Solving a Sequencing Problem in the Vertebrate Mitochondrial Control Region using Phylogenetic Comparisons

Abstract

The mitochondrial control region (mtCR) of the bird-of-paradise, Phonygammus keraudrenii, the Trumpet Manucode, contains a unique arrangement of homopolymers and short tandem repeats. Homopolymers occur within a few hundred bases of each other, trapping sequence information between unsequenceable barriers. A comparative strategy, involving other manucode species, allowed the prediction of primer sites in the inaccessible region. The method is suggested for similar sequencing problems.

• Phonygammus keraudrenii
• Manucodes
• Bird-of-paradise
• Avian mitochondrial control region
• Homopolymers