Characterization of the Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae)

Abstract

Metopaulias depressus is a non-marine crab endemic to Jamaica that dwells in rainforest bromeliads and exhibits elaborate active parental care behavior. Current genomic resources on M. depressus are rare, limiting the understanding of its adaptation to terrestrial life in species that evolved from marine ancestors. This study reports the complete mitochondrial genome of M. depressus assembled using Sanger sequencing. The AT-rich mitochondrial genome of M. depressus is 15,765 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 691 bp-long intergenic space is assumed to be the control region (CR) or D-loop. A set of selective pressure analyses indicate that the entirety of the PCGs experience purifying selection. Cox1, cox2, nad5, cox3, and atp6 experience strong purifying selection, and atp8 experiences weak purifying selection compared to the rest of the PCGs. The secondary structures of most tRNA genes exhibit a standard ‘cloverleaf’ structure, with the exception of trnS1, which lacks the dihydroxyuridine (DHU) arm but not the loop, the trnH gene, which lacks the thymine pseudouracil cytosine (T) loop but not the arm, and trnM, which exhibits an overly developed T loop. A maximum likelihood phylogenetic analysis based on all PCGs indicated that M. depressus is more closely related to the genera Clistocoeloma, Nanosesarma, and Parasesarma than to Chiromantes, Cristarma, Geosesarma, and Orisarma. This study contributes to deciphering the phylogenetic relationships within the family Sesarmidae and represents a new genomic resource for this iconic crab species.

The First Complete Mitochondrial Genome of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) and Phylogenetic Relationships within Infraorder Brachyura

“…The rrnL and rrnS genes of E. crenata are 1398 bp and 819 bp in length, respectively. Consistent with many Brachyura crabs [15,16], rrnL and rrnS are typically separated by trnV (gta) (Table 2). The AT and GC content of rRNAs are 78.3% and 21.7%, and the AT skew and GC skew are 0.022 and 0.29, respectively, suggesting an apparent bias toward the use of A and G.…”

“…However, it can be used as direct evidence of evolutionary relationships between species [36]. Gene order and strand arrangement in E. crenata is unidentical to that reported before in co-order species with mitochondrial genomes deposited in Genbank, i.e., Perisesarma bidens, Parasesarma tripectinis, and Metopaulias depressus [16,37,38]. After comparison and analysis with the ancestor of Decapoda [15], we found that E. crenata had a trnH-cac translocation, where the trnH-cac shifted into trnE-gaa and trnF-ttc, instead of the usual location between nad5 and nad4.…”

“…The RSCU values indicate that the six most commonly used codons are TTA (Leu), AGA (Ser), TCT (Ser), CCT (Pro), ACT (Thr), GCT (Ala) ( Figure 2 ). Based on RSCU and amino acid composition in the PCGs, comparative analyses showed that the codon usage pattern of E. crenata is not conserved, varying from those of most Brachyuran species, such as Grapsus albolineatus and Metopaulias depressus [ 15 , 16 ]. In particular, leucine (9.8%) was found to be used less than serine, and AGA (Ser) plays a key role in the codon usage.…”

“…Thus, the investigations about the species mitogenomes in Goneplacidae and their phylogenetic relationships within the infraorder Brachyura are worthy of great attention. Up to now, the phylogenetic relationships within the infraorder Brachyura of several crabs belonging to some families, i.e., Grapsidae, Sesarmidae, Panopeidae, have been studied [ 15 , 16 , 17 ]. However, the species mitogenomes in the family Goneplacidae have never been reported, nor have their phylogenies within the infraorder Brachyura.…”