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

Abstract

Characterizing the complete mitochondrial genome (mitogenome) of an organism is useful for genomic studies in taxonomy and evolution. The mitogenomic characteristics of Eucrate crenata (Decapoda: Brachyura: Goneplacidae) have never been studied. The present study decodes the first mitogenome of E. crenata by high-throughput sequencing (HTS). The length of the mitogenome is 15,597 bp, and it contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL), and 22 transfer RNA genes. There are 14 and 23 genes observed on the heavy and light strands, respectively. E. crenata possesses a trnH-cac translocation, with the trnH-cac shifted between trnE-gaa and trnF-ttc instead of the usual location between nad5 and nad4 in decapods. Phylogenetic analyses based on the current dataset of 33 Brachyuran mitogenomes indicate that E. crenata. is closely related to Ashtoret lunaris of Matutidae. The similar codon usage and rearrangements in the two species provide evidence for their close phylogenetic relationship. Positive selection analysis showed that one residue located in cox1 was identified as a positively selected site with high BEB value (>95%), indicating that this gene was under positive selection pressure. This study is the first complete mitogenome record for the family Goneplacidae, and the results obtained may improve the understanding of the phylogeny of Goneplacidae in Brachyura.

Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.)

“…For example, the valine codons GTC and GTG were rare, whereas GTT and GTA's synonymous codons were prevalent (Table 2). In the mitogenome of Leucoma salicis [60] and Eucrate crenata [47] a similar tendency was observed. The pattern of codons for the frequently used amino acids like Phe, Leu, Ile, Asn and Ser of C. acuta are similar to most noctuoid mitogenomes [48,61,62].…”

“…The protein-coding genes are found scattered on both heavy and light strands, covering 71.93% of the total mt genome of C. acuta, and-11,077 bp long. These PCGs include cytochrome c oxidase, NADH dehydrogenase, Cytochrome B, and ATPase, commonly found in most insect species belonging to Lepidopteran order [21,[46][47][48].…”

“…Our findings are consistent with those of Liu et al [55], Dai et al [22], Dai et al [56], Li et al [57] Chen et al [58] and Riyaz et al [48] who also reported the presence of single "T" as a termination codon for the cox1 and cox2 genes in the majority of Lepidopteran species. This incomplete termination codon "T" in lepidopteran mt genes might get polyadenylated to TAA codon during translation [46,47,59]. Numerous studies have demonstrated that the nucleotides 'A' and 'T' are generally overrepresented in metazoan mitogenomes, which causes bias in the corresponding encoded amino acids [21].…”

Characterization and Phylogenetic Analysis of the First Complete Mitochondrial Genome of Gnathophyllum americanum (Guérin-Méneville, 1855) (Malacostraca: Decapoda: Palaemonidae)

“…The longest overlap was 17 bp, between atp6 and cox3. In Decapoda, mitochondrial gene overlap was reported in many species [12][13][14]. The most common locations were atp6/atp8 and nad4l/nad4, but locations were also observed at different genes.…”