Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

Abstract

Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In this study, the complete mitogenomes of two hermit crabs, Dardanus arrosor and Dardanus aspersus, were sequenced for the first time and compared with other published mitogenomes of Paguroidea. Each of the two mitogenomes contains an entire set of 37 genes and a putative control region, but they display different gene arrangements. The different arrangements of the two mitogenomes might be the result of transposition, reversal, and tandem duplication/random loss events from the ancestral pancrustacean pattern. Genome sequence similarity analysis reveals the gene rearrangement in 15 Paguroidea mitogenomes. After synteny analysis between the 15 Paguroidea mitogenomes, an obvious rearranged region is found in D. aspersus mitogenome. Across the 13 protein-coding genes (PCGs) tested, COI has the least and ND6 has the largest genetic distances among the 15 hermit crabs, indicating varied evolution rates of PCGs. In addition, the dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. The phylogenetic analyses based on both gene order and sequence data present the monophyly of three families (Paguridae, Coenobitidae, and Pylochelidae) and the paraphyly of the family Diogenidae. Meanwhile, the phylogenetic tree based on the nucleotide sequences of 13 PCGs shows that two Dardanus species formed a sister group with five Coenobitidae species. These findings help to better understand the gene rearrangement and phylogeny of Paguroidea, as well as provide new insights into the usefulness of mitochondrial gene order as a phylogenetic marker.

The complete mitochondrial genome of the hermit crab Diogenes Edwardsii (Anomura: Diogenidae) and phylogenetic relationships within infraorder Anomura

“…The A + T contents of PCGs and third codon positions in D. Edwardsii mitogenome are 69.08% and 72.30%, respectively. The strong AT-bias in the third codon positions is similar to many species in the infraorder Anomura, i.e., Dardanus arrosor, Shinkaia crosnieri and Pagurus longicarpus [11,33,34].…”

“…Whether or not the same explanation works on our results remains di cult to predict at this time due to the scarcity of information regarding DNA replication of invertebrate mitochondria. For most families of the order Decapoda, congeners belonging to the same family possess identical gene arrangement generally [11], which has particularly been con rmed based on the reported crab mitogenomes [37][38][39]. However, comparing with the reported mitogenomes of the species Clibanarius infraspinatus and Dardanus arrosor belonging to the same family Diogenidae, the D. Edwardsii mitogenome shows distinctive gene arrangement [11,40].…”

“…For the D. Edwardsii mitogenome, the AT skew is -0.110, and the GC skew is 0.233, which indicates bias toward T and G. This asymmetry often occurs on Anomura species [11,[33][34][35]. In mammals, the duration of single-stranded state of the "heavy-stranded" genes during mitochondrial DNA replication can explain this asymmetry [36].…”

“…For most families of the order Decapoda, congeners belonging to the same family possess identical gene arrangement generally [11], which has particularly been con rmed based on the reported crab mitogenomes [37][38][39]. However, comparing with the reported mitogenomes of the species Clibanarius infraspinatus and Dardanus arrosor belonging to the same family Diogenidae, the D. Edwardsii mitogenome shows distinctive gene arrangement [11,40]. For instance, nad5 located between trnH-cac and trnF-ttc in the mitogenome of D. Edwardsii, instead of the common location between trnF-phe and trnH-his in the mitogenomes of Clibanarius infraspinatus and Dardanus arrosor.…”

“…Hermit crabs (the superfamily Paguroidea Latreille, 1802) are one of the best known and most diverse consisting of Coenobitidae, Diogenidae, Paguridae, Parapaguridae, Pylochelidae and Pylojacquesidae, with more than 1,100 species inhabiting diverse biotopes from intertidal to deep seas [10]. The hermit crabs represent an intermediate group of crustaceans from Macrura to Brachyura, which occupy a key position in crustacean evolution [11]. These species are unique because they have asymmetrical bodies that allow them to live in gastropod shells.…”