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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    • "In sum, we show that RPM provides the most rigorous method to identify optimal codons (File S1), and thus use these codon lists for all analyses. Another complementary method usedtofurther confirm optimal codon lists is to compare codon use between ribosomal protein genes (RPGs), which typically are highly expressed, and lowly expressed genes (Heger and Ponting 2007; Wang et al. 2011). Thus, we repeated our analyses of RSCU using RSCU RPGs = RSCU RPGs – RSCU CDS with Lowest 5% Expression (File S2) and found that the results of these analyses also support the existence of AT3 optimal codons in G. bimaculatus and O. fasciatus, and GC3 codons for P. hawaiensis. "
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    ABSTRACT: In protein coding genes, synonymous codon usage and amino acid composition correlate to expression in some eukaryotes, and may result from translational selection. Here, we studied large-scale RNA-seq data from three divergent arthropod models, including cricket (Gryllus bimaculatus), milkweed bug (Oncopeltus fasciatus) and the amphipod crustacean Parhyale hawaiensis, and tested for optimization of codon and amino acid usage relative to expression level. We report strong signals of AT3 optimal codons (those favored in highly expressed genes) in G. bimaculatus and O. fasciatus, whilst weaker signs of GC3 optimal codons were found in P. hawaiensis, suggesting selection on codon usage in all three organisms. Further, in G. bimaculatus and O. fasciatus, high expression was associated with lowered frequency of amino acids with large size/complexity (S/C) scores in favor of those with intermediate S/C values; thus selection may favor smaller amino acids whilst retaining those of moderate size for protein stability or conformation. In P. hawaiensis, highly transcribed genes had elevated frequency of amino acids with large and small S/C scores, suggesting a complex dynamic in this crustacean. In all species, the highly transcribed genes appeared to favor short proteins, high optimal codon usage, specific amino acids, and were preferentially involved in cell-cycling and protein synthesis. Together, based on examination of 1,680,067, 1,667,783 and 1,326,896 codon sites in G. bimaculatus, O. fasciatus, and P. hawaiensis respectively, we conclude that translational selection shapes codon and amino acid usage in these three Pancrustacean arthropods.
    G3-Genes Genomes Genetics 09/2015; 5(11). DOI:10.1534/g3.115.021402 · 3.20 Impact Factor
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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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