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. 2021 Mar 22:9:e10677.
doi: 10.7717/peerj.10677. eCollection 2021.

Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels

Julian Valdes #  1 , Sergio Sebastian Samoluk #  1 , Cristian Simón Abdala  2 , Diego Baldo  3 , Guillermo Seijo  1   4
Affiliations

Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels

Julian Valdes et al. PeerJ. .

Abstract

Liolaemus is the most specious genus of the Squamata lizards in South America, presenting exceptional evolutionary radiation and speciation patterns. This recent diversification complicates the formal taxonomic treatment and the phylogenetic analyses of this group, causing relationships among species to remain controversial. Here we used Next-Generation Sequencing to do a comparative analysis of the structure and organization of the complete mitochondrial genomes of three differently related species of Liolaemus and with different reproductive strategies and ploidy levels. The annotated mitochondrial genomes of ca. 17 kb are the first for the Liolaemidae family. Despite the high levels of sequence similarity among the three mitochondrial genomes over most of their lengths, the comparative analyses revealed variations at the stop codons of the protein coding genes and the structure of the tRNAs among species. The presence of a non-canonical dihydrouridine loop is a novelty for the pleurodonts iguanians. But the highest level of variability was observed in two repetitive sequences of the control region, which were responsible for most of the length heterogeneity of the mitochondrial genomes. These tandem repeats may be useful markers to analyze relationships of closely related species of Liolaemus and related genera and to conduct population and phylogenetic studies.

Keywords: Liolaemus species; Lizards; Mitochondrial genomes; Tandem repeats.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Map of the complete mitogenome of Liolaemus darwinii. Ph: Cristian Abdala.
Figure 2
Figure 2. Alignment of the Liolaemus species mitogenomes.
The sequence of L. parthenos mitogenome was compared to those of L. darwinii (A) and L. millcayac (B) using mVISTA for the alingment. Grey arrows above the alignment indicate genes and their orientation.
Figure 3
Figure 3. Nucleotide diversity of the PCGs in the mitogenomes of Liolaemus species.
Figure 4
Figure 4. (A) Abundance of codon families. Relative Synonymous Codon Usage (RSCU) in the 13 PCGs in the mitogenomes of Liolaemus darwinii, (B) L. parthenos (C) and L. millcayac (D).
Figure 5
Figure 5. The ratios of non-synonymous (Ka) versus synonymous (Ks) substitutions (Ka/Ks ratios) of the 13 PCGs in the mitogenomes of Liolaemus especies.
Figure 6
Figure 6. Stem-and-loop structures in the typical position for OL between the tRNAAsn and tRNAcys genes in the mitogenomes of Liolaemus species.
The box in the stem denotes the potential 3′-GCC-5′ light-strand elongation start point (Macey, Schulte & Larson, 2000).
Figure 7
Figure 7. Features in control regions of Liolaemus lizards. The CR is divided into three domains: Domain 1 (TAS), Domain 2 (CD) and domain 3 (CSB).
The two types of AT-rich sequences of the CRs are indicated as (AxTy)n and (TA)y. P: tRNAPro, F: tRNAPhe.
See this image and copyright information in PMC

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