Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci U S A

Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 03/2007; 104(8):2767-72. DOI: 10.1073/pnas.0606204104
Source: PubMed


We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of approximately 65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).

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Available from: Andrew Shedlock, Aug 01, 2014
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    • "SYSTEMATIC BIOLOGY identification of high-quality orthologs. More importantly , there are several difficult questions within the backbone phylogeny of jawed vertebrates, such as the position of lungfishes relative to tetrapods (Hedges 2009), the root of teleost fishes (e.g., Inoue et al. 2001; Near et al. 2012), the relationships among the three extant amphibian orders (e.g., Zhang et al. 2005; Fong et al. 2012), the position of turtles within Amniota (e.g., Shedlock et al. 2007; Chiari et al. 2012), and the root of placental mammals (e.g., McCormack et al. 2012; Song et al. 2012). Moreover, the interordinal relationships of neoavian birds have also received considerable attention (e.g., Hackett et al. 2008; McCormack et al. 2013; Jarvis et al. 2014). "
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    ABSTRACT: Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4,682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias towards specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email:
    Systematic Biology 08/2015; DOI:10.1093/sysbio/syv059 · 14.39 Impact Factor
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    • "Comparisons of the SSR content of avian and lizard genomes support this, confirming that bird genomes contain substantially less SSR content than does the lizard genome (Fig. 6); this trend was also observed in analogous comparisons to a snake genome sample [26]. It has been hypothesized that SSR evolution and turnover has been particularly slow in non-mammalian vertebrates [2], which is consistent with our findings of highly similar abundances of SSR loci across all bird genomes that we examined (Fig. 6), although this and other studies suggest this may not be the case in squamate reptiles like the Anolis lizard [45], [46]. "
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    ABSTRACT: As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
    PLoS ONE 09/2014; 9(9):e106649. DOI:10.1371/journal.pone.0106649 · 3.23 Impact Factor
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    • "composition for several reptiles (Shedlock et al. 2007; Alf€ oldi et al. 2011). However, all paralogs contained at least one CpG island, usually within introns (fig. "
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    ABSTRACT: Members of a gene family expressed in a single species often experience common selection pressures. Consequently, the molecular basis of complex adaptations may be expected to involve parallel evolutionary changes in multiple paralogs. Here, we use bacterial artificial chromosome library scans to investigate the evolution of the voltage-gated sodium channel (Nav) family in the garter snake Thamnophis sirtalis, a predator of highly toxic Taricha newts. Newts possess tetrodotoxin (TTX), which blocks Nav’s, arresting action potentials in nerves and muscle. Some Thamnophis populations have evolved resistance to extremely high levels of TTX. Previous work has identified amino acid sites in the skeletal muscle sodium channel Nav1.4 that confer resistance to TTX and vary across populations. We identify parallel evolution of TTX resistance in two additional Nav paralogs, Nav1.6 and 1.7, which are known to be expressed in the peripheral nervous system and should thus be exposed to ingested TTX. Each paralog contains at least one TTX-resistant substitution identical to a substitution previously identified in Nav1.4. These sites are fixed across populations, suggesting that the resistant peripheral nerves antedate resistant muscle. In contrast, three sodium channels expressed solely in the central nervous system (Nav1.1–1.3) showed no evidence of TTX resistance, consistent with protection from toxins by the blood–brain barrier. We also report the exon–intron structure of six Nav paralogs, the first such analysis for snake genes. Our results demonstrate that the molecular basis of adaptation may be both repeatable across members of a gene family and predictable based on functional considerations.
    Molecular Biology and Evolution 08/2014; 31(11). DOI:10.1093/molbev/msu237 · 9.11 Impact Factor
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