Dataset Information

Complete mitochondrial genome of the spiny rock crab Thalamita crenata (ruppell, 1830) (Crustacea: Decapoda: Portunidae) from China coast and its phylogeny.

ABSTRACT: To understand the evolution of the swimming crab Thalamita crenata, the complete mitochondrial genome of T. crenata from China was sequenced and analyzed. The circular mitogenome sequence was 15,787?bp in length, made up of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The overall mitogenome composition was 34.40% for A, 11.55% for G, 35.31% for T, and 18.74% for C, respectively, with a high A?+?T content of 69.71%. Phylogenetic analysis showed that T. crenata was closest to the genus Charybdis.

SUBMITTER: Xie Z

PROVIDER: S-EPMC7800823 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome of the spiny rock crab Thalamita crenata (rüppell, 1830) (Crustacea: Decapoda: Portunidae) from China coast and its phylogeny.

Xie Zhuofang Z Lai Tinghe T Waiho Khor K Tan Huaqiang H Ma Hongyu H

Mitochondrial DNA. Part B, Resources 20181030 2

To understand the evolution of the swimming crab Thalamita crenata, the complete mitochondrial genome of T. crenata from China was sequenced and analyzed. The circular mitogenome sequence was 15,787 bp in length, made up of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The overall mitogenome composition was 34.40% for A, 11.55% for G, 35.31% for T, and 18.74% for C, respectively, with a high A + T content of 69.71%. Phylogenetic analy ...[more]

PMID: 33474399

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Project description:The objectives of this work are to use gene sequence data to assess the hypothesis that the Lithodinae arose from ancestors with uncalcified abdomens in shallow waters of the North-East Pacific, investigate the monophyly and interrelationships of genera within the Lithodinae and to estimate the scale and minimum number of biogeographic transitions from the shallow environment to the deep sea and vice versa. To do this, phylogenetic analysis from three mitochondrial and three nuclear markers was conducted using minimum evolution, maximum likelihood and Bayesian methods. The Lithodinae as defined to include North Pacific genus Cryptolithodes may be paraphyletic, with the Hapalogastrinae and Cryptolithodes as sister taxa. This implies that the soft-bodied abdomen of the Hapalogastrinae might not be plesiomorphic for the Lithodidae. Paralomis, Lopholithodes, Phyllolithodes, Lithodes and Neolithodes share a common ancestor, from which the North Pacific Hapalogastrinae did not descend. Lithodid ancestors are likely to have had a north Pacific, shallow water distribution and to have had planktotrophic larvae. North Pacific genus Paralithodes is paraphyletic; P. brevipes is the most basal member of the genus (as sampled) while P. camtschaticus and P. platypus are more closely related to the genera Lithodes and Neolithodes. Genera Lithodes, Neolithodes and Paralomis (as sampled) are monophyletic if Glyptolithodes is included within Paralomis. Lopholithodes is closely related to, but not included within, the Paralomis genus. Paralomis is divided into at least two major lineages: one containing South Atlantic, West African, and Indian Ocean species, and the other containing Pacific and South American species. Several species of Paralomis do not resolve consistently with any other groups sampled, implying a complex and possibly rapid global evolution early in the history of the genus. Relationships within the Lithodes genus vary between analytical methods, suggesting that conclusions may not be stable. Consistently, however, Indian Ocean and Pacific forms-L. murrayi, L. longispina and L. nintokuae form a group separated from Atlantic species such as L. santolla, L. confundens, L. maja and L. ferox.

Project description:BACKGROUND: The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. RESULTS: We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. CONCLUSIONS: Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

Dataset Information

Complete mitochondrial genome of the spiny rock crab Thalamita crenata (ruppell, 1830) (Crustacea: Decapoda: Portunidae) from China coast and its phylogeny.

Publications

Complete mitochondrial genome of the spiny rock crab <i>Thalamita crenata</i> (rüppell, 1830) (Crustacea: Decapoda: Portunidae) from China coast and its phylogeny.

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