Genome assemblies and transcripts of Lacerta viridis and Lacerta bilineata
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ABSTRACT:
PROVIDER: PRJEB24178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| OFHU01.dat.gz | Other | |||
| OFHU01.fasta.gz | Fasta.gz | |||
| OFHU01.master.dat | Other | |||
| OFHV01.dat.gz | Other |
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Project description:Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
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Project description:Understanding the conditions that promote the evolution of reproductive isolation, and thus speciation. Here we empirically test some of the key predictions of speciation theory (Coyne 2004; Kohn 2005) by experimentally evolving the initial stages of speciation in yeast. After allowing replicate populations to adapt to two divergent environments, we observed the consistent, de novo evolution of two forms of postzygotic isolation: reduced rate of mitotic reproduction and reduced efficiency of meiotic reproduction. In general, divergent selection resulted in greater reproductive isolation than parallel selection, as predicted by ecological speciation theory. Our experimental system allowed for the first controlled comparison of the relative importance of ecological and genetic mechanisms of isolation, and the novel ability to quantify the effects of antagonistic epistasis. For mitotic reproduction, hybrid inferiority was conditional upon the selective environments and was both ecological and genetic in basis. In contrast, isolation associated with meiotic reproduction was unconditional and was caused solely by genetic mechanisms. Overall, our results show that adaption to divergent environments promotes the evolution of isolation through antagonistic epistasis, providing evidence of a plausible common avenue to speciation and adaptive radiation in nature (Schluter 2000,2001: Funk 2006) Keywords: Speciation, antagonistic epistasis, divergent adaptation
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Project description:Proteins are ubiquitous macromolecules displaying a vast repertoire of chemical and enzymatic functions making them suitable candidates for chemosignals used in intraspecific communication. Proteins are present in skin gland secretions of vertebrates but their identity, and especially, their functions, remain largely unknown. Many species of lizards possess femoral glands, i.e. epidermal organs primarily involved in the production and secretion of chemosignals playing a pivotal role in mate choice and intrasexual communication. The lipophilic fraction of femoral glands has been well studied in lizards. In contrast, proteins have been the focus of only a handful of investigations. Here, we study the identity, inter-individual expression patterns and functionality of proteins present in femoral glands of sand lizards (Lacerta agilis) by applying mass-spectrometry proteomics. Our results showed that the total number of proteins varied substantially among individuals. None of the identified femoral gland proteins could be directly linked to chemical communication in lizards, although this result hinges on protein annotation in databases in which squamate semiochemicals are poorly represented. In contrast to our expectations, proteins consistently expressed across individuals were related to immune system, antioxidant activity and lipid metabolism as the main functions, adding support to the hypothesis that proteins in reptilian epidermal glands have other functions besides chemical communication. Interestingly, we found that major histocompatibility complex class I (MHC) expression is enriched in femoral gland secretions. Previously, MHC was hypothesized to have been coopted to serve a semiochemical function in sand lizards, specifically in partner recognition. We speculate with the possibility that MHC proteins could be linked to semiochemical function in sand lizards.
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