Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

  title={Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles},
  author={Athanasia C. Tzika and Rapha{\"e}l Helaers and Gerrit Schramm and Michel C. Milinkovitch},
  pages={19 - 19}
BackgroundReptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation.ResultsHere, we use 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species: the Nile crocodile… 
Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics
The Reptilian Transcriptomes Database 2.0 is presented, which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages and is a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles.
De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)
This dataset represents a major increase in genomic resources for the tuatara, increasing the number of annotated gene sequences from just 60 to almost 16,000, which will facilitate future research in sex determination, genome evolution, local adaptation and population genetics of tu atara, as well as inform studies on amniote evolution.
Reptile genomes open the frontier for comparative analysis of amniote development and regeneration.
The current diversity of available reptile genomes is reviewed, with an emphasis on their evolutionary relationships, and it is highlighted how these genomes have and will continue to facilitate research in developmental and regenerative biology.
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
Next-generation sequencing is used to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish, and provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.
Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates
It is reported that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and a strong GC3-heterogeneity to be already present in the tetrapod ancestor, and the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, in agreement with the gBGC hypothesis.
Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in Yellow Catfish (Pelteobagrus fulvidraco) Brain
This work identifies a set of annotated genes that are candidate factors affecting sexual dimorphism as well as simple sequence repeat (SSR) and single nucleotide variation (SNV) in yellow catfish.
More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
The resulting phylogeny provides overwhelming support for the hypothesis that turtles evolved from a common ancestor of birds and crocodilians, rejecting the hypothesized relationship between turtles and lepidosaurs.
Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles
This work recovers strong support for turtles sharing a more recent common ancestor with archosaurs, and tests the hypothesis with an expanded miRNA presence/absence dataset, and employs more rigorous criteria for miRNA annotation.
The First Chameleon Transcriptome: Comparative Genomic Analysis of the OXPHOS System Reveals Loss of COX8 in Iguanian Lizards
The first chameleon transcriptome is presented, obtained using deep sequencing (SOLiD), adding a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.
The draft genomes of softshell turtle and green sea turtle yield insights into the development and evolution of the turtlespecific body plan
The results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.


Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird
The results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles.
A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences
This resource provides the most comprehensive set of EST sequences available for an individual ectothermic reptile species, increasing the number of snake ESTs 50-fold and identifying genes that appear to be under evolutionary selection and those that are sex-specific.
Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate
BackgroundUnderstanding the genetic basis of adaptive changes has been a major goal of evolutionary biology. In complex organisms without sequenced genomes, de novo transcriptome assembly using a
Patterns of Vertebrate Isochore Evolution Revealed by Comparison of Expressed Mammalian, Avian, and Crocodilian Genes
Analyses of third-codon-position GC content provided conclusive evidence that the poikilothermic alligator has GC-rich isochores, like homeothermic birds and mammals, and placed these results in a theoretical framework able to unify available models of isochore evolution.
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome
A megabase-scale phylogenomic analysis of the Reptilia suggests 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.
Complete mitochondrial genome suggests diapsid affinities of turtles.
  • R. ZardoyaA. Meyer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
The results challenge the classic view of turtles as the only survivors of primary anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.
Genome evolution in Reptilia, the sister group of mammals.
The recent sequencing of the chicken and zebra finch genomes has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds.
Turtle isochore structure is intermediate between amphibians and other amniotes.
A comparative analysis of a new set of expressed genes of the red-eared slider turtle and orthologs of the turtle genes in mammalian, archosaurian, amphibian, and amphibian genomes indicates that the isochore structure of turtles is intermediate between that of amphibians and other amniotes.
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
It is concluded that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost‐effective, and reliable method for development of functional genomic tools for nonmodel species.
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms to facilitate genomics studies in corals and other non-model systems.