Dataset Information

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura.

ABSTRACT: We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both ?- and ?-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the ?-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis.

SUBMITTER: Basso A

PROVIDER: S-EPMC5481413 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

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The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura.

Basso Andrea A Babbucci Massimiliano M Pauletto Marianna M Riginella Emilio E Patarnello Tomaso T Negrisolo Enrico E

Scientific reports 20170622 1

We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both α- and β-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the β-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study con ...[more]

PMID: 28642542

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Project description:BackgroundAparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes.ResultsA new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs.ConclusionsGeological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.

Project description:Portunoidea (Heterotremata) is a morphologically disparate taxon of true crabs (Brachyura) best-known for many of its representatives being considered “swimming crabs”. The term “swimming crab”, however, sometimes refers to a distinct taxon (traditionally to Portunidae within Portunoidea), and sometimes to a certain morphotype in which the 5th pereiopod (P5) has a specific shape that facilitates swimming. We use the term “P5-swimming crab” or “P5-swimmer” herein, not only to restrict it to the morphotype, but also to distinguish the swimming in question from other kinds of swimming in Brachyura. The evolution of P5-swimming crabs has not yet been satisfactorily investigated. In particular, it is not known whether the morphotype evolved several times independently in different lineages of Portunoidea or whether it evolved only once and was lost in several lineages. Ours is the first approach combining molecular with morphological data to result in a new phylogenetic positioning of some members of Portunoidea. For the first time, data from the axial skeleton and extrinsic musculature are used. Morphological examinations reveal that the axial skeleton and extrinsic musculature in P5-swimming crabs are more diverse than previously thought, with the exception of the P5 anterior coxa muscle, which originates at the median plate in all P5-swimmers. Ancestral state reconstructions based on parsimony reveal that the stem species of Portunoidea already showed the morphotype of a P5-swimming crab, but with a long merus which probably resulted in less effective P5-swimming than in extant P5-swimming crab species with a short merus. Several other extant taxa represent a reversal of the P5-swimmer morphotype to varying degrees, with some extant species showing a complete reversal of unambiguous P5-swimming crab character states—one example being the well-known common shore crab Carcinus maenas. The absence of a connection between interosternite 7/8 and the sella turcica (the secondary loss of the “brachyuran sella turcica”) in the stem species of Heterotremata, resulting in a junction plate which forms a cavity that offers room and attachment sites for the P5 extrinsic musculature is uncovered as preadaptation to the P5-swimmer morphotype in Heterotremata. This preadaptation is missing in Podotremata and Thoracotremata, the other two traditional main taxa of Brachyura. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-022-00467-8.

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Dataset Information

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura.

Publications

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura.

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