High divergence across the whole mitochondrial genome in the “pan-Antarctic” springtail Friesea grisea: Evidence for cryptic species? Giulia Torricelli a,1 , Antonio Carapelli a, ⁎ ,1 , Peter Convey b , Francesco Nardi a , Jeffrey L. Boore c , Francesco Frati a a Department of Evolutionary Biology, University of Siena, Via A. Moro 2, 53100 Siena, ITALY b British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK c DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA and Genome Project Solutions, Inc., 1024 Promenade Street, Hercules, CA 94547, USA abstract article info Article history: Received 23 July 2009 Received in revised form 14 September 2009 Accepted 15 September 2009 Available online 25 September 2009 Received by M. Di Giulio Keywords: Collembola Antarctica mtDNA Cryptic species Collembola are one of the few hexapod groups adapted to live in the harsh environmental conditions of Antarctic terrestrial ecosystems. Diversity is limited to a few species that can be very abundant in coastal deglaciated sites. A remarkable lack of overlap in Collembola species composition is evident between Western and Eastern Antarctica, and Friesea grisea is currently the only species whose distribution is thought to span these two main regions of the continent. However, our analysis of the complete sequences of the mitochondrial genomes from specimens obtained from each of the two regions showed unexpected genetic divergence, well above the average levels observed between populations belonging to the same species, and so indicating that these are actually separate species, despite their lack of distinguishing morphology. Detailed analysis of the two genomes showed the presence of a non-coding region observed between trnS (uga) and nad1. Other features of these mitochondrial genomes, such as base compositional bias, secondary structure features of tRNAs and the presence of regulatory elements in the control region, are described and discussed from an evolutionary standpoint. © 2009 Elsevier B.V. All rights reserved. 1. Introduction The mitochondrial DNA (mtDNA) of Metazoa is a circular, double- stranded molecule, usually ranging between 14 and 17 kb in length, that encodes for 13 protein coding genes (PCGs) required for the assembly of the respiratory chain complexes (subunits 6 and 8 of the ATPase [atp6 and atp8], cytochrome c oxidase subunits 1 to 3 [cox1-3], apo cytochrome b [cob] and NADH dehydrogenase subunits 1 to 6 and 4L [nad1-6 and nad4L]), 2 genes encoding for ribosomal RNAs (small and large subunits [rrnS and rrnL]) and 22 genes encoding for transfer RNAs (trnXs) necessary for the translation of the mitochondrial proteins. There are two tRNA genes for each of the amino acids leucine and serine, since each can be specified by two codon families, and these are differentiated by anticodon. Typically, mitochondrial genomes have a compact gene organization with no introns and few intergenic nucleotides, with the exception of a single large non-coding region (named “control region”, or “A+T-rich” region in arthropods), containing the main regulatory elements for the replication and transcription of the mtDNA (see Boore, 1999). One of the most remarkable features of animal mtDNAs is the strand-specific bias in nucleotide composition, with one strand being rich in A and C (thus, with positive AT- and negative CG-skews) and the other in T and G (having negative AT- and positive GC-skews) (Perna and Kocher, 1995; Hassanin et al., 2005). This base compositional asymmetry is particularly evident at synonymous codon positions of PCGs where the major selective constraint is exerted by overall base composition rather than the encoded amino acid. In addition, due to the peculiar asymmetry of the mtDNA replication system (Bogenhagen and Clayton, 2003), compositional deviations in nucleotide frequencies are usually more severe in clusters of genes that remain displaced in a single-strand state for a protracted period of time (Reyes et al., 1998). Gene 449 (2010) 30–40 Abbreviations: (Mitochondrial genes) atp6 and atp8, genes for ATP synthase subunits 6 and 8; cox1–3, genes for subunits I–III of cytochrome c oxidase; cob, gene for cytochrome b; nad1–6 and nad4L, genes for subunits 1–6 and 4L of NADH dehydrogenase; rrnL and rrnS, genes for the large and small subunits of ribosomal RNA; trnX, genes encoding for transfer RNA molecules with corresponding amino acids denoted by the one-letter code and anticodon indicated in parentheses (xxx) when necessary. (Other abbreviations) AP (or ap), Antarctic Peninsula; BAS, British Antarctic Survey; bp, base pair; GTR+I+Γ, General time reversible+Invariant+Gamma; J-strand, DNA strand where the majority of the mitochondrial genes are encoded; kb, kilobase; ML, Maximum Likelihood; mt, mitochondrial; Mya, Million Years; N-strand, DNA strand where the minority of the mitochondrial genes are encoded; O N , origin of the N-strand replication; O J , origin of the J-strand replication; PCG, Protein Coding Gene; PCR, Polymerase Chain Reaction; PNRA, Progetto Nazionale Ricerche in Antartide; RSCU, Relative Synonymous Codon Usage; VL (or vl), Victoria Land. ⁎ Corresponding author. E-mail addresses: torricelli5@unisi.it (G. Torricelli), carapelli@unisi.it (A. Carapelli), pcon@bas.ac.uk (P. Convey), nardifra@unisi.it (F. Nardi), JLBoore@GenomeProjectSolutions.com (J.L. Boore), frati@unisi.it (F. Frati). 1 These authors contributed equally to this work. 0378-1119/$ – see front matter © 2009 Elsevier B.V. All rights reserved. doi:10.1016/j.gene.2009.09.006 Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene