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Comparative molecular evolution and phylogenetic utility of 3′-UTRs and introns in Galliformes

MOLECULAR PHYLOGENETICS AND EVOLUTION 2010年第2期56卷 536-542页

作者： Bonilla, Amber J. Braun, Edward L. Kimball, Rebecca T. Univ Florida Dept Biol Gainesville FL 32611 USA

Many phylogenetic studies have used nuclear introns or coding exons, but few have included untranslated regions (UTRs). Here we compare the phylogenetic utility and patterns of molecular evolution for 3'-UTRs and introns from five unlinked loci in Galliformes (Ayes). 3'-UTRs evolved at slower rates and exhibited greater spatial clustering of sites with similar evolutionary rates than associated introns, though they exhibited similar overall model complexities. Base compositions differed between the 3'-UTR and associated intron for two of five loci, suggesting that base composition was not exclusively driven by isochore structure. Phylogenies estimated using individual and concatenated 3'-UTRs were more similar to an independent reference tree than those based upon introns, though all phylogenies were largely congruent. However, some 3'-UTRs were difficult to amplify, potentially limiting their use in phylogenetic studies. This study suggests that 3'-UTRs and introns can exhibit distinct patterns of molecular evolution and that they provide useful phylogenetic signal. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Game birds Untranslated regions Evolutionary rates Base composition Tree distances non-coding dna Isochore

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Absence of close-facing retrotransposons: A comparison of molecular data and theory

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JOURNAL OF THEORETICAL BIOLOGY 2010年第2期264卷 205-210页

作者： Bousios, Alexandros Waxman, David Pearce, Stephen R. Univ Sussex Sch Life Sci Brighton BN1 9QG E Sussex England

Retrotransposons occur in extremely large numbers in many eukaryotic genomes. However, little is known of the factors which affect the distribution of close proximity elements. In this work we investigate the frequency of close facing retrotransposons in a plant species with extremely high numbers of retrotransposons. Molecular observations are compared with predictions of a mathematical model that assumes a uniform probability of retrotransposon insertion into the genome. The mathematical model plays the role of a null hypothesis. We find that compared with the predictions of the model, there is a statistically significant deficit of identical copies of facing retroelements that are close to one another. This suggests that an efficient mechanism exists that removes or limits close facing retroelements. (C) 2009 Elsevier Ltd. All rights reserved.

关键词： Genome structure Retroelement non-coding dna Copy number Distribution

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A multi-gene estimate of phylogeny in the nightjars and nighthawks (Caprimulgidae)

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MOLECULAR PHYLOGENETICS AND EVOLUTION 2010年第2期55卷 443-453页

作者： Han, Kin-Lan Robbins, Mark B. Braun, Michael J. Univ Florida Dept Biol Gainesville FL 32611 USA Smithsonian Inst Natl Museum Nat Hist Dept Vertebrate Zool Suitland MD 20746 USA Univ Maryland Behav Ecol Evolut & Systemat Program College Pk MD 20740 USA Univ Kansas Nat Hist Museum Div Ornithol Lawrence KS 66045 USA Biodivers Inst Lawrence KS 66045 USA

Caprimulgidae is a cosmopolitan family of nocturnal and crepuscular insectivorous birds comprising the nightjars, nighthawks, and relatives. Sexual selection and convergence or parallelism in plumage and behavior have made it difficult to discern evolutionary relationships in this group. In order to provide a framework for comparative studies of this family, a molecular phylogeny was reconstructed using mitochondrial cytochrome b, and nuclear c-myc and growth hormone dna sequences. Likelihood, parsimony and Bayesian analyses agree in placing Eurostopodus species and Caprimulgus enarratus, a Malagasy endemic, as the earliest branches of the tree. The remaining taxa are divided among four well-supported clades, three in the New World and one in the Old World. Insertion/deletion events, common in non-coding sequences, provide additional support in resolving the phylogeny. Neither of the traditional subfamilies, Caprimulginae (nightjars) and Chordeilinae (nighthawks), is monophyletic, suggesting that the morphological specializations characterizing "nighthawks" evolved multiple times and the "nightjar" body plan is an old and conservative one. The large genus Caprimulgus is polyphyletic with respect to many other genera in the family, which are often defined by derived plumage traits that likely reflect sexual selection or ecological specialization. A taxonomic revision of the family is proposed based on the combined tree, including naming a new genus for C. enarratus. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Caprimulgidae Nightjars Nighthawks Molecular phylogeny Cytochrome b c-myc Growth hormone Convergence Sexual selection Evolution Indels non-coding dna

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Evidence for two independent functional variants for androgenetic alopecia around the androgen receptor gene

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EXPERIMENTAL DERMATOLOGY 2010年第11期19卷 1026-1028页

作者： Cobb, Joanna E. Zaloumis, Sophie G. Scurrah, Katrina J. Harrap, Stephen B. Ellis, Justine A. Royal Childrens Hosp Murdoch Childrens Res Inst Parkville Vic 3052 Australia Univ Melbourne Dept Physiol Melbourne Vic Australia Univ Melbourne Ctr Mol Environm Genet & Analyt Epidemiol Melbourne Vic Australia

The gene encoding the androgen receptor (AR) is associated with male pattern baldness (androgenetic alopecia - AGA). In case-control and family analyses, we mapped AR and the adjacent intergenic regions. We found evidence for association with two independent loci, one upstream and previously described and the other downstream and apparently novel. The haplotype comprising these SNPs was strongly associated with AGA (P = 3.75 x 10-5) in 1195 men. We also replicated association with a recently reported non-coding region on chromosome 20 and found that its association with AGA was less strong and independent of that of AR. Our results will help focus future efforts to further define AGA genetic risk.

关键词： androgen receptor ectodysplasin A2 receptor male pattern baldness non-coding dna

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Patterns of dna-Sequence Divergence Between Drosophila miranda and D. pseudoobscura

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JOURNAL OF MOLECULAR EVOLUTION 2009年第6期69卷 601-611页

作者： de Proce, Sophie Marion Halligan, Daniel L. Keightley, Peter D. Charlesworth, Brian Univ Edinburgh Sch Biol Sci Inst Evolutionary Biol Edinburgh EH9 3JT Midlothian Scotland

Contrary to the classical view, a large amount of non-coding dna seems to be selectively constrained in Drosophila and other species. Here, using Drosophila miranda BAC sequences and the Drosophila pseudoobscura genome sequence, we aligned coding and non-coding sequences between D. pseudoobscura and D. miranda, and investigated their patterns of evolution. We found two patterns that have previously been observed in comparisons between Drosophila melanogaster and its relatives. First, there is a negative correlation between intron divergence and intron length, suggesting that longer non-coding sequences may contain more regulatory elements than shorter sequences. Our other main finding is a negative correlation between the rate of non-synonymous substitutions (d (N)) and codon usage bias (F (op)), showing that fast-evolving genes have a lower codon usage bias, consistent with strong positive selection interfering with weak selection for codon usage.

关键词： D. pseudoobscura D. miranda non-coding dna Intron length Codon usage

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Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements

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BIOINFORMATICS 2009年第5期25卷 578-584页

作者： Taher, Leila Ovcharenko, Ivan Natl Lib Med Computat Biol Branch Natl Ctr Biotechnol Informat NIH Bethesda MD 20894 USA

Motivation: Several functional gene annotation databases have been developed in the recent years, and are widely used to infer the biological function of gene sets, by scrutinizing the attributes that appear over- and underrepresented. However, this strategy is not directly applicable to the study of non-coding dna, as the non-coding sequence span varies greatly among different gene loci in the human genome and longer loci have a higher likelihood of being selected purely by chance. Therefore, conclusions involving the function of non-coding elements that are drawn based on the annotation of neighboring genes are often biased. We assessed the systematic bias in several particular Gene Ontology (GO) categories using the standard hypergeometric test, by randomly sampling non-coding elements from the human genome and inferring their function based on the functional annotation of the closest genes. While no category is expected to occur significantly over- or underrepresented for a random selection of elements, categories such as 'cell adhesion', 'nervous system development' and 'transcription factor activities' appeared to be systematically overrepresented, while others such as 'olfactory receptor activity'-underrepresented. Results: Our results suggest that functional inference for non-coding elements using gene annotation databases requires a special correction. We introduce a set of correction coefficients for the probabilities of the GO categories that accounts for the variability in the length of the non-coding dna across different loci and effectively eliminates the ascertainment bias from the functional characterization of non-coding elements. Our approach can be easily generalized to any other gene annotation database.

关键词： .Databases GO categories functional inference gene annotation non-coding dna

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Phylogeny of the eudicot order Malpighiales: analysis of a recalcitrant clade with sequences of the petD group II intron

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PLANT SYSTEMATICS AND EVOLUTION 2009年第3-4期282卷 201-228页

作者： Korotkova, Nadja Schneider, Julio V. Quandt, Dietmar Worberg, Andreas Zizka, Georg Borsch, Thomas Univ Bonn Nees Inst Biodivers Plants D-5300 Bonn Germany Univ Leipzig Dept Systemat Bot Leipzig Germany Tech Univ Dresden Inst Bot Plant Phylogenet & Phylogenom Grp D-8027 Dresden Germany Res Inst Senckenberg Dept Bot & Mol Evolut Frankfurt Germany Goethe Univ Frankfurt Frankfurt Germany

Malpighiales are one of the most diverse orders of angiosperms. Molecular phylogenetic studies based on combined sequences of coding genes allowed to identify major lineages but hitherto were unable to resolve relationships among most families. Spacers and introns of the chloroplast genome have recently been shown to provide strong signal for inferring relationships among major angiosperm lineages and within difficult clades. In this study, we employed sequence data of the petD group II intron and the petB-petD spacer for a set of 64 Malpighiales taxa, representing all major lineages. Celastrales and Oxalidales served as outgroups. Sequence alignment was straightforward due to frequent microstructural changes with easily recognizable motifs (e. g., simple sequence repeats), and well defined mutational hotspots. The secondary structure of the complete petD intron was calculated for Idesia polycarpa as an example. Domains I and IV are the most length variable parts of the intron. They contain terminal A/T-rich stem-loop elements that are suggested to elongate independently in different lineages with a slippage mechanism earlier reported from the P8 stem-loop of the trnL intron. Parsimony and Bayesian analyses of the petD dataset yielded trees largely congruent with results from earlier multigene studies but statistical support of nodes was generally higher. For the first time a deep node of the Malpighiales backbone, a clade comprising Achariaceae, Violaceae, Malesherbiaceae, Turneraceae, Passifloraceae, and a Lacistemataceae-Salicaceae lineage received significant statistical support (83% JK, 1.00 PP) from plastid dna sequences.

关键词： Malpighiales Angiosperms Molecular evolution Group II introns non-coding dna

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Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus

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JOURNAL OF MOLECULAR EVOLUTION 2009年第3期69卷 249-259页

作者： Piganeau, Gwenael Vandepoele, Klaas Gourbiere, Sebastien Van de Peer, Yves Moreau, Herve Observ Oceanol LOB UMR7621 CNRS F-66651 Banyuls Sur Mer France Univ Paris 06 UMR 7621 Lab Arago F-66651 Banyuls Sur Mer France VIB Dept Plant Syst Biol B-9052 Ghent Belgium Univ Ghent Dept Mol Genet B-9052 Ghent Belgium Univ Perpignan UMR 5244 Lab Biol & Ecol Tropicale & Mediterraneenne F-66860 Perpignan France

We used a phylogenetic footprinting approach, adapted to high levels of divergence, to estimate the level of constraint in intergenic regions of the extremely gene dense Ostreococcus algae genomes (Chlorophyta, Prasinophyceae). We first benchmarked our method against the Saccharomyces sensu stricto genome data and found that the proportion of conserved non-coding sites was consistent with those obtained with methods using calibration by the neutral substitution rate. We then applied our method to the complete genomes of Ostreococcus tauri and O. lucimarinus, which are the most divergent species from the same genus sequenced so far. We found that 77% of intergenic regions in Ostreococcus still contain some phylogenetic footprints, as compared to 88% for Saccharomyces, corresponding to an average rate of constraint on intergenic region of 17% and 30%, respectively. A comparison with some known functional cis-regulatory elements enabled us to investigate whether some transcriptional regulatory pathways were conserved throughout the green lineage. Strikingly, the size of the phylogenetic footprints depends on gene orientation of neighboring genes, and appears to be genus-specific. In Ostreococcus, 5' intergenic regions contain four times more conserved sites than 3' intergenic regions, whereas in yeast a higher frequency of constrained sites in intergenic regions between genes on the same dna strand suggests a higher frequency of bidirectional regulatory elements. The phylogenetic footprinting approach can be used despite high levels of divergence in the ultrasmall Ostreococcus algae, to decipher structure of constrained regulatory motifs, and identify putative regulatory pathways conserved within the green lineage.

关键词： Phylogenetic footprinting non-coding dna cis-regulatory elements Saccharomyces Ostreococcus

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Pan-vertebrate conserved non-coding sequences associated with developmental regulation

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Briefings in Functional Genomics and Proteomics 2009年第4期8卷 256-265页

作者： Elgar, Greg School of Biological and Chemical Sciences Queen Mary University of London London E1 4NS Mile End Rd United Kingdom

Whilst coding sequences are readily recognised in vertebrate genomes using computational approaches, the identification of non-coding regulatory sequences has traditionally been much more difficult, due to their small size and, as a general rule, low sequence homology between genomes. Nevertheless, a small proportion of non-coding sequence is very highly conserved across the entire vertebrate radiation. This review will look at the specific properties of these sequences, how they have been identified and assayed functionally, and current progress in the quest to identify and understand the underlying language and grammar encoded within them. I will also discuss the evolution of these elements, and examine their emerging and likely roles in disease. Together these analyses are starting to unravel how conserved non-coding regions function at the molecular level. © The Author 2009. Published by Oxford University Press.

关键词： Bioinformatics CNEs Comparative genomics non-coding dna Regulatory sequence Vertebrate evolution

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Structural families of genomic microsatellites

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GENE 2008年第1-2期408卷 124-132页

作者： Subirana, Juan A. Messeguer, Xavier Univ Politecn Cataluna Dept Engn Quim E-08028 Barcelona Spain Univ Politecn Cataluna Dept Llenguatges & Sist Informat E-08034 Barcelona Spain

We present an analysis of tandem repeats of short sequence motifs (microsatellites) in twelve eukaryotes for which a large part of the genome has been sequenced and assembled. The pattern of motif abundance varies significantly in different species, but it is very similar in different chromosomes of the same species. The most abundant repeats can be classified in two main families. The first family has a rigid conformation, with purines in one strand and pyrimidines in the complementary strand, mainly A(n)/T(n) and (AG)(n)/(CT)(n). The second family has alternating, flexible sequences, such as (AT)(n), (AC)(n) and related sequences. In the pluricellular organisms the relative frequency of both families is rather constant. These observations indicate that microsatellites have structural information and may be involved in the organization of chromatin fibers and in chromosome architecture in general. An additional intriguing finding is the absence of microsatellites with sequences which appear to be forbidden, such as (AATT)(n). Additional tables and references are given as supplementary material. (c) 2007 Elsevier B.V. All rights reserved.

关键词： dna structure chromatin fibers non-coding dna dna repeats

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