The complete mitochondrial genome of the subterranean crustaceanMetacrangonyx longipes(Amphipoda): A unique gene order and extremely short control region

Abstract

Metazoan mitochondrial genomes usually consist of the same gene set, but some taxonomic groups show a considerable variety in gene order and nucleotide composition. The mitochondrial genomes of 37 crustaceans are currently known. Within the malacostracan superorder Peracarida, only three partial mitogenome sequences and the complete sequence of Ligia oceanica (Isopoda) are available.Frequent translocation events have changed the mitochondrial gene order in crustaceans, providing an opportunity to study the patterns and mechanisms of mitogenome rearrangement and to determine their impact on phylogenetic reconstructions. Here we report the first complete nucleotide sequence of an amphipod species, Metacrangonyx longipes, belonging to a phylogenetically enigmatic family occurring in continental subterranean waters. The genome has 14,113 base pairs (bp) and contains the usual 13 protein coding genes and two rRNA subunits, but only 21 out of the typical 22 tRNA genes of Metazoa. This is the shortest mitogenome described thus far for a crustacean and also one of the richest in AT (76.03%). The genome compactness results from a very small control region of 76 bp, the occurrence of frequent gene overlap, and the absence of large non-coding fragments. Six of the protein-coding genes have unusual start codons.Comparison of individual protein coding genes with the sequences known for other crustaceans suggests that nad2, nad6, nad4L and atp8 show the highest divergence rates. Metacrangonyx longipes shows a unique crustacean mitogenome gene order, differing even from the condition found in Parhyale hawaiiensis (Amphipoda), whose coding sequence has also been completed in the present study.

Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea)

“…In previous studies we obtained the sequence information and complete or nearly complete mitochondrial genome of 21 metacrangonyctid specimens belonging to 10 species plus six taxa that are not formally described yet, covering the entire geographical range of the family (Table 1) [12, 16]. The sequence coverage of mitogenomes ranged from 4.3 to 5.7 × for the shearing/shotgun sequencing approach, to between 80–178 × and 59–281 × for the Roche GS Junior and Roche FLX approaches, respectively (see Table 1).…”

“…Aside of two species of Caprella [14, 15], the few known amphipod mitogenomes derive from species placed in distant genera and families. Here we analyse 21 metacrangonyctid mitochondrial complete or nearly complete genome sequences (including the 20 mitogenomes reported in [12] plus one previously obtained by us, Metacrangonyx longipes from Mallorca [16]), to explore their phylogenetic signal and to perform a comparative intra-familiar genomic analysis. We have compared them also with the mitogenomic features displayed by other amphipod families.…”

Complete mitochondrial genome of the groundhopperAlulatettix yunnanensis(Insecta: Orthoptera: Tetrigoidea)

“…The closed circular mtDNA molecule spanning 14 -39 kbp typically consists of a canonical set of 37 genes that encode for 13 proteins, 2 ribosomal RNAs (rRNA), and 22 transfer RNAs (tRNA). Apart from a major noncoding region (termed the control region or the AþT region in hexapods), these genes are compact, have no introns, and have few intergenic spacer (Boore 1999;Taanman 1999;Bauzà-Ribot et al 2009;Kim et al 2011). Because of the simple and uniform organization, such as low frequency of intermolecular genetic recombination, maternal inheritance, and relatively rapid evolutionary rate, the mtDNA has been extensively used for studying population structures, phylogeography, and phylogenetic relationships at various taxonomic levels (Wilson et al 1985;Moore 1995;Ito et al 2010).…”

The complete mitochondrial genome of Gammarus roeselii (Crustacea, Amphipoda): insights into mitogenome plasticity and evolution

“…The gene content generally is highly conserved, with 37 genes encoding for 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one control region (CR) containing regulatory elements for transcription and replication. In amphipods, mitogenomic features such as alterations in gene order, strand bias reversion, presence of additional tRNA genes and CR duplication have been reported and could be used to explore amphipod evolutionary history at various taxonomic levels (Bauzà-Ribot et al, 2009;Ito et al, 2010;Ki et al, 2010;Kilpert & Podsiadlowski, 2010;Krebes & Bastrop, 2012;Pons et al, 2014;Aunins et al, 2016;Romanova et al, 2016c).…”

“…By contrast, the small and circular mt genome is more easily accessible. As a consequence, more than 20 amphipod mt genomes have been sequenced, although many are incomplete (Bauzà-Ribot et al, 2009;Ito et al, 2010;Ki et al, 2010;Kilpert & Podsiadlowski, 2010;Bauzà-Ribot et al, 2012;Krebes & Bastrop, 2012;Shin et al, 2012;Pons et al, 2014;Aunins et al, 2016;Lan et al, 2016;Romanova et al, 2016a, b, c;Stokkan et al, 2016;Macher et al, 2017a).…”