitrogen, added and absorbed,was apparently stored rather than used for structural growth.The RG of the roots was less affected by RA. V_max, for net nitrateuptake increased with RA up to 0.11 d^–1, but decreasedat higher RA. The decline in V_max coincided with a build-upof nitrate stores in both roots and shoots. V_max, expressedper unit nitrogen in the plants (the relative V_max, was higherthan required for maintenance of growth (up to 30-fold) at lowRA, whereas at higher RA the relative V_max decreased. Kineticpredictions of steady-state external nitrate concentrationsduring N-limited growth ranged from 0.2 to 5.0 mmol m^–3over the RG range 0.02 to 0.11 d_–1. It is suggested thatthe nitrate uptake system is not under specific regulation atlow RA, but co-ordinated with root protein synthesis and growthin general. At RA higher than 0.11 d_–1, however, specificregulation of nitrate uptake, possibly via root nitrate pools,become important. The three cultivars showed very similar growthand nitrate uptake characteristics. Key words: Barley, growth, nitrogen limitation, nitrate uptake, kinetics