The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa Anke Braband a, * ,1 , Stephen L. Cameron b,1 , Lars Podsiadlowski c , Savel R. Daniels d , Georg Mayer e a Institute of Biology, Comparative Zoology, Humboldt Universität zu Berlin, Philippstr. 13, D-10115 Berlin, Germany b Australian National Insect Collection CSIRO Entomology, Canberra, ACT 2601, Australia c Institute of Evolutionary Biology & Ecology, Universität Bonn, An der Immenburg 1, D-53121 Bonn, Germany d Department of Botany and Zoology, University of Stellenbosch Private Bag X1, Matieland 7602, South Africa e Institute of Biology II: Molecular Evolution & Animal Systematics, University of Leipzig, Talstrasse 33, D-04103 Leipzig, Germany article info Article history: Received 20 January 2010 Revised 8 May 2010 Accepted 13 May 2010 Available online 20 May 2010 Keywords: Arthropods Gene order Onychophora Phylogeny Velvet worms abstract The ancestral genome composition in Onychophora (velvet worms) is unknown since only a single spe- cies of Peripatidae has been studied thus far, which shows a highly derived gene order with numerous translocated genes. Due to this lack of information from Onychophora, it is difficult to infer the ancestral mitochondrial gene arrangement patterns for Panarthropoda and Ecdysozoa. Hence, we analyzed the complete mitochondrial genome of the onychophoran Opisthopatus cinctipes, a representative of Peripa- topsidae. Our data show that O. cinctipes possesses a highly conserved gene order, similar to that found in various arthropods. By comparing our results to those from different outgroups, we reconstruct the ancestral gene arrangement in Panarthropoda and Ecdysozoa. Our phylogenetic analysis of protein-cod- ing gene sequences from 60 protostome species (including outgroups) provides some support for the sis- ter group relationship of Onychophora and Arthropoda, which was not recovered by using a single species of Peripatidae, Epiperipatus biolleyi, in a previous study. A comparison of the strand-specific bias between onychophorans, arthropods, and a priapulid suggests that the peripatid E. biolleyi is less suitable for phylogenetic analyses of Ecdysozoa using mitochondrial genomic data than the peripatopsid O. cinctipes. Ó 2010 Elsevier Inc. All rights reserved. 1. Introduction Studies of animal mitochondrial genomes have become a useful tool for inferring the evolutionary relationships of animals for two reasons. First, the mitochondrial sequence data can be directly used to infer phylogenetic relationships and, second, offer the pos- sibility to trace back the evolution of gene rearrangements, thus, providing an additional source of information for phylogenetic reconstructions (e.g., Boore et al., 1995, 1998; Blanchette et al., 1999; Dowton et al., 2002; Bleidorn et al., 2007). As close relatives to arthropods (Nielsen, 2001; Kusche et al., 2002; Mallatt and Giribet, 2006; Roeding et al., 2007; Dunn et al., 2008), Onychophora or velvet worms are an important group for understanding the evolution of Panarthropoda and Ecdysozoa (Fig. 1). So far, however, complete mitochondrial geno- mic data are available only from one species of Peripatidae, Epipe- ripatus biolleyi, which has a highly derived gene order and numerous gene rearrangements (Podsiadlowski et al., 2008). Moreover, the use of mitochondrial sequence data from this spe- cies for a phylogenetic analysis resulted in an unresolved polyto- my within the Ecdysozoa. This might be due to a strand bias in this species, which highly deviates from that of arthropods (Rota-Stabelli and Telford, 2008). In the present study, we investigate the complete mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsi- dae). We compare the mitochondrial gene arrangement patterns between arthropods, onychophorans, and other ecdysozoans to clarify the major transformation events and reconstruct the ances- tral mitochondrial gene order in Onychophora, Panarthropoda, and Ecdysozoa. Furthermore, we perform an amino acid-based phylo- genetic analysis of Panarthropoda and Ecdysozoa to clarify the phylogenetic position of Onychophora. In addition to O. cinctipes, we include data from another representative of Peripatopsidae, Metaperipatus inae, to increase taxon sampling. A detailed analysis of the mitochondrial genome of M. inae is presented in another pa- per from this issue (Braband et al., 2010) as it is beyond the scope of the present work to describe the complex pattern of gene rear- rangements and genome composition in this species. 1055-7903/$ - see front matter Ó 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2010.05.011 * Corresponding author. E-mail address: phylogenetics@arcor.de (A. Braband). 1 These authors contributed equally to this work. Molecular Phylogenetics and Evolution 57 (2010) 285–292 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev