Duplicate Control Regions in Avian Mitochondrial Genomes


Markus Delitz

MSc Student
Advisor: Elisabeth Haring

Natural History Museum Vienna;
Unit for Integrative Zoology, Department of Evolutionary Biology
University of Vienna


The mitochondrial genome of birds differs from that of other vertebrates by its gene order. Moreover, within the class of birds two different gene orders have been described which can be classified as Standard Avian Gene Order (SAGO) and Derived Avian Gene Order (DAGO). They differ regarding their control region (CR) and gene order. SAGO harbors the CR between the tRNA glutamic acid gene (E) and tRNA phenylalanine gene (F), instead of between the tRNA proline gene (P) and F in other vertebrates. In DAGO the CR is located between the tRNA threonine gene (T) and P and additionally there is a duplicated CR called pseudo control region (ΨCR) -- between E and F, at the original site of the CR in SAGO. DAGO arose several times independently in the avian radiation. The second CR was originally named non-protein coding sequence (nc) and ΨCR, but later other designations were used in various bird orders and families, e.g.,CR2. In the current literature it is stated, that the origin for the second CR and the different gene orders in birds is due to a duplication followed by degeneration of several genes. Although, the functionality of the duplicated CRs is still subject of current research, current literature is in favour towards regarding the duplicated CR as possessing no functionality. In my work I will analyse all avian full mitochondrial genome sequences present currently in NCBI Reference Sequence Database (RefSeq) concerning their gene order, intragenomic similarity between CR and ΨCR and possible secondary structures being present in CR and ΨCR.