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).

Download full-text


Available from: Andrew Shedlock, Aug 01, 2014
1 Follower
24 Reads
  • Source
    • "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]. "
    [Show abstract] [Hide abstract]
    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
  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    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
  • Source
    • "Much progress in our understanding of morphological evolution stands to be made from the simultaneous phylogenetic analysis of parareptiles, basal stem diapsids, and crown reptiles; however, no relevant matrices have so far been constructed (Lee 2013). If the morphological hypothesis that turtles represent the extant sister group of living reptiles accurately reflects turtle origins, it would indicate that virtually the entire genome (Matsuda et al. 2005; Shedlock et al. 2007), including mitochondrial genes (Zardoya and Meyer 1998; Kumazawa and Nishida 1999), ribosomal RNA genes (Hedges and Poling 1999), protein coding genes (Hedges and Poling 1999; Iwabe et al. 2005; Shen et al. 2011; Tzika et al. 2011; Chiari et al. 2012; Fong et al. 2012; Lu et al. 2013; Shaffer et al. 2013; Wang et al. 2013), ultraconserved elements (Crawford et al. 2012), and miRNAs (this study), exhibit astonishing levels of homoplasy in a surprisingly congruent pattern. However, applying a 'genes as characters' approach, Lu et al. (2013) argued that the turtle þ archosaur hypothesis could be an artifact of large, concatenated alignments overburdened by gene heterogeneity—likely the single largest source of systematic error in phylogenomic analyses (Jeffroy et al. 2006; Salichos and Rokas 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using miRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super-alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.
    Evolution & Development 05/2014; 16(4). DOI:10.1111/ede.12081 · 2.72 Impact Factor
Show more