The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

Abstract

In this study, the complete mitochondrial (mt) genome sequence of the South China deep‐sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep‐sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep‐sea benthic environment; based on their large size, Bathynomus is included in the “supergiant group” of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein‐coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date. Although the overall genome organization is typical for metazoans, the mt genome of Bathynomus sp. shows a number of derived characters, such as an inversion of 10 genes when compared to the pancrustacean ground pattern. Rearrangements in some genes (e.g., cob, trnT, nad5, and trnF) are shared by nearly all isopod mt genomes analyzed thus far, and when compared to the putative isopod ground pattern, five rearrangements were found in Bathynomus sp. Two tRNAs exhibit modified secondary structures: The TΨC arm is absent from trnQ, and trnC lacks the DHU. Within the class Malacostraca, trnC arm loss is only found in other isopods. Phylogenetic analysis revealed that Bathynomus sp. (Cymothoida) and Sphaeroma serratum (Sphaeromatidea) form a single clade, although it is unclear whether Cymothoida is monophyletic or paraphyletic. Moreover, the evolutionary rate of Bathynomus sp. (dN/dS [nonsynonymous mutational rate/synonymous mutational rate] = 0.0705) is the slowest measured to date among Cymothoida, which may be associated with its relatively constant deep‐sea environment. Overall, our results may provide useful information for understanding the evolution of deep‐sea Isopoda species.

The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade

“…Gene order rearrangements in this group of animals were discussed in detail in previous studies [4,11,32], so here we only briefly discuss the idiosyncrasies of the new mitogenome. Cymothoa indica also exhibits a completely unique order with a large number of rearrangements (Fig 1).…”

“…Furthermore, isopod mitogenomes generally exhibit a large number of gene order rearrangements [4,11], and some groups of isopods even possess a non-standard, linearised, mitogenome organisation and unique tRNA-encoding mechanisms [12–16]. As the evolution of mitogenomic architecture appears to be highly discontinuous [17,18], with some major animal taxa exhibiting a highly conserved mitochondrial architecture (most vertebrates being a good example), and other taxa exhibiting a rapidly-evolving architecture [17–21], we hypothesise that isopods might present an important model system to study the complex dynamics of the evolution of mitochondrial genomic architecture.…”

Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep‐sea habitats

“…We compared Ka/Ks ratios Low Ka/Ks ratios were also reported for mt PCGs from the deepsea giant isopod Bathynomus sp. (Shen et al, 2017). The mt PCGs work in close association with nuclear-encoded subunits in protein complexes involved in oxidative phosphorylation system (Burton & Barreto, 2012).…”

“…Due to their fundamental roles in oxidative phosphorylation responsible for energy production (Saraste, 1999), mt PCGs are generally thought to evolve primarily under constant purifying selection (Oliveira, Raychoudhury, Lavrov, & Werren, 2008). During the past decade, mt genomes had been intensively investigated for the study of molecular evolution, population genetics, and inferring phylogeny (Boore, 1999; Shen et al., 2017). …”

The first complete mitochondrial genome of the Mariana Trench Freyastera benthophila (Asteroidea: Brisingida: Brisingidae) allows insights into the deep‐sea adaptive evolution of Brisingida

“…relationship and therefore have become more popular in recent years (Fan, Hu, Wen, & Zhang, 2011;Shen, Ma, Ren, & Zhao, 2009;Shen et al, 2017). Up to now, the complete mitochondrial genomes have been reported in many marine organisms, such as sea cucumber (Fan et al, 2011;Perseke et al, 2010;Scouras, Beckenbach, Arndt, & Smith, 2004;Sun, Qi, & Kong, 2010), sea urchin (Cantatore, Roberti, Rainaldi, Gadaleta, & Saccone, 1989;De Giorgi, Martiradonna, Lanave, & Saccone, 1996;Qureshi & Jacobs, 1993), brittle star (Perseke et al, 2008(Perseke et al, , 2010Scouras et al, 2004;Smith, Arndt, Gorski, & Fajber, 1993), sea lily (Perseke et al, 2008;Scouras & Smith, 2006), shellfish (Plazzi, Ribani, & Passamonti, 2013;Ren, Liu, Jiang, Guo, & Liu, 2010), and crab (Liu & Cui, 2010;Yang & Yang, 2008).…”