Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes)

The control region (<i>CR</i>) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two <i>CRs</i>, and the second control region (<i>CR2</i>) may enhance replication and transcription; however, the <i>CR2</i> in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from <i>Alaudala cheleensis</i>, <i>Eremophila alpestris</i>, <i>Alauda razae</i>, and <i>Calandrella cinerea</i> and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of <i>CR2</i>. The mitochondrial gene orders were conserved in all published lark mitogenomes, with <i>Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2</i> with tandem repeat-<i>trnF-rrnS</i>. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of <i>CR2</i> may occur in their common ancestor. <i>CR</i> sequence and phylogeny analysis indicated <i>CR2</i> tandem repeats were generated within <i>CR2</i>, originating in the ancestor of all larks, rather than inherited from <i>CR1</i>. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the <i>CR2</i> containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.