Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

The reconstruction of phylogenetic history is predicated on being able to accurately establish hypotheses of character homology, which involves sequence alignment for studies based on molecular sequence data. In an empirical study investigating nucleotide sequence alignment, we inferred phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based on complete small-subunit rDNA sequences, using six different multiple-alignment procedures: manual alignment based on the secondary structure of the 18S rRNA molecule, and automated similarity-based alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM computer programs. Trees were constructed using neighboring-joining, weighted-parsimony, and maximum- likelihood methods. All of the multiple sequence alignment procedures yielded the same basic structure for the estimate of the phylogenetic relationship among the taxa, which presumably represents the underlying phylogenetic signal. However, the placement of many of the taxa was sensitive to the alignment procedure used; and the different alignments produced trees that were on average more dissimilar from each other than did the different tree-building methods used. The multiple alignments from the different procedures varied greatly in length, but aligned sequence length was not a good predictor of the similarity of the resulting phylogenetic trees. We also systematically varied the gap weights (the relative cost of inserting a new gap into a sequence or extending an already-existing gap) for the ClustalW program, and this produced alignments that were at least as different from each other as those produced by the different alignment algorithms. Furthermore, there was no combination of gap weights that produced the same tree as that from the structure alignment, in spite of the fact that many of the alignments were similar in length to the structure alignment. We also investigated the phylogenetic information content of the helical and nonhelical regions of the rDNA, and conclude that the helical regions are the most informative. We therefore conclude that many of the literature disagreements concerning the phylogeny of the Apicomplexa are probably based on differences in sequence alignment strategies rather than differences in data or tree-building methods.      

南京地区人群MN、Hp、Tf、Bf、GLOI、EsD、EAP表型分布及基因频率调查

南京地区人群ＭＮ、Ｈｐ、Ｔｆ、Ｂｆ、ＧＬＯＩ、ＥｓＤ、ＥＡＰ表型分布及基因频率调查达建章淑华（南京医科大学法医学教研室,南京２１００２９）（江苏省中医院,南京２１００００）ＩｎｖｅｓｔｉｇａｔｉｏｎｓｏｎｔｈｅＰｈｅｎｏｔｙｐｅＤｉｓｔｒｉｂｕｔｉｏ...     

Sports genetics: the PPARA gene and athletes’ high ability in endurance sports. A systematic review and meta-analysis

A meta-analysis was performed with the aim of re-evaluating the role of the peroxisome proliferator activated receptor alpha (PPARA) gene intron 7 G/C polymorphism (rs4253778) in athletes’ high ability in endurance sports. Design: A meta-analysis of case control studies assessing the association between the G/C polymorphisms of the PPARA gene and endurance sports was conducted. The Cochrane Review Manager software was used to compare the genotype and allele frequencies between endurance athletes and controls to determine whether a genetic variant is more common in athletes than in the general population. Five studies, encompassing 760 endurance athletes and 1792 controls, fulfilled our inclusion criteria. The pooled odds ratio (and confidence intervals, CIs) for the G allele compared to the C allele was 1.65 (95% CI 1.39-1.96). The pooled OR for the GG genotype compared to the GC genotype was 1.79 (95% CI 1.44-2.22), and for the GG genotype compared to the CC genotype 2.37 (95% CI 1.40-3.99). There was no evidence of heterogeneity (I² =0%) or of publication bias. Athletes with high ability in endurance sports had a higher frequency of the GG genotype and G allele.     

Colour polymorphism and genetic strains in Avion intermedins from Flores, Azores (Mollusca: Pulmonata)

Thirty specimens of Arion intermedins from Flores (and Corvo) were electrophoretically (PAGE) assayed for 11 enzymes, yielding information about 14 putative loci in two colour morphs of this species. One of these colour variants was tentatively identified as A. pascalianus (P morph). Except for the Mdh locus, all loci in A. intermedins sensu lato from Flores were monomorphic. Mdh , however, was diallelic for Mdh₁₀₀ and Mdh₁₂₂. This latter electromorph was absent in A. intermedins sensu stricto from Flores, but present in the P morph and A. intermedins from Belgium. As a consequence A. intermedins sensu lato from Flores consists of two genetic strains defined by the Mdh alleles. The genetic identity between these strains (7) is 0.929. The genetic identity between the P morph and A. intermedins sensu stricto in Flores is 0.951, while between the P morph and Belgian A. intermedins it is 0.973. These values suggest that the supposed A. pascalianus from Flores is only a colour morph of A. intermedins. This paper also provides the first published record of this species from the island of Corvo.     

A lectin from the lichenized Basidiomycete Dictyonema glabratum

A lectin with hemagglutinating activity has been isolated from an aqueous extract of the symbiotic phenotype of Dictyonema glabratum and its cyanobacterial photobiont Scytonema sp. The purified lectin had a pI of 6.8 and its molecular mass was investigated by electrospray ionization mass spectrometry, gel filtration and SDS-PAGE, which indicated its native conformation as a dimer formed by two identical subunits of 16540 Da. The lectin is a glycoprotein with a low degree of glycosylation, containing galactose, xylose, glucose and mannose as neutral monosaccharides, in addition to glucosamine, which could indicate both N - and O -linkages. Amino acid analysis showed the predominance of nonpolar residues such as phenylalanine. Agglutination of human erythrocytes required divalent cations, which is affected by addition of EDTA. The lectin was more stable at 30 °C or less for at least 1 h and between pH 5.0 and 7.0. Among the various compounds tested for hemagglutination inhibition, N -acetylgalactosamine was the most active. The potential role of this lectin in recognition of the compatible cyanobacterial photobiont is discussed.     

StGA2ox1 is induced prior to stolon swelling and controls GA levels during potato tuber development

The formation and growth of a potato ( Solanum tuberosum ) tuber is a complex process regulated by different environmental signals and plant hormones. In particular, the action of gibberellins (GAs) has been implicated in different aspects of potato tuber formation. Here we report on the isolation and functional analysis of a potato GA 2-oxidase gene ( StGA2ox1 ) and its role in tuber formation. StGA2ox1 is upregulated during the early stages of potato tuber development prior to visible swelling and is predominantly expressed in the subapical region of the stolon and growing tuber. 35S-over-expression transformants exhibit a dwarf phenotype, reduced stolon growth and earlier in vitro tuberization. Transgenic plants with reduced expression levels of StGA2ox1 showed normal plant growth, an altered stolon swelling phenotype and delayed in vitro tuberization. Tubers of the StGA2ox1 suppression clones contain increased levels of GA₂₀, indicating altered GA metabolism. We propose a role for StGA2ox1 in early tuber initiation by modifying GA levels in the subapical stolon region at the onset of tuberization, thereby facilitating normal tuber development and growth.     

外源水杨酸对总状绿绒蒿种子萌发及生理特性的影响

以总状绿绒蒿（Meconopsis racemosa Maxim.）为实验材料,通过不同浓度水杨酸（SA）浸种处理,研究了SA在不同温度条件下对总状绿绒蒿种子萌发质量和相关生理特性的影响。结果表明,在5~30℃条件下,对总状绿绒蒿种子萌发都有不同程度影响,但在15~25℃条件下,萌发效果比较显著（P<0.05）,其中20℃萌发效果极为显著（P<0.01）;0.1~1.0 mmol·L^-1 SA浸种预处理明显促进了总状绿绒蒿种子的萌发,其萌发指数、发芽势、萌发率在0.1~0.7 mmol·L^-1 SA范围内呈显著增长趋势,其中0.7 mmol·L^-1 SA处理效果极为显著（P<0.01）;（3） SA浸种后总状绿绒蒿种子内可溶性蛋白质和脯氨酸含量的变化同种子的萌发和生长呈相似趋势,用0.7 mmol·L^-1 SA处理后,种子内可溶性蛋白质和脯氨酸的含量达到最高。通过SA浸种可以提高总状绿绒蒿种子的萌发率;并且SA在高温和低温条件下对其萌发有一定的缓解作用。     

Leaf Blade Dimensions of Rice (Oryza sativa L. and Oryza glaberrima Steud.). Relationships between Tillers and the Main Stem

The effects of genotype and environment on the leaf area indexof rice are well documented, but the rules governing leaf areadistribution among main stem and tillers are less well understood.This study investigated the ontogenetic patterns of leaf bladearea and dimensions on the main stem and tillers of three ricecultivars, IAC47, Javaé (Oryza sativa L.) and CG14 (O.glaberrima Steud.) grown in pots without competition among plants.No differences in phyllochron were observed among culms, butleaves on tillers appeared 0.5 to 0.8 phyllochrons earlier thanthe genealogically corresponding leaves on the main stem (systemof Katayama). Cohorts were thus not fully synchronized. Allculms produced their largest leaves soon after panicle initiation(PI), despite differences in tiller age. Leaves that appearedsubsequently were smaller owing to reduced length but not width,which remained constant. Three different hypothetical rulesgoverning the behaviour of culms were tested: (1) tillers behaveas clones of the main stem; (2) cohorts behave uniformly, and(3) behaviour is determined by leaf position (sum of genealogicalleaf and tiller indices). The results were best explained byhypotheses (2) and (3), with leaf blade width and length showingmarkedly different patterns. Copyright 2001 Annals of BotanyCompany Phenology, phyllochron, leaf area, leaf position, leaf cohorts, summed leaf position, leaf blade length and width