Abstract
Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
Highlights
Amphipods are widely spread in both marine and freshwater habitats[1]
Comparative studies across these seven superfamilies indicated that most amphipod mitochondrial genomes shared typical metazoan gene content comprising 37 genes—13 protein coding genes (PCGs), 2 ribosomal genes, and 22 transfer genes, as well as a putative non-coding control region (CR)[22,23,24]
The mitochondrial DNAs of Metacrangonyctidae (Hadzioidea) showed an opposite strand nucleotide bias to that observed in the majority of crustacean mitochondrial genomes, but this reversal of strand bias has seldom been seen in other amphipod superfamilies[24]
Summary
MT-2017 specimens were trapped; many H. gigas specimens were collected in that depth range (Table S1). An approximately complete mitochondrial genome of the hadal Halice sp. MT-2017 from the Mariana Trench clustered robustly with the abyssal species collected at 2567.6 m from the Iceland Basin[28], and separated from others in shallower water (289.4–510.9 m) using Bayesian and maximum likelihood methods based on partial cytochrome c oxidase subunit I (cox1) barcodes (Fig. S1). The vertical and geographic distribution of Halice discovered in hadal trenches and Icelandic waters conformed to the “tropical submergence” hypothesis, which proposed that closely related species lived in shallower waters. Feature rrnL trnL1(tag) nad[1] trnP(tgg) nad[5] trnF(gaa) trnE(ttc) trnV(tac) trnN(gtt) trnS1(tct) trnA(tgc) trnQ(ttg) trnC(gca) trnY(gta) trnI(gat) trnM(cat) nad[2] trnW(tca) cox[1] trnL2(taa) cox[2] trnK(ttt) trnD(gtc) atp[8] atp[6] cox[3] trnG(tcc) nad[3] trnR(tcg) trnH(gtg) nad[4] nad4L trnT(tgt) nad[6] cytb trnS2(tga) rrnS control region
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