The complete mitochondrial genomes of two vent squat lobsters, <i>Munidopsis lauensis</i> and <i>M. verrilli</i>: Novel gene arrangements and phylogenetic implications

Sun, Shao'e; Sha, Zhongli; Wang, Yanrong

doi:10.1002/ece3.5542

Cited by 13 publications

(9 citation statements)

References 99 publications

(129 reference statements)

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“…The mitochondrial genomes (mitogenomes) provide rich phylogenetic information not only in the sequences, but also in the genomic rearrangements (Boore, 1999;Sun et al, 2003;Tan et al, 2017). In the Decapoda, novel mitochondrial gene orders have been reported across a range of lineages, such as brachyurans (Zhang et al, 2020;Wang et al, 2021), anomurans (Sun et al, 2019;Gong et al, 2020), and caridean shrimps (Ye et al, 2021). By analyzing 246 decapod mitogenomes, Tan et al (2019) found that a large number of mitochondrial gene orders in decapods deviated from the ancestral arthropod ground pattern and unevenly distributed among infraorders, but there was limited evidence for correlations between gene rearrangement events and species ecology or lineage-specific nucleotide substitution rates.…”

Section: Introductionmentioning

confidence: 99%

Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)

et al. 2022

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Thoracotremata is a group of Brachyura, with 1,248 extant species. To date, parts of the thoracotreme phylogeny are not yet resolved and require further investigation. In this study, 12 new mitogenomes from the four thoracotreme superfamilies were sequenced. They contain a standard set of 37 genes, and vary in size from 15,422 (Hapalocarcinus marsupialis Stimpson, 1858 sensu lato) to 16,490 bp [Arcotheres sinensis (Shen, 1932)]. Combined with 58 thoracotreme mitochondrial genomes (mitogenomes) from GenBank, we described the evolution of gene rearrangement and the internal phylogenetic relationships of Thoracotremata, and evaluated the phylogenetic position of Cryptochiroidea and Pinnotheroidea. Nine distinct patterns of mitochondrial gene order (MGO) among thoracotreme mitogenomes are identified, with four MGOs newly found in Thoracotremata. All other gene orders are the result of transformational pathways originating from brachyuran gene order (BraGO). The different gene orders have variable levels of gene rearrangements, which involve both tRNAs and protein-coding genes. No link between variable gene arrangements (breakpoint distances) and nucleotide substitution rates (branch lengths) is found in thoracotreme crabs. The symbiotic groups, the cryptochiroid and pinnotheroid crabs, display variable MGOs (CryGO, Pin1GO, and Pin2GO), providing evidence for possible correlations of rearranged MGOs to the adaptations to specialized lifestyles. In our phylogenetic analyses, Cryptochiridae (Cryptochiroidea) show close relationship with an Ocypodoidea lineage (Camptandriidae/Xenophthalmidae/Dotillidae). Pinnotheridae (Pinnotheroidea) form the basal monophyletic clade.

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Section: Introductionmentioning

confidence: 99%

Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)

et al. 2022

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“…Recent studies have also found positive selection in ATP genes for many deep-sea animals, such as sea anemone [ 77 ] and shrimp [ 25 ], indicating potential adaptation to marine extreme environments. ATP dehydrogenase not only is the last enzyme complex in the respiratory chain, but also is a part of the regulatory system of complex V [ 78 ]. The atp6 subunit plays an important role in the assembly of F0 proton in ATP synthase, which suggest that mutation in the atp6 gene may affect the production of ATP [ 79 ].…”

Section: Resultsmentioning

confidence: 99%

The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

Cai

et al. 2020

PLoS ONE

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Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

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“…Our conclusion is in accordance with previous workers, who suggested that gene rearrangements, to some extent, contain phylogenetic information. For example, Shao et al 64 compared the mitochondrial gene arrangements of 12 anomurans and found that Munidopsis lauensis and M. verrilli are most closely related to Shinkaia crosnieri . Based on the comparative analysis of mitochondrial gene arrangement within Coleoidea, Akasaki et al 65 concluded that order Octopoda might be the most ancestral among this subclass Coleoidea.…”

Section: Discussionmentioning

confidence: 99%

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

Zhang

Meng

Wei

et al. 2021

Sci Rep

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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.

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The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

Cited by 13 publications

References 99 publications

Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)

Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)

The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

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

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