The complete mitochondrial genome of
            <i>Lacerta bilineata</i>
            and comparison with its closely related congener
            <i>L. Viridis</i>

Kolora, Sree Rohit Raj; Faria, Rui; Weigert, Anne; Schaffer, Stefan; Grimm, Annegret; Henle, Klaus; Sahyoun, Abdullah H.; Stadler, Peter F.; Nowick, Katja; Bleidorn, Christoph; Schlegel, Martin

doi:10.3109/19401736.2015.1111349

Cited by 6 publications

(6 citation statements)

References 15 publications

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“…Sequences of complete mitochondrial DNAs of Darevskia species were deposited in GenBank with accession numbers MH481130-37; MG704915-21. In all the species we have > 20X ; the observed lengths of the protein coding genes were similar to those found in other reptile mitochondrial genomes [38,40,41,62]. (Fig 2A and 2B).…”

Section: Genome Organisationsupporting

confidence: 83%

“…[35]). Mitogenomes of other species included in the analysis were: Podarcis muralis (Acc # NC011607, FJ460597; [15]), P. siculus (Acc # NC011609, FJ460598; [15]), Lacerta viridis (Acc # NC008328 [39]) L. agilis (Acc # NC021766, KC990830; Qin & Tao, unpublished), L. bilineata (Acc # KT722705, NC028440; [40], Takydromus tachydromoides (Acc # NC008773 [41], T. amurensis (Acc # NC030209, KU641018; [42]) T. sexlineatus (Acc # NC022703, KF425529 [43]), T. wolteri (Acc # NC018777, JX181764; [44]), Zootoca vivipara (Acc # NC026867 [45]) and Phoenicolacerta kulzeri (Acc # FJ460596 (16)), Eremias argus (Acc # IQ086345, NC016755; Kim et al, unpublished), E. multiocellata (Acc # KJ664798, KM257724; NC025304 [46]), E. przewalskii (Acc # KM507330, NC025929; [47]), E. stummeri (Acc # NC029878, KT372881; [48]) E. vermiculata (Acc # NC025320, KP981389, KM104865; [46]) (Acc # KP981388; [46]), and E. velox (Acc # KM359148; [48] E. brenchleyi (Acc # EF490071; NC011764 Rui et al, unpublished).…”

Section: Genome Assemblymentioning

confidence: 99%

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Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

et al. 2020

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We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Nextgeneration sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intrageneric topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/ NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.

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Section: Genome Organisationsupporting

confidence: 83%

Section: Genome Assemblymentioning

confidence: 99%

Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

et al. 2020

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“…The time of population divergence between L. viridis and L. bilineata was estimated as at least 1.15 Mya (per generation), whereas the previously estimated mitochondrial divergence time was 2.6–3.4 Mya [33, 69]. Lacerta viridis and L. bilineata show a high level of genome-wide differentiation (F ST = 0.688).…”

Section: Discussionmentioning

confidence: 92%

Divergent evolution in the genomes of closely related lacertids,Lacerta viridisandL. bilineata, and implications for speciation

et al. 2018

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Background 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. Findings 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. Conclusion 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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“…Mitochondrial genomes have been used as phylogenetic tools in various studies, including European green lizards (Bernt et al, 2013a;B€ ohme et al, 2007a;Kehlmaier et al, 2020;Kolora et al, 2017;Mendes et al, 2016;Perseke et al, 2013). Recent improvements in determining whole genomes raised the number of animal mitogenomes to some 10,000 (NCBI RefSeq).…”

Section: Mitochondrial Genomes As Phylogenetic Toolsmentioning

confidence: 99%

“…For phylogenetic analyses three published mitogenomes were included: L. viridis (AM176577.1), Adriatic clade (ERS4631750), L. bilineata (KT722705.1) and another L. viridis mitogenome determined by Kolora et al (2017) but submitted to ENA within this study (ERZ1645122, Table S1). For a comprehensive inference, phylogenetic trees were based on nucleotide sequences of all 13 protein-coding genes concatenated with all rRNA-and tRNA-coding sequences.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Mitogenome evolution in the Lacerta viridis complex (Lacertidae, Squamata) reveals phylogeny of diverging clades

Jauss

Solf

Kolora

et al. 2021

Systematics and Biodiversity

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In order to elucidate mitochondrial evolution and resolve the phylogeny of the widely distributed European green lizards (Lacerta viridis complex), we determined 16 mitochondrial genomes from a representative sampling of the four previously identified major clades corresponding to L. bilineata (western distribution range), L. viridis (most of the eastern distribution range), the unnamed Adriatic (or West Balkan) and the Turkish þ south-eastern European clades. The mitogenomes were on average 17,162 bp long with a canonical vertebrate gene inventory of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a long non-coding Control Region. We detected several almost completely clade-specific insert and tandem-repeat signatures. Phylogenetic analyses using all 13 protein-coding genes as well as rRNA-and tRNA-coding sequences from a total of 20 mitogenomes inferred a resolved branching pattern of the four divergent clades. The Turkish clade is strongly supported as sister to all other members of the complex. Within the monophylum comprising the remaining clades, L viridis is sister to a clade containing L. bilineata and the Adriatic clade. Unexpectedly, one specimen of western Italy (Calambrone, Pisa)which is within the distribution range of L. bilineataclustered together with the Adriatic clade with high bootstrap support, calling for further research on the biogeography of the L. viridis complex. Integrating our results with those of previous studies suggest that the lineages have reached the level of distinct taxa, but to determine whether they have become fully independent lineages on the species level requires further research that tackles nuclear genomic variation of all four clades and the viability of hybrids and gene flow within putative hybrid zones.

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The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis

Cited by 6 publications

References 15 publications

Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

Divergent evolution in the genomes of closely related lacertids,Lacerta viridisandL. bilineata, and implications for speciation

Mitogenome evolution in the Lacerta viridis complex (Lacertidae, Squamata) reveals phylogeny of diverging clades

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