Abstract
BackgroundComparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012).ResultsWe present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure.ConclusionsNext-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.
Highlights
Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level
Mitochondrial gene order in all taxa was identical to that previously reported for M. longipes [16], where trnL2 (UUR) gene appears between cox1 and cox2 as in the putative pancrustacean pattern
This pancrustacean pattern is assumed to derive from a translocation of this gene with respect to the arthropod presumed ground pattern, but it shows many rearrangements compared to the hypothetical ancestral pancrustacean gene order [16,17,18]
Summary
Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The metazoan mitochondrial genome (mitogenome) usually consists of a single compact circular DNA with a highly conserved gene content. It harbours the coding capacity for 13 proteins of four complexes of the respiratory chain, two ribosomal RNAs, and 22 genes coding for the tRNA set, including two gene copies for each leucine and serine tRNAs [1]. A wealth of data on DNA sequence and gene organization of metazoan mitogenomes has been gathered in the last decades, with about 4000 complete mitochondrial genomes already deposited in DNA sequence databases (RefSeq release 64), of which two thirds correspond to vertebrates [5]. Within the malacostracan peracarid order Amphipoda, the sequences of species within the genera Parhyale (Hyalidae), Caprella (Caprellidae), Onisimus (Lysianassidae), Gondogeneia (Pontogeneiidae), Gammarus (Gammaridae), Eulimnogammarus (Eulimnogammaridae), Pseudoniphargus (Pseudoniphargidae), Bahadzia (Hadziidae) and Metacrangonyx (Metacrangonyctidae) have been reported or are deposited in sequence databases ([11] and references therein; NCBI RefSeq database)
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
