The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella)

Xiao-Xin Bi,Ai-Yun Wang,Li Zhang,Mei-Dong Jing,Pei-Yong Feng,Ling Huang

doi:10.1590/s1415-47572012005000034

Abstract

The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general.

Highlights

The phylogenetic analysis of primates has attracted much attention because of the potential for defining and understanding the processes that mold, shape and transform the human genome
polymerase chain reaction (PCR) amplifications were done in a Mycycler Gradient thermocycler using a final volume of 50 mL that contained 20-50 ng of genomic DNA (0.5 mL), 2.5 mM of each dNTP (4 mL), 10 mM of each primer (1 mL), 5 mL of 10x buffer, 0.25 mL of Taq polymerase (5 U/mL; Takara) and 38.3 mL of sterile distilled water
The complete mitogenome consisted of two rRNAs, 22 tRNAs, 13 protein-coding genes (PCGs) and a control region

Summary

Introduction

The phylogenetic analysis of primates has attracted much attention because of the potential for defining and understanding the processes that mold, shape and transform the human genome. The complete mitogenomes of 46 primate species have been sequenced, including five platyrrhine species (Aotus lemurinus, Ateles belzebuth, Callicebus donacophilus, Cebus albifrons and Saimiri sciureus) (Arnason et al, 2000; Hodgson et al, 2009). Several molecular phylogenetic and cytogenetic studies of C. apella have been reported (Moreira, 2002; Amaral et al, 2008; Wildman et al, 2009; Nieves et al, 2011; Perelman et al, 2011), the complete mitogenome sequence of this species has not yet been described.

Results

Conclusion