TY - JOUR AB - We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%-28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%-22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types. AU - Piednoël, M.* AU - Aberer, A.J.* AU - Schneeweiss, G.M.* AU - Macas, J.* AU - Novak, P.* AU - Gundlach, H. AU - Temsch, E.M.* AU - Renner, S.S.* C1 - 11723 C2 - 30770 SP - 3601-3611 TI - Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of orobanchaceae. JO - Mol. Biol. Evol. VL - 29 IS - 11 PB - Oxford Univ. Press PY - 2012 SN - 0737-4038 ER - TY - JOUR AB - A quickly growing number of characteristics reflecting various aspects of gene function and evolution can be either measured experimentally or computed from DNA and protein sequences. The study of pairwise correlations between such quantitative genomic variables as well as collective analysis of their interrelations by multidimensional methods have delivered crucial insights into the processes of molecular evolution. Here, we present a principal component analysis (PCA) of 16 genomic variables from Saccharomyces cerevisiae, the largest data set analyzed so far. Because many missing values and potential outliers hinder the direct calculation of principal components, we introduce the application of Bayesian PCA. We confirm some of the previously established correlations, such as evolutionary rate versus protein expression, and reveal new correlations such as those between translational efficiency, phosphorylation density, and protein age. Although the first principal component primarily contrasts genomic change and protein expression, the second component separates variables related to gene existence and expressed protein functions. Enrichment analysis on genes affecting variable correlations unveils classes of influential genes. For example, although ribosomal and nuclear transport genes make important contributions to the correlation between protein isoelectric point and molecular weight, protein synthesis and amino acid metabolism genes help cause the lack of significant correlation between propensity for gene loss and protein age. We present the novel Quagmire database (Quantitative Genomics Resource) which allows exploring relationships between more genomic variables in three model organisms-Escherichia coli, S. cerevisiae, and Homo sapiens. AU - Theis, F.J. AU - Latif, N.* AU - Wong, P. AU - Frishman, D. C1 - 6259 C2 - 29082 CY - Oxford SP - 2501-2512 TI - Complex principal component and correlation structure of 16 yeast genomic variables. JO - Mol. Biol. Evol. VL - 28 IS - 9 PB - Oxford Univ. Press PY - 2011 SN - 0737-4038 ER - TY - JOUR AB - Recent publications have revealed that the evolution of phosphosites is influenced by the local protein structures and whether the phosphosites have characterized functions or not. With knowledge of the wide functional range of phosphorylation, we attempted to clarify whether the evolutionary conservation of phosphosites is different among distinct functional modules. We grouped the phosphosites in the human genome into the modules according to the functional categories of KEGG (Kyoto Encyclopedia of Genes and Genomes) and investigated their evolutionary conservation in vertebrate genomes from mouse to zebrafish. We have found that the phosphosites in the vertebrate-specific functional modules (VFMs), such as cellular signaling processes and responses to stimuli, are evolutionarily more conserved than those in the basic functional modules (BFMs), such as metabolic and genetic processes. The phosphosites in the VFMs are also significantly more conserved than their flanking regions, whereas those in the BFMs are not. These results hold for both serine/threonine and tyrosine residues, although the fraction of phosphorylated tyrosine residues is increased in the VFMs. Moreover, the difference in the evolutionary conservation of the phosphosites between the VFMs and BFMs could not be explained by the difference in the local protein structures. There is also a higher fraction of phosphosites with known functions in the VFMs than BFMs. Based on these findings, we have concluded that protein phosphorylation may play more dominant roles for the VFMs than BFMs during the vertebrate evolution. As phosphorylation is a quite rapid biological reaction, the VFMs that quickly respond to outer stimuli and inner signals might heavily depend on this regulatory mechanism. Our results imply that phosphorylation may have an essential role in the evolution of vertebrates. AU - Wang, Z.* AU - Ding, G.* AU - Geistlinger, L. AU - Li, H.* AU - Liu, L.* AU - Zeng, R.* AU - Tateno, Y.* AU - Li, Y.* C1 - 5439 C2 - 28523 CY - Oxford, England SP - 1131-1140 TI - Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. JO - Mol. Biol. Evol. VL - 28 IS - 3 PB - Oxford Univ. Press PY - 2011 SN - 0737-4038 ER - TY - JOUR AB - A unique combination of genetic features and a rich stock of information make the flowering plant genus Oenothera an appealing model to explore the molecular basis of speciation processes including nucleus-organelle coevolution. From representative species, we have recently reported complete nucleotide sequences of the 5 basic and genetically distinguishable plastid chromosomes of subsection Oenothera (I-V). In nature, Oenothera plastid genomes are associated with 6 distinct, either homozygous or heterozygous, diploid nuclear genotypes of the 3 basic genomes A, B, or C. Artificially produced plastome-genome combinations that do not occur naturally often display interspecific plastome-genome incompatibility (PGI). In this study, we compare formal genetic data available from all 30 plastome-genome combinations with sequence differences between the plastomes to uncover potential determinants for interspecific PGI. Consistent with an active role in speciation, a remarkable number of genes have high Ka/ Ks ratios. Different from the Solanacean cybrid model Atropa/tobacco, RNA editing seems not to be relevant for PGIs in Oenothera. However, predominantly sequence polymorphisms in intergenic segments are proposed as possible sources for PGI. A single locus, the bidirectional promoter region between psbB and clpP, is suggested to contribute to compartmental PGI in the interspecific AB hybrid containing plastome I (AB-I), consistent with its perturbed photosystem II activity. AU - Greiner, S.* AU - Wang, X. AU - Herrman, R.G.* AU - Rauwolf, U.* AU - Mayer, K.F.X. AU - Haberer, G. AU - Meurer, J.* C1 - 1671 C2 - 25952 SP - 2019-2030 TI - The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data. JO - Mol. Biol. Evol. VL - 25 IS - 9 PB - Oxford Univ. Press PY - 2008 SN - 0737-4038 ER - TY - JOUR AB - Short-chain alcohol dehydrogenases (SCAD) constitute a large and diverse family of ancient origin. Several of its members play an important role in human physiology and disease, especially in the metabolism of steroid substrates (e.g., prostaglandins, estrogens, androgens, and corticosteroids). Their involvement in common human disorders such as endocrine-related cancer, osteoporosis, and Alzheimer disease makes them an important candidate for drug targets. Recent phylogenetic analysis of SCAD is incomplete and does not allow any conclusions on very ancient divergences or on a functional characterization of novel proteins within this complex family. We have developed a 3D structure-based approach to establish the deep-branching pattern within the SCAD family. In this approach, pairwise superpositions of X-ray structures were used to calculate similarity scores as an input for a tree-building algorithm. The resulting phylogeny was validated by comparison with the results of sequence-based algorithms and biochemical data. It was possible to use the 3D data as a template for the reliable determination of the phylogenetic position of novel proteins as a first step toward functional predictions. We were able to discern new patterns in the phylogenetic relationships of the SCAD family, including a basal dichotomy of the 17beta-hydroxysteroid dehydrogenases (17beta-HSDs). These data provide an important contribution toward the development of type-specific inhibitors for 17beta-HSDs for the treatment and prevention of disease. Our structure-based phylogenetic approach can also be applied to increase the reliability of evolutionary reconstructions in other large protein families. AU - Breitling, R. AU - Laubner, D. AU - Adamski, J. C1 - 9994 C2 - 22337 SP - 2154-2161 TI - Structure-based phylogenetic analysis of short-chain alcohol dehydrogenases and reclassification of the 17beta-hydroxysteroid dehydrogenase family. JO - Mol. Biol. Evol. VL - 18 PB - Oxford Univ. Press PY - 2001 SN - 0737-4038 ER -