Gene rearrangements in the mitochondrial genome of Chiromantes eulimene (Brachyura: Sesarmidae) and phylogenetic implications for Brachyura

Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.

Section: Resultssupporting

confidence: 83%

“…Gene rearrangements in the mitogenomes of crabs are relatively common 1 , 19 , 20 . So far, several hypotheses have been suggested to help explain gene rearrangements in animal mitogenomes.…”

Section: Introductionmentioning

confidence: 99%

The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura

Xia

Liu

et al. 2022

“…In addition, they have a compact size, maternal inheritance, conserved features in their gene organization, a lack of extensive recombination, and a higher mutation rate than nuclear sequences 3 – 5 . These sequences been extensively used in comparative and evolutionary genomics 6 , species identification, population genetics 7 , molecular evolutionary and phylogenetic analyses and taxonomic diagnosis in marine biological studies 8 – 10 . In particular, phylogenetic analysis based on complete mitogenomes proved that the resolution of inferred phylogenetic trees was improved compared with that of trees based on partial gene fragments 11 .…”

Section: Introductionmentioning

confidence: 99%

Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships

Jiao

Xia

Yan

et al. 2021

Neritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.

“…S3 , S4 ). The lack of DHU arm in tRNA-Ser (TCT) is thought to be a common phenomenon in metazoan mitogenomes 12 , 53 . The 16S rRNA and 12S rRNA genes of D. arrosor and D. aspersus are located between ND1 and tRNA-Val and between tRNA-Val and CR, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Generally, the gene order in most vertebrate mitogenomes is considered conserved. However, extensive mitochondrial gene rearrangements have been observed in invertebrate mitogenomes, such as in cephalopods 9 , bivalves 10 , insects 11 , and crabs 12 , 13 . The gene rearrangement within a lineage has been supposed to be phylogenetically informative; therefore, comparative analysis of mitochondrial gene order has been proved to be a valuable phylogenetic tool.…”

Section: Introductionmentioning

confidence: 99%

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

Zhang

Meng

Wei

et al. 2021

Self Cite

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.