The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes.

BACKGROUND: China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. RESULTS: Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense, and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo-nad1) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo-trnL2 and pseudo-rrnL) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. CONCLUSIONS: This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures.

Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species?

The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum, utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late Holocene, accompanied by a recent population bottleneck. Species distribution modeling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently, genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance.

Fiddler crabs from highly disturbed beaches are more sensitive to human presence.

The presence of humans frequently modifies the behavior of animals, particularly their foraging patterns, compromising energetic demands. The fiddler crab Leptuca leptodactyla inhabits mangroves with high degrees of anthropogenic influence. Thus, we tested if populations living in highly anthropized mangroves respond differently from those living in more protected areas. We predict that individuals from touristy areas will be more tolerant to humans and will resume their activities sooner after disturbance. To do so, we conducted an experiment that consisted in the approach of an observer to the burrows, recording the response of individuals to the stimuli. The experiment took place in July 2022, in Ubatuba, São Paulo, Brazil. We analysed the duration and latency of various behaviors of a total of 80 adult males from two populations (high and low anthropogenic influence). Contrary to our predictions, individuals from the anthropized population were less tolerant, spending more time inside their burrows and taking longer to resume their activities. Therefore, fiddler crabs were not habituated to human presence. These results help us understand the learning process in invertebrates and their ability to select stimuli, contributing to understanding the impacts of human-wildlife interactions.

Identification and functional characterization of C-type lectins and crustins provide new insights into the immune response of Portunus trituberculatus.

A meticulous understanding of the immune characteristics of aquaculture animals is the basis for developing precise disease prevention and control strategies. In this study, four novel C-type lectins (PtCTL-5, PtCTL-6, PtCTL-7 and PtCTL-8) including a single carbohydrate-recognition domain (CRD), and four novel crustins (Ptcrustin-1, Ptcrustin-2, Ptcrustin-3 and Ptcrustin-4) with a single whey acidic protein (WAP) domain were identified from the swimming crab Portunus trituberculatus. Tissue distribution analysis indicated that most of the target genes were predominantly expressed in the hepatopancreas in all examined tissues, except for Ptcrustin-1 which were mainly expressed in the gills. Our results showed that the eight genes displayed various transcriptional profiles across different tissues. In hemocytes, the PtCTL-7 responded quickly to Vibrio alginolyticus and exhibited much more strongly up-regulation than other three PtCTLs. The Ptcrustin-1 rapidly responded to V. alginolyticus within 3 h in all the three tested tissues. Furthermore, recombinant proteins of PtCTL-5 and PtCTL-8 were successfully obtained, and both of them displayed bacterial binding activities toward V. alginolyticus, V. harveyi and Staphylococcus aureus, and only showed antibacterial activity against V. harveyi. These findings provided new insights into the diverse immune response of P. trituberculatus and laid theoretical foundations for the development of precise disease prevention and control strategies in P. trituberculatus farming. Moreover, the specific anti-V. harveyi activities exhibited by rPtCTL-5 and rPtCTL-8 suggested their promising application prospects for controlling diseases caused by V. harveyi.

Phylogenetic relationships of Grapsoidea and insights into the higher phylogeny of Brachyuran.

Decapoda is one of the most diverse crustacean orders, and has become an important research subject. However, the phylogenetic relationships among the main lineages of Decapoda remain uncertain, especially in the order Brachyura. Herein, we sequenced the whole mitochondrial genome of V. litterata and constructed a phylogenetic tree to understand its phylogenetic relationships with other species. The results showed that the mitochondrial genome of V. litterata was generally similar to mitogenomes of Metazoa reported in the literature, with a size of 16,247 bp, 37 genes, and a control region. Both AT-skew and GC-skew were negative, indicating more abundant Cs and Ts than Gs and As. The gene arrangement of V. litterata is identical to those of Eriocheir hepuensis, Cyclograpsus granulosus, Hemigrapsus sanguineus, Helicana wuana, and Helice tientsinensis but differs from the pancrustacean ground pattern and typical arrangement of Brachyuran crabs. Phylogenetic reconstruction showed that V. litterata belongs to the Varunidae.

The complete mitochondrial genome of the sand bubbler crab Scopimera globosa and its phylogenetic position.

The mitochondrial genome has become commonly used for the molecular phylogenetic analysis of animals. Most phylogenetic studies on brachyurans using mitogenome sequences have indicated the paraphyly of superfamilies Grapsoidea and Ocypodoidea but taxon sampling remains limited. The phylogenetic position of Scopimera has been tested in several previous studies using nuclear and/or mitochondrial DNA sequences, but the phylogenetic relationship within the family remains to be resolved. We newly sequenced the complete mitochondrial genome of the sand bubbler crab Scopimera globosa (Ocypodoidea: Dotillidae). Scopimera globosa was clustered with Ilyoplax despite the morphological similarity between Scopimera and Dotilla. The mitochondrial gene order of S. globosa was unique, whereas that of other genera in the family was the same. These results suggest that phylogenetic analysis based on mitogenome sequences and gene order comparison would provide a more robust phylogeny of Dotillidae.

The complete mitochondrial genome of the red-jointed brackish-water fiddler crab Minuca minax (LeConte 1855) (Brachyura: Ocypodidae): New family gene order, and purifying selection and phylogenetic informativeness of protein coding genes.

Minuca minax is a semi-terrestrial crustacean that commonly lives in low salinity, riverine habitats along the shores of the eastern United States. This study reports, for the first time, the complete mitochondrial genome of M. minax. The AT-rich mitochondrial genome of M. minax is 15,937 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 737 bp long intergenic space is assumed to be the D-loop. Most of the PCGs and tRNA genes are encoded in the L-strand. The gene order observed in the mitochondrial genome of M. minax is new although almost identical to that reported in confamiliar species. In all other confamiliar species to which M. minax is compared, the positions of the trnQ gene and the trnI gene are switched. KA/KS ratios calculated for all mitochondrial PCGs show values of <1, indicating that these PCGs are evolving under purifying selection. A maximum likelihood phylogenetic analysis (concatenated PCGs [n = 13], 15 species) supports the monophyly of the subfamilies Ocypodinae and Gelaminidae. Mitochondrial PCGs have enough phylogenetic information to reveal relationships supporting higher taxonomic levels within this family. The knowledge of a complete mitochondrial genome from the red-jointed brackish-water fiddler crab M. minax contributes to the better understanding of meta-population connectivity and the mechanisms involved in the adaptation of marine organisms to near-limnic conditions.

Genetic Identification of all Four Mangrove Mud Crab Species (genus Scylla) Using Multiple Molecular Markers.

Misleading identification and subsequent publications on biological, molecular, and aquaculture data of mangrove mud crab (genus Scylla de Hann 1833) is a major concern in many countries. In this study, multiple molecular markers were used for genetic identification of all four known mud crab species under genus Scylla collected from India, Philippines, Myanmar, Malaysia and Indonesia. Internal Transcribed Spacer (ITS-1), Polymerase chain reaction (PCR)-Restriction Fragment Length Polymorphism (PCR-RFLP) and PCR-based species-specific markers were used to resolve taxonomic ambiguity. PCR-RFLP techniques using NlaIV and BsaJI restriction endonucleases were efficient to differentiate four different mud crab species under genus Scylla with specific fragment profile. The results also justified the use of ITS-1 and PCR-based species-specific markers to identify mud crab species available in many countries quite rapidly and effectively. Several new molecular markers generated during the study are reported here to resolve the taxonomic ambiguity of Scylla species and the results reconfirmed that India is only having two commonly available mud crab species which was reported by the authors earlier.

The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura.

Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (- 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.

Characterization of the complete mitochondrial genome of Helice latimera and its phylogenetic implications in Brachyura.

Mitochondrial genomes (mitogenomes) help advance our learning of molecular evolution and phylogenetic relationships. The mitogenome of H. latimera is 16,246 bp in length, which typically contains 37 animal mitogenome genes consisting of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, as well as a control region. The AT content of H. latimera is 69.1%. The A + T skew of the mitogenome of H. latimera was slightly negative (-0.017). The size of Thirteen PCGs is from 162 bp to 1731 bp. Twenty-two tRNA genes ranged from 62 to 73 bp and were highly A + T biased. All tRNA genes owed a typical cloverleaf structure, not including the trnS1 gene lacking a dihydroxyuridine arm. One PCG, two rRNAs, and 12 of the tRNAs were rearranged compared to the pancrustacean gene order. Phylogenetic analysis revealed the locationt of H. latimera among the Varunidae family.

Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs.

Brachyuran crabs comprise the most species-rich clade among the crustacean order Decapoda and are divided into several major superfamilies. However, the monophyly of the superfamilies Ocypodoidea and Grapsoidea in their current compositions within the Brachyura remains inconclusive. In this study, the complete mitochondrial genome (mitogenome) of Uca lacteus (Ocypodoidea, Ocypodidae) was sequenced, annotated, and compared with those of other Brachyuran crabs. The circular mitogenome of U. lacteus is 15,661 base pairs long and contains the entire set of 37 genes and an A + T-rich region typically observed in decapod mitogenomes. Secondary structures of several tRNAs are partly missing (trnS1), and the number of bases is significantly decreased (trnD and trnF), as discovered in many other metazoans. We compared the gene order of U. lacteus with other species of Ocypodidae and found that they are consistent. The gene rearrangement of Ocypodidae is also identical to that of the ancestor of Brachyura. However, the order of the trnH gene varies from the rearrangement of ancestral Decapoda. Accordingly, we hypothesized that this rearrangement of trnH underwent a translocation during the evolution from Decapoda to Brachyura. The phylogenetic relationship of the 81 Brachyura species and one outgroup was recovered based on 13 protein-coding genes. This analysis confirmed that U. lacteus belongs to the family Ocypodidae and established a paraphyletic relationship between Ocypodoidea and Grapsoidea.

Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea.

Grapsoidea and Ocypodoidea, two of the most abundant and economically important groups in Brachyura, are of great commercial value to fisheries and aquaculture. However, the taxonomy of Ocypodoidea and Grapsoidea has long been highly disputed. Previous studies have investigated this problem through phylogenetic analysis based on limited taxonomic sampling, with different reports proposing either monophyly or paraphyly, but no definitive conclusion has been reached. In this study, the complete mitogenome of Macrophthalmus pacificus (Ocypodoidea, Macrophthalmidae) is reported on and the relationship between Ocypodoidea and Grapsoidea is further investigated. Sequencing the M. pacificus mitogenome, which is a closed circular molecule containing a typical 37 genes, preliminarily determined the ancestral gene order of Macrophthalmidae, which is consistent with previous studies. Comparative analyses of gene order among Ocypodoidea and Grapsoidea revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) have the same rearrangement, which confirms previous research. Larger data analysis revealed that these two families (Varunidae and Macrophthalmidae) cluster into a monophyletic clade as sister groups. Rearrangement and phylogeny lines of evidence is concluded that Varunidae and Macrophthalmidae may be of common origin. Furthermore, the remaining Ocypodoidea and Grapsoidea families mix paraphyletically in the phylogenetic tree. Therefore, both gene rearrangement and phylogenetic analysis support the paraphyly of Ocypodoidea and Grapsoidea, which reinforces this view. These findings provide important information regarding Brachyura's phylogenetic relationships, which demonstrates the advantage of mitogenome sequence data in phylogenetic studies.

The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura.

In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (-0.010) and GC-skew (-0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.

Marine species formation along the rise of Central America: The anomuran crab Megalobrachium.

The evolution of marine neotropical shallow water species is expected to have been greatly affected by physical events related to the emergence of the Central American Isthmus. The anomuran crab Megalobrachium, a strictly neotropical porcellanid genus, consists of four species in the West Atlantic (WA) and nine in the East Pacific (EP). Dispersal is limited to a relatively short planktonic phase, which lasts approximately two weeks. We obtained DNA sequences of three mitochondrial and two nuclear genes of all but one species of Megalobrachium to construct a time-calibrated phylogeny of the genus and its historical phylogeography, based on the reconstruction of ancestral areas. The topology of the phylogenetic trees of Megalobrachium produced by Bayesian Inference (BI) and Maximum Likelihood (ML) were virtually congruent. The genus is monophyletic with respect to other porcellanids. Ancestral area reconstruction indicates that it arose in the eastern Pacific 18 million years ago and diversified into at least 13 species that are currently formally recognized and three additional species indicated by our data. Most morphological variation appears to have followed phylogenetic differentiation, though some cryptic speciation has also occurred. Four geminate clades in this genus implicate the gradual emergence of the Central American Isthmus in this diversification, but events preceding the final separation of the oceans as well as within-ocean events after the cessation of water connections were also important.

Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae).

We present here a combined mitogenome gene order dataset totalling 62% of the known genera of East Asian potamiscine freshwater crabs that includes first-time mitogenome data for 14 species and gene order data from 37 other species of potamiscines. A surprisingly high number of mitogenome gene order rearrangements were found in the taxa studied (comprising nine different rearrangements and seven major patterns, one of which has two sub-arrangements). Our phylogenetic reconstructions indicate that the mitogenome gene order rearrangements are associated with the evolutionary history of potamiscine lineages. We also used a new Event-based Maximum Parsimony method to reconstruct ancestral gene orders, which takes into consideration gene duplication, pseudogeneticization, and tandem duplication random loss. Furthermore, shared mitogenome gene order patterns were used to inform the taxonomic placement of Sinopotamon parvum, and the cryptic diversity in Potamiscus. The remarkably frequent mitogenome rearrangements in potamiscine freshwater crabs have great potential to contribute to our understanding of the evolutionary history of these highly diverse decapods in East Asia.

Evolution of digestive enzyme genes associated with dietary diversity of crabs.

Crabs feed on a wide range of items and display diverse feeding strategies. The primary objective of this study was to investigate 10 digestive enzyme genes in representative crabs to provide insights into the genetic basis of feeding habits among crab functional groups. Crabs were classified into three groups based on their feeding habits: herbivores (HV), omnivores (OV), and carnivores (CV). To test whether crabs' feeding adaptations matched adaptive evolution of digestive enzyme genes, we examined the 10 digestive enzyme genes of 12 crab species based on hepatopancreas transcriptome data. Each of the digestive enzyme genes was compared to orthologous sequences using both nucleotide- (i.e., PAML and Datamonkey) and protein-level (i.e., TreeSAAP) approaches. Positive selection genes were detected in HV crabs (AMYA, APN, and MGAM) and CV crabs (APN, CPB, PNLIP, RISC, TRY, and XPD). Additionally, a series of positive selection sites were localized in important functional regions of these digestive enzyme genes. This is the first study to characterize the molecular basis of crabs' digestive enzyme genes based on functional feeding group. Our data suggest that HV crabs have evolved an enhanced digestion capacity for carbohydrates, and CV crabs have acquired digestion capacity for proteins and lipids.

Identification of a transforming growth factor-ß type I receptor transcript in Eriocheir sinensis and its molting-related expression in muscle tissues.

The transforming growth factor-ß (TGF-ß) signaling pathway is conserved across animals, and knowledge of its roles during the molt cycle in crustaceans is presently very limited. This study investigates the roles of the TGF-ß receptor in molting-related muscle growth in Eriocheir sinensis. Using the RT-PCR and RACE techniques, we obtained a 1722 bp cDNA sequence encoding a transforming growth factor-ß type I receptor in Eriocheir sinensis, designated EsTGFBRI, which contains a 124 bp 5'-untranslated region, a 20 bp partial 3'-untranslated region and a 1578 bp open reading frame encoding 525 amino acids. The deduced EsTGFBRI contains an N-terminal 24 amino acid signal peptide, an activin type I and II receptor domain, a transmembrane helix region, a glycine-serine-rich motif, and a conserved serine/threonine kinase catalytic domain including an activation loop. The qRT-PCR results showed that EsTGFBRI gene was highly expressed in the intermolt testis and ovary in mature crabs. In juvenile crabs, the mRNA levels of EsTGFBRI in claw and abdominal muscles in the later premolt D3-4 stage were significantly higher than those in the intermolt C and postmolt A-B stages. There was no significant change in EsTGFBRI mRNA levels in walking leg muscles during the molt cycle. The results suggest that EsTGFBRI is probably play roles in molting-related muscle growth in E. sinensis. This study provides a necessary basis for elucidating the functions of TGF-ß-like signaling mediated by TGFBRI in molting-related muscle growth in crustaceans.

The distribution of the freshwater crab Fredius reflexifrons (Ortmann, 1897) (Brachyura, Pseudothelphusidae) in an Environmental Protection Area of the Planalto da Ibiapaba, Northeastern Brazil.

Freshwater crabs are important components of aquatic ecosystems; however, their distributions are restricted because of characteristics of their life history, which hinder conservation strategies. Fredius reflexifrons is a widely distributed freshwater crab of the Amazon basin with relictual occurrences in small wetlands on the Planalto da Ibiapaba in Northeastern Brazil. Habitat degradation, destruction of forest patches, channeling of water bodies, and the use of land for legume cropping can seriously impact the species by leading to the extinction of its relic populations, which have limited distributions in the Área de Proteção Ambiental (APA; Environmental Protection Area) Bica do Ipu of the Planalto da Ibiapaba. The objectives of this study were to assess the distribution of F. reflexifrons in APA Bica do Ipu, identify the main impacts from anthropic activities, suggest potential actions to mitigate these impacts, besides providing recommendations for the expansion of the APA. Fredius reflexifrons was recorded in eleven sites in the Planalto da Ibiapaba, of which nine are new records and five are not located within the APA. These findings evidence the need of expanding the APA to encompass the newly known distribution of F. reflexifrons in order to assure its protection.

The complete mitochondrial genome of Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) and comparison with other Brachyuran crabs.

Mitochondrial DNA (mtDNA) is an extrachromosomal genome which can provide important information for evolution and phylogenetic analysis. In this study, we assembled a complete mitogenome of a crab Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) from next generation sequencing reads at the first time. P. pictum is a mudflat crab, belonging to the Sesarmidae family (subfamily Sesarminae), which is perched on East Asia. The 15,716 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (CR). The control region spanns 420 bp. The genome composition was highly A+T biased 75.60% and showed negative AT-skew (-0.03) and negative GC-skew (-0.47). Compared with the ancestor of Brachyura, the gene order of Sesarmidae has several differences and the gene order of P. pictum is typical for mitogenomes of Sesarmidae. Phylogenetic tree based on nucleotide sequences of mitochondrial 13 PCGs using BI and ML determined that P. pictum has a sister group relationship with Parasesarma tripectinis and belongs to Sesarmidae.

Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs.

Recent fossil calibrated molecular phylogenies have revealed that the Brachyura underwent rapid radiation during the Cretaceous and Early Tertiary, resulting in many early diverging lineages separated by short internodes that remain difficult to resolve. Here we present the first phylogenomic analyses of Brachyura using transcriptome data from 30 brachyuran species and 22 families. Analyses were carried out on a dataset containing 372 putative homologous loci (246,590 bps) and included data from 21 newly generated transcriptomes. With minor exceptions, all phylogenetic analyses recovered a congruent, highly resolved and well supported brachyuran phylogeny. Consistent with previous work, this phylogeny suggests that primary freshwater crabs diverged early in brachyuran evolution, falling sister to Thoracotremata, thus supporting recent proposal for establishment of subsection Potamoida for primary freshwater crabs. The interfamilial relationships among heterotremes were well resolved in our analyses but those within Thoracotremata remained problematic. Phylogenomic analyses clearly provide a powerful means for resolving brachyuran relationships, but future studies would benefit greatly from increased taxon sampling of transcriptome data.