Heger A, Ponting CP. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res 17: 1837-1849

Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.
Genome Research (Impact Factor: 14.63). 01/2008; 17(12):1837-49. DOI: 10.1101/gr.6249707
Source: PubMed


The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding genes were predicted using established Drosophila melanogaster genes as templates, with recovery rates ranging from 81%-97% depending on species divergence and on genome assembly quality. Orthology and paralogy assignments were shown to be self-consistent among the different Drosophila species and to be consistent with regions of conserved gene order (synteny blocks). Next, we investigated the rates of diversification among these species' gene repertoires with respect to amino acid substitutions and to gene duplications. Constraints on amino acid sequences appear to have been most pronounced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages. Codons predicted to have been subject to positive selection were found to be significantly over-represented among genes with roles in immune response and RNA metabolism, with the latter category including each subunit of the Dicer-2/r2d2 heterodimer. The vast majority of gene duplications (96.5%) and synteny rearrangements were found to occur, as expected, within single Müller elements. We show that the rate of ancient gene duplications was relatively uniform. However, gene duplications in terminal lineages are strongly skewed toward very recent events, consistent with either a rapid-birth and rapid-death model or the presence of large proportions of copy number variable genes in these Drosophila populations. Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins.

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    • "Thicker branches have been classified as undergoing episodic diversifying selection by the sequential likelihood ratio test at corrected p≤0.05. Previous studies have found that antiviral Dicer2 is under intense positive selection in Drosophila melanogaster and across the Drosophila phylogeny (Obbard et al., 2006; Heger and Ponting, 2007; Kolaczkowski et al., 2011). A study conducted by Mukherjee et al. (2012) established that Dicer2 DEAD (Aspartate-Glutamate-Alanine-Aspartate) box protein/Helicase and PAZ domains have experienced positive selection in flies using branch-sites analyses to identify adaptive protein-coding changes. "
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    ABSTRACT: Dicer, an ribonuclease type III type endonuclease, is the key enzyme involved in biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs), and thus plays a critical role in RNA interference through post transcriptional regulation of gene expression. This enzyme has not been well studied in the Indian water buffalo, an important species known for disease resistance and high milk production. In this study, the primary coding sequence (5,778 bp) of bubaline dicer (GenBank: AB969677.1) was determined and the bubaline Dicer1 biocomputationally characterized to determine the phylogenetic signature among higher eukaryotes. The evolutionary tree revealed that all the transcript variants of Dicer1 belonging to a specific species were within the same node and the sequences belonging to primates, rodents and lagomorphs, avians and reptiles formed independent clusters. The bubaline dicer1 is closely related to that of cattle and other ruminants and significantly divergent from dicer of lower species such as tapeworm, sea urchin and fruit fly. Evolutionary divergence analysis conducted using MEGA6 software indicated that dicer has undergone purifying selection over the time. Seventeen divergent sequences, representing each of the families/taxa were selected to study the specific regions of positive vis-à-vis negative selection using different models like single likelihood ancestor counting, fixed effects likelihood, and random effects likelihood of Datamonkey server. Comparative analysis of the domain structure revealed that Dicer1 is conserved across mammalian species while variation both in terms of length of Dicer enzyme and presence or absence of domain is evident in the lower organisms.
    Asian Australasian Journal of Animal Sciences 02/2015; 28(6). DOI:10.5713/ajas.14.0767 · 0.54 Impact Factor
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    • "Filtering, and Expression Human, mouse, dog, cow, dolphin, and platypus genomes and gene annotations were obtained from Ensembl (Flicek et al., 2013), the genome and gene annotation of minke whale were obtained from Yim et al. (2014). In total, 21,069, 22,275, 19,292, 19,988, 15,769, 17,936, 20,496, and 22,733 human, mouse, dog, cow, dolphin, platypus, minke whale, and bowhead whale genes, respectively, were used to construct orthology mappings using OPTIC (Heger and Ponting, 2007). Briefly, OPTIC builds phylogenetic trees for gene families by first assigning orthology relationships based on pairwise orthologs computed using PhyOP (Goodstadt and Ponting, 2006). "
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    ABSTRACT: Graphical Abstract Highlights d Genome and two transcriptomes of the bowhead whale, the longest-lived mammal d Bowhead-specific mutations in genes associated with cancer and aging (e.g., ERCC1) d Duplications in genes associated with DNA repair, cell cycle, and aging (e.g., PCNA) d Changes in genes related to thermoregulation (UCP1) and other bowhead traits Correspondence In Brief The bowhead whale is the longest-lived mammal, possibly living over 200 years. Keane et al. sequence the bowhead genome and transcriptome and perform a comparative analysis with other cetaceans and mammals. Changes in bowhead genes related to cell cycle, DNA repair, cancer, and aging suggest alterations that may be biologically relevant.
    Cell Reports 01/2015; 10(1):112-122. DOI:10.1016/j.celrep.2014.12.008 · 8.36 Impact Factor
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    • "Orthology assignments and orthologous groups were defined using the OPTIC pipeline [10,98]. Orthology assignments are based upon the computation of pairwise orthologs using PhyOP [99] using BLASTP searches with an E-value threshold of 10-5 and a minimum size cut-off equal to 75% of the smaller sequence. "
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    ABSTRACT: Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
    Genome biology 03/2013; 14(3):R28. DOI:10.1186/gb-2013-14-3-r28 · 10.81 Impact Factor
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