Mitochondrial Genome of Grapsus albolineatus and Insights into the Phylogeny of Brachyura
1
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
2
Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224007, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2025, 15(5), 679; https://doi.org/10.3390/ani15050679
Submission received: 9 January 2025
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Revised: 8 February 2025
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Accepted: 20 February 2025
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Published: 26 February 2025
(This article belongs to the Section Animal Genetics and Genomics)
Simple Summary
The diverse crustacean group Brachyura, which consists of over 7000 species, possesses important crab mitogenomes that are valuable for molecular evolution and phylogenetic studies. Among these species, Grapsus albolineatus stands out due to its unique rearrangements in comparison to the Pancrustacean ground pattern and other Brachyura species. Mitogenomes play a crucial role in subfamily-level phylogenetics within Brachyura and have the potential to aid in the systematic classification of other Brachyuran species.
Abstract
Brachyura is among the most diverse groups of crustaceans, with over 7000 described species. Crab mitogenomes are important for understanding molecular evolution and phylogenetic relationships. Grapsus albolineatus exhibits specific rearrangements compared with the Pancrustacean ground pattern and other Brachyura species. The gene arrangement of G. albolineatus is similar to that of ancestral crustaceans, barring that of the translocated trnH gene. In phylogenetic analyses, the Bayesian inference estimation was observed to be superior to the maximum likelihood estimation when the nodal support values were compared. Considering the results of the gene rearrangement pattern and phylogenetic analysis, we speculate that G. albolineatus belongs to Grapsidae. Our comparative study indicated that mitogenomes are a useful phylogenetic tool at the subfamily level within Brachyura. The findings indicate that mitogenomes could be a useful tool for systematics in other Brachyuran species.
1. Introduction
The mitochondria, an organelle of eukaryotic cells, has its own genome. It is commonly referred to as the mitochondrial genome. The mitochondrial genome, as a unique and easily accessible genetic marker, is characterised by a high mutation rate, high replication number, and maternal inheritance [1]. The metazoan mitochondrial genome is a double-stranded, circular, covalently closed molecule. Metazoans have a small mitochondrial genome, measuring approximately 16–20 kbp in length [2]. The mitochondrial genome comprises 13 protein-coding genes (PCGs), including seven nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits (NADH dehydrogenase subunit [ND] 1, ND2, ND3, ND4, ND5, ND6, and ND4l), cytochrome b (cytb), three cytochrome c oxidases (cytochrome C oxidase subunit [CO] I, COII, and COIII), and two adenosine triphosphate (ATP) synthase subunits (ATPase subunit [ATPase] 6 and ATPase8). Twenty-two transfer ribonucleic acid (RNA) genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding control region (also known as an adenine–thymine [AT]-rich region in invertebrates) regulate mitogenomic transcription and replication [3].
Nearly 7000 described species and 98 families make up the infraorder Brachyura [4]. The evolutionary history of the Brachyura can be viewed as an example of evolutionary radiation, where different directions of adaptive evolution (freshwater, marine, and intertidal) occurred due to different survival environments during the process of evolution. This ultimately resulted in the highly diverse group that we see today [5]. Correctly understanding the taxonomic status of species and constructing robust phylogenetic relationships are crucial for tracing the origin and evolution of the Brachyura. In the early stages, Guinot et al. [6] used the location of the male and female reproductive openings (gonopores) of crabs as a basis for classification of species in the Brachyura, and the Brachyura species were divided into three lineages, the Pototremata, the Heterotremata and the Thoracotremata. Under Guinot’s classification system, the Pototremata is divided into the Dromiacea and the Archaeobrachyura. The Heterotremata and the Thoracotremata are collectively referred to as Eubrachyura [7]. However, some other scholars did not use the theory of the Pototremata. Martin and Davis [5] identify the Dromiacea and the Eubrachyura as the two major taxa of the Brachyura. At the same time, Homolodromioidea in Archaeobrachyura was classified into Dromiacea, and Raninoidea and Cyclodorippoidea were placed under the newly created Rainoida in Eubrachyura. The results of the Tsang study showed that Homolodromioidea and Dromiacea have a sister-group relationship, providing support for Homolodromioidea to be classified into Dromiacea [8]. Other studies have shown that Homolodromioidea is more closely related to Raninoidea and Cyclodorippoidea, suggesting that Homolodromioidea should be moved from Dromiacea to the newly created Homoloida [9,10].
With the development of sequencing technology, particularly next-generation sequencing, the time and cost associated with sequencing have significantly decreased, making mitochondrial genome sequences easy to obtain [11]. Currently, mitochondrial genomic analysis is widely used in phylogenetic analysis, biogeography [12,13], population genetics [14], medicine, and ecology [15,16]. Tang et al.’s comparative study of the mitochondrial deoxyribonucleic acid (DNA) of Helice wuana and its relatives provides important evidence in terms of the origin, germline evolution, and the specific genetic structure formation of H. wuana [17]. The mitochondrial genome comprises 37 genes, theoretically possessing great rearrangement potential; however, based on the existing results, genetic rearrangements are infrequent. In conclusion, the same genetic rearrangement among different species is not likely due to convergent evolution but is more likely to predict a certain phylogenetic relationship among species. Therefore, analysing the genetic rearrangement is more suitable for understanding the superior phylogenetic relationship [18,19,20].
Grapsus albolineatus belongs to the genus Grapsus and is classified into Grapsoidea and Grapsidae. G. albolineatus is mainly found in Taiwan and Guangdong (including Hainan Island) in China, Japan, Hawaii, and Australia [21,22]. Herein, we sequenced the complete mitochondrial genome of G. albolineatus and compared it with other species of Brachyura. We inferred phylogenetic trees by analysing the amino acid and nucleotide sequences of 13 PCGs and analysed the genetic rearrangement patterns to understand the phylogenetic positions of G. albolineatus in Brachyura. At the end of the study, we downloaded other mitochondrial genomes of Brachyura crabs to obtain the phylogenetic status of Grapsoidea.
2. Materials and Methods
2.1. Sampling and DNA Extraction
We collected the mature crabs (G. albolineatus) from Xiamen, Fujian Province, China. Before DNA extraction, the specimen was stored in aerated tap water maintained at 21 ± 1 °C for 1 week. We extracted DNA from muscle tissue samples using an Aidlab Genomic DNA Extraction Kit (Aidlab, Beijing, China). The extracted DNA was stored at −20 °C until amplification.
2.2. PCR Amplification and Sequencing
Before amplifying the mitogenome of G. albolineatus, we designed a set of universal primers [17] using the Primer Premier 5.0 software. The primers were synthesised by the Beijing Sunbiotec Company, Beijing, China. We amplified DNA fragments using an Aidlab Extraction Kit per the manufacturer’s instructions. PCR was performed in a 50 μL reaction mixture containing 5 μL of 10× Taq plus Buffer (Mg2+), 4 μL of deoxynucleoside triphosphate, 2 μL of each of the primers, 2 μL of DNA, 34.5 μL of double-distilled water (ddH2O), and 0.5 μL of Taq DNA polymerase RED. The PCR conditions were as follows: 94 °C for 3 min, followed by 35 cycles of 30 s at 90 °C, annealing for 35 s at 49–58 °C (depending on the primer combination), elongation at 72 °C for 0.5–4 min (depending on the fragment length) and the final extension step at 72 °C for 10 min. We used agarose gel electrophoresis (1% w/v) to separate the PCR products and the Aidlab DNA Gel Extraction Kit for purification. Finally, we ligated the purified products into Tvector and sequenced them (Sangon Biotech, Shanghai, China).
2.3. Sequencing and Analysis
We annotated the sequence of G. albolineatus using the BLAST version 2.2.28 search function of the National Centre for Biotechnology Information (NCBI) (https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 12 March 2022)). The mitogenome of G. albolineatus was edited and assembled using the SeqMan software version 7 from the DNASTAR package (DNAStar Inc., Madison, WI, USA) [21]. It was visualised using the online tool OrganellarGenomeDRAW (OGDRAW) (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html (accessed on 12 March 2022)), and the annotated sequence was represented on a graphical map [23]. The tRNAscan-SE webserver was used to predict the cloverleaf secondary structures of 22 tRNAs in G. albolineatus [24]. MEGA X was used to evaluate the relative synonymous codon usage value and nucleotide composition of the mitogenomes [25]. The nucleotide composition skewness was calculated using the following formulas [26]: AT skew = [A − T]/[A + T]; guanine–cytosine (GC) skew = [G − C]/[G + C].
2.4. Phylogenetic Analysis
The whole mitogenomes of 41 Brachyura species, along with their taxonomic status, were retrieved from the NCBI GeneBank. We used the mitogenome of Alpueus distinguendus as an outgroup taxon. The GeneBank ID is listed in Table 1. Subsequently, we used the Multiple Alignment using Fast Fourier Transform (MAFFT) selection for G-INS-i to align the nucleotide and amino acid sequences of 13 PCGs from these species with the invertebrate mitochondrial code [27]. We used Gblocks to identify and remove the unreliable parts of the MAFFT alignment results [28]. The 13 PCG sequences were combined using the Concatenate Sequence function of the PhyloSuite software version 1.2.3 [29]. In addition, we used Bayesian inference (BI) and maximum likelihood (ML) estimation. We selected the best molecular evolution model for the sequences for evolutionary inference using PartitionFinder2 [30]. Finally, we entered the Partitionfinder2 results into MrBayes v3.2 and IQ-TREE [31,32]. The MrBayes software version 3.2 ran for ten million generations with four chains and sampled every 100 generations with a 5000-generation burn-in step. The average standard deviation of the split frequency was <0.01, based on the convergence. The IQ-TREE software version 2 ran with 1000 bootstrapped replicates. The results were assessed using the Tracer v1.6 software. The effective sample size (ESS) value was >200 [33], which revealed that the simultaneous chains in the Markov chain Monte Carlo were convergent. The phylogenetic trees were visualised using the online tool, Interactive Tree Of Life [34].
3. Results and Discussion
3.1. Mitogenome Organisation and Nucleotide Composition
The mitogenome of G. albolineatus is a closed circular molecule in structure with a length of 15,580 bp (Figure 1). Similar to that of other Brachyuran species, the mitogenome of G. albolineatus has 13 PCGs, 22 tRNAs, two rRNAs, and one AT-rich region. A total of 37 genes were observed, of which 14 (trnH, trnF, nad5, nad4, nad4L, trnP, nad1, trnL1, rrnL, tranV, rrnS, trnQ, trnC, and trnY) are transcribed on the light strand and 23 are transcribed on the heavy strand (Table 2). The nucleotide composition (A, 33.4%; T, 34%; C, 19.2%; and G, 11.8%) had a high AT bias. The AT-rich region constituted 67.4% of the total nucleotides. The calculated AT and GC skews were −0.01 and −0.26, respectively. Other listed Brachyuran species had negative GC skew values, and only nine species had a slightly positive AT skew value (Table 3).
3.2. Protein-Coding Genes
As presented in Table 2, the 13 PCGs ranged from 159 bp (atp8) to 1731 bp (nad5) in length. The PCG region in the mitogenome of G. albolineatus was 11,184 bp and composed of 13 genes (nad1–6, nad4L, cox1–3, atp6, atp8, and cytb). Twelve PCGs in G. albolineatus use the ATN codon as the start codon, except for the atp8 gene, which has CTG as the start codon. Furthermore, ten PCGs contain a canonical stop codon (TCG (serine) or TAA (termination)), whereas the stop codons of the genes cox1, cox, and cytb contain only a single T nucleotide (Table 2).
The codon usage of the PCGs is demonstrated in Table 4. The results revealed that the mitogenome of G. albolineatus has 3728 codons. The codon usage of G. albolineatus was skewed towards A or T. Other Brachyura species yielded similar results [35,36]. The relative synonymous codon usage values of G. albolineatus are indicated in Figure 2, which confirmed our results.
3.3. Transfer RNA and Ribosomal RNA Genes and Control Region
The two rRNAs (rrnL and rrnS) of G. albolineatus were 1328 bp and 827 bp in length, respectively. A trnV gene was observed between rrnL and rrnS; this arrangement is shared by other metazoans [37]. The mitogenome of G. albolineatus contains 22 tRNA genes (Figure 3, Table 2), each 64–71 nucleotides long, for a total length of 1480 bp. Furthermore, eight tRNAs (trnH, trnF, trnP, trnL1, tranV, trnQ, trnC, and trnY) were transcribed on the light strand. The cloverleaf structures of the tRNAs predicted by tRNAscan-SE are demonstrated in Figure 3. However, the trns1 gene is an exception, since it has a bigger dihydroxyuridine arm and an extra arm. This finding is consistent with that of other Brachyuran species [38,39,40]. The control region between rrnS and trnI is 616 nucleotides long and contains the mitotic genome replication and transcription initiation site.
3.4. Gene Arrangement
The arrangement of genes in the mitogenome is an effective tool to study phylogenetic relationships [41]. We compared the gene order of the whole mitogenome of G. albolineatus to the Pancrustacean ground pattern (cox1, L2, cox2, K, D, atp8, atp6, cox3, G, nad3, A, R, N, S1, E, F, nad5, H, nad4, nad4L, T, P, nad6, cytb, S2, L1, rrnL, V, rrnS, CR, I, Q, M, nad2, W, C, and Y) [42,43]. Except for the translocation of trnH, the gene sequence was observed to be identical (Figure 4). This phenomenon is not unique to G. albolineatus, as other Brachyuran species also exhibit similar tRNA rearrangements. We obtained eight gene order patterns from the selected Brachyuran species. The gene order of G. albolineatus is identical to that of the other seven families (Figure 4), suggesting a sister-group relationship. As demonstrated in Figure 4, the gene order of 13 PCGs and 2 rRNAs was unchanged, even though the tRNAs were translocated. The observed tRNA rearrangements, particularly the relocation of trnH, could be explained by several mechanisms. One hypothesis is tandem replication of partial mitogenomes followed by the loss of supernumerary genes [43,44,45]. However, this explanation may not fully account for the specific relocation of trnH without affecting other genes. An alternative hypothesis is tRNA remolding, a process in which tRNAs undergo structural and functional changes, potentially leading to their relocation within the mitogenome. tRNA remolding has been documented in metazoan mitochondrial genomes, where tRNAs can acquire new identities or functions through mutations in their anticodon loops or other structural modifications [46,47]. In the case of G. albolineatus, the relocation of trnH could be a result of such remolding events, which may have provided a selective advantage or been neutral in terms of evolutionary fitness. The gene order of G. albolineatus is consistent with that of other Brachyuran species, supporting its placement within the broader phylogenetic framework of Brachyura. However, the unique relocation of trnH raises questions about the evolutionary forces driving such changes. While the lack of recombination in mitochondrial genomes limits the mechanisms by which gene order can be rearranged, tRNA remolding offers a plausible explanation for the observed patterns. Further studies, including comparative analyses of tRNA sequences and structures across Brachyuran species, are needed to test this hypothesis and clarify the evolutionary history of trnH relocation. In contrast to G. albolineatus, the gene order of PCGs and tRNAs in Xenograpsidae species shows significant changes, consistent with previous studies [48,49]. This suggests that different evolutionary pressures or mechanisms may be at play in different Brachyuran lineages. On the other hand, the gene order of Varunidae species (M. longipes, P. subquadrata, and E. sinensis) is identical, supporting their classification within Grapsidae and Varunidae, as previously reported [50,51]. These findings highlight the diversity of mitogenome evolution within Brachyura and underscore the importance of considering both gene order and tRNA remolding in phylogenetic analyses.
3.5. Phylogenetic Analysis
We selected Brachyura species that were highly similar to G. albolineatus using the BLAST function of NCBI. We used both nucleotide and amino acid sequences of 13 PCGs in the 40 Brachyura species, listed in Table 1, to analyse the phylogeny of G. albolineatus. We constructed phylogenetic trees using BI and ML estimation with identical topologies (Figure 5 and Figure 6). G. albolineatus and Pachygrapsus carssipes were clustered in the same branch of the phylogenetic tree and had high nodal support values. Therefore, we hypothesised that they have a sister-group relationship, implying that G. albolineatus belongs to the Grapsidae family, which is consistent with the findings of a previous study [50].
The topologies of the phylogenetic trees were nearly identical to that observed in a previous study [10], particularly in the placement of G. albolineatus within Grapsidae. However, some discrepancies were observed, especially within the Grapsidae superfamily. For instance, the phylogenetic trees based on amino acid and nucleotide sequences showed different topologies in this group, and the nodal support values in certain regions were relatively low. The classification of Grapsidae has historically been complex due to morphological similarities and convergent evolution among species. Molecular data, while powerful, can sometimes yield conflicting results due to incomplete lineage sorting, hybridisation, or rapid diversification events [52]. Recent studies have highlighted the challenges in resolving Grapsidae phylogeny, particularly when using mitochondrial genomes alone [17,38,39]. Differences in evolutionary rates between nucleotide and amino acid sequences can lead to conflicting topologies. Amino acid sequences are generally more conserved, while nucleotide sequences may capture more recent evolutionary changes, leading to discrepancies in tree construction [51,53]. Mitochondrial gene order and tRNA rearrangements have been shown to play a significant role in Brachyuran phylogeny. Studies on Helice latimera and Sesarmops sinensis have demonstrated that gene rearrangements can provide additional phylogenetic signals, but they can also complicate tree reconstruction if not properly accounted for [39,54]. Recent advances in mitogenomic research have provided valuable insights into the phylogeny of Grapsidae and Brachyura. Studies on Helice wuana and Clistocoeloma sinensis have revealed extensive gene rearrangements and tRNA remolding events, which can influence phylogenetic reconstructions [17,43]. The ongoing development of DNA sequencing technologies and bioinformatics tools has revolutionised phylogenetic studies. High-throughput sequencing allows for the rapid generation of mitogenomic data, while advances in computational power enable the analysis of large datasets with complex evolutionary models [51,52]. These advancements will undoubtedly enhance our ability to resolve phylogenetic relationships within Brachyura and other taxa. With the emergence of long-read sequencing, previously unresolved or misclassified regions, such as those labelled as “non-coding” in invertebrates, have been increasingly clarified. This technological constraint may impact the completeness and accuracy of the assembled mitogenome, potentially overlooking critical genomic features [55]. Research on the higher phylogeny of Brachyura has highlighted the importance of integrating multiple data types, including nuclear and mitochondrial genomes, to resolve deep evolutionary relationships [56,57].
4. Conclusions
In this study, we analysed the whole mitogenome of G. albolineatus. Using gene arrangement patterns and phylogenetic analysis, we suggested that G. albolineatus belongs to the Grapsidae family. Meanwhile, using phylogenetic trees based on amino acid and nucleotide sequences, we discovered that the topologies in the Grapsoidea superfamily differed and the nodal support values in the area were low. We believe the classification of the Grapsoidea superfamily was not ideal. With the rapid advancement of the PCR technique, further research on the mitogenome will aid in more accurate classification of crabs.
Author Contributions
Q.L. and B.T. conceived and designed the study. S.T., X.Z. and Y.C. performed the molecular experiments and data analysis. S.T. and X.Z. drafted the manuscript. X.Z., S.T. prepared all figures and tables. X.Z., S.T. and Q.L. performed the phylogenetic analyses. X.Z., S.T., Q.L. and B.T. assisted in the drafting of the manuscript. All authors have read and agreed to the published version of the manuscript.
Funding
This work was funded by the National Natural Science Foundation of China (32270487). The study was sponsored by the Qinglan Project of Jiangsu Province and the “Outstanding Young Talents” of YCTU.
Institutional Review Board Statement
The animal study protocol was approved by the School of Wetlands, Yancheng Teachers University (20200301).
Informed Consent Statement
Not applicable.
Data Availability Statement
The datasets generated for this study can be found in the GenBank accession no. MF198247.
Conflicts of Interest
The authors declare no competing interests.
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Figure 1.
Circular map of the mitogenome of Grapsus albolineatus. Protein-coding and ribosomal genes are presented with standard abbreviations. Transfer RNA (tRNA) genes are shown by single-letter abbreviations, except for S1 = AGN, S2 = UCN, L1 = CUN, and L2 = UUR. The thick lines outside the circle indicate the heavy strand, whereas those inside the circle indicate the light strand.
Figure 1.
Circular map of the mitogenome of Grapsus albolineatus. Protein-coding and ribosomal genes are presented with standard abbreviations. Transfer RNA (tRNA) genes are shown by single-letter abbreviations, except for S1 = AGN, S2 = UCN, L1 = CUN, and L2 = UUR. The thick lines outside the circle indicate the heavy strand, whereas those inside the circle indicate the light strand.
Figure 2.
The relative synonymous codon usage (RSCU) values of the mitogenome of Grapsus albolineatus.
Figure 2.
The relative synonymous codon usage (RSCU) values of the mitogenome of Grapsus albolineatus.
Figure 3.
Putative secondary structure of the transfer RNA (tRNA) genes of the mitogenome of Grapsus albolineatus.
Figure 3.
Putative secondary structure of the transfer RNA (tRNA) genes of the mitogenome of Grapsus albolineatus.
Figure 4.
The gene order patterns of the Brachyuran species used in this study.
Figure 5.
Phylogenetic tree inferred from the nucleotide sequences of 13 protein-coding genes (PCGs) of the mitogenome using Bayesian inference (BI) and maximum likelihood (ML) estimation. The Bayesian posterior probability (BPP) and bootstrap value (BP) of each node are shown as BPP/BP, with maxima of 1.00/100.
Figure 5.
Phylogenetic tree inferred from the nucleotide sequences of 13 protein-coding genes (PCGs) of the mitogenome using Bayesian inference (BI) and maximum likelihood (ML) estimation. The Bayesian posterior probability (BPP) and bootstrap value (BP) of each node are shown as BPP/BP, with maxima of 1.00/100.
Figure 6.
Phylogenetic tree inferred from the amino acid sequences of 13 protein-coding genes (PCGs) of the mitogenome using Bayesian inference (BI) and maximum likelihood (ML) estimation. The Bayesian posterior probability (BPP) and bootstrap value (BP) of each node are shown as BPP/BP, with maxima of 1.00/100.
Figure 6.
Phylogenetic tree inferred from the amino acid sequences of 13 protein-coding genes (PCGs) of the mitogenome using Bayesian inference (BI) and maximum likelihood (ML) estimation. The Bayesian posterior probability (BPP) and bootstrap value (BP) of each node are shown as BPP/BP, with maxima of 1.00/100.
Table 1.
List of the Brachyuran species used in this study.
| Species | Family | Size (bp) | Accession No. |
|---|---|---|---|
| Grapsus albolineatus | Grapsidae | 15,580 | MF198247 |
| Chionoecetes japonicus pacificus | Majidae | 15,341 | AB735678 |
| Scylla serrata | Portunidae | 15,721 | HM590866 |
| Scylla paramamosain | Portunidae | 15,824 | JX457150 |
| Austinograea alayseae | Bythograeidae | 15,611 | KC581803 |
| Umalia orientalis | Raninidae | 15,466 | KM365084 |
| Eriocheir sinensis | Varunidae | 16,350 | KP064329 |
| Gandalfus puia | Bythograeidae | 15,548 | KR002727 |
| Maja crispata | Majidae | 16,592 | KY650651 |
| Maja squinado | Majoidea | 16,598 | KY650652 |
| Xenograpsus ngatama | Xenograpsidae | 16,106 | KY985236 |
| Ashtoret lunaris | Matutidae | 15,807 | LK391941 |
| Mictyris longicarpus | Mictyridae | 15,548 | LN611670 |
| Metaplax longipes | Varunidae | 16,424 | MF198248 |
| Charybdis bimaculata | Portunidae | 15,712 | MG787408 |
| Terrapotamon thungwa | Potamidae | 16,156 | MW697078 |
| Portunus trituberculatus | Portunidae | 16,026 | NC_005037 |
| Callinectes sapidus | Portunidae | 16,263 | NC_006281 |
| Pseudocarcinus gigas | Eriphiidae | 15,515 | NC_006891 |
| Scylla serrata | Portunidae | 15,775 | NC_012565 |
| Scylla tranquebarica | Portunidae | 15,833 | NC_012567 |
| Scylla olivacea | Portunidae | 15,723 | NC_012569 |
| Charybdis japonica | Portunidae | 15,738 | NC_013246 |
| Xenograpsus testudinatus | Xenograpsidae | 15,798 | NC_013480 |
| Gandalfus yunohana | Bythograeidae | 15,567 | NC_013713 |
| Alpheus distinguendus | Alpheidae | 15,700 | NC_014883 |
| Austinograea rodriguezensis | Bythograeidae | 15,611 | NC_020312 |
| Pachygrapsus crassipes | Grapsidae | 15,652 | NC_021754 |
| Ranina ranina | Raninidae | 15,557 | NC_023474 |
| Thalamita crenata | Portunidae | 15,787 | NC_024438 |
| Charybdis feriata | Portunidae | 15,660 | NC_024632 |
| Homologenus malayensis | Homolidae | 15,793 | NC_026080 |
| Portunus pelagicus | Portunidae | 16,157 | NC_026209 |
| Monomia gladiator | Portunidae | 15,878 | NC_037173 |
| Nanosesarma minutum | Sesarmidae | 15,637 | NC_040977 |
| Chiromantes haematocheir | Sesarmidae | 15,899 | NC_042142 |
| Etisus anaglyptus | Xanthidae | 16,435 | NC_042208 |
| Austruca lactea | Ocypodidae | 15,659 | NC_042401 |
| Pseudohelice subquadrata | Varunidae | 16,898 | NC_042685 |
| Ovalipes punctatus | Ovalipidae | 16,084 | NC_042695 |
| Longpotamon depressum | Potamidae | 16,537 | NC_057478 |
Table 2.
Annotation of the complete mitochondrial genome of Grapsus albolineatus.
| Gene | Direction | Location | Size (bp) | Intergenic Nucleotides | Start Codon | Stop Codon |
|---|---|---|---|---|---|---|
| cox1 | F | 1–1534 | 1534 | ATG | T | |
| trnL2 | F | 1535–1599 | 65 | |||
| cox2 | F | 1610–2297 | 688 | ATG | T | |
| trnK | F | 2298–2366 | 69 | |||
| trnD | F | 2367–2430 | 64 | |||
| atp8 | F | 2431–2589 | 159 | GTG | TAA | |
| atp6 | F | 2583–3257 | 675 | −7 | ATT | TAA |
| cox3 | F | 3257–4048 | 792 | −1 | ATG | TAA |
| trnG | F | 4048–4110 | 63 | −1 | ||
| nad3 | F | 4111–4461 | 351 | ATC | TAA | |
| trnA | F | 4460–4523 | 64 | −2 | ||
| trnR | F | 4530–4593 | 64 | |||
| trnN | F | 4595–4659 | 65 | |||
| trnS1 | F | 4664–4730 | 67 | |||
| trnE | F | 4733–4800 | 68 | |||
| trnH | R | 4804–4868 | 65 | |||
| trnF | R | 4873–4937 | 65 | |||
| nad5 | R | 4990–6720 | 1731 | ATG | TAA | |
| nad4 | R | 6765–8102 | 1338 | ATG | TAG | |
| nad4L | R | 8096–8398 | 303 | −7 | ATG | TAA |
| trnT | F | 8413–8478 | 66 | |||
| trnP | R | 8479–8545 | 67 | |||
| nad6 | F | 8548–9051 | 504 | ATT | TAA | |
| cytb | F | 9051–10,185 | 1135 | −1 | ATG | T |
| trnS2 | F | 10,186–10,253 | 68 | |||
| nad1 | R | 10,281–11,246 | 966 | ATT | TAA | |
| trnL1 | R | 11,252–11,318 | 67 | |||
| rrnL | R | 11,319–12,646 | 1328 | |||
| trnV | R | 12,647–12,719 | 73 | |||
| rrnS | R | 12,720–13,546 | 827 | |||
| CR | - | 13,547–14,762 | 616 | |||
| trnI | F | 14,164–14,229 | 67 | |||
| trnQ | R | 14,227–14,297 | 71 | |||
| trnM | F | 14,305–14,375 | 71 | |||
| nad2 | F | 14,376–15,386 | 1011 | ATG | TAG | |
| trnW | F | 15,385–15,453 | 69 | −2 | ||
| trnC | R | 15,453–15,516 | 64 | −1 | ||
| trnY | R | 15,517–15,680 | 64 |
Table 3.
Nucleotide composition and skewness of the mitochondrial genome.
| Species | Size (bp) | A (%) | T (%) | C (%) | G (%) | A + T (%) | A + T Skew | C + G Skew |
|---|---|---|---|---|---|---|---|---|
| G. albolineatus | 15,580 | 33.4 | 34 | 20.5 | 12.1 | 67.4 | −0.01 | −0.26 |
| C. jpacificus | 15,341 | 34.6 | 37 | 17.2 | 11.1 | 71.6 | −0.033 | −0.215 |
| S. serrata | 15,721 | 33.4 | 35.8 | 19.5 | 11.3 | 69.2 | −0.034 | −0.266 |
| S. paramamosain | 15,824 | 34.9 | 38.2 | 16.8 | 10.2 | 73.1 | −0.045 | −0.247 |
| A. alayseae | 15,611 | 34.5 | 32.4 | 21.9 | 11.3 | 66.9 | 0.032 | −0.321 |
| U. orientalis | 15,466 | 33.1 | 34.9 | 20.2 | 11.8 | 68 | −0.027 | −0.262 |
| E. sinensis | 16,350 | 35.3 | 36.4 | 17.6 | 10.7 | 71.7 | −0.015 | −0.245 |
| G. puia | 15,548 | 35.1 | 34.8 | 19.8 | 10.3 | 69.9 | 0.006 | −0.313 |
| M. crispata | 16,592 | 33.6 | 36.7 | 18.6 | 11.1 | 70.3 | −0.044 | −0.25 |
| M. squinado | 16,598 | 33.7 | 37.1 | 18.2 | 11 | 70.8 | −0.047 | −0.245 |
| X. ngatama | 16,106 | 36.1 | 36.8 | 17.5 | 9.6 | 72.9 | −0.01 | −0.293 |
| A. lunaris | 15,807 | 34.8 | 35.4 | 18.7 | 11.1 | 70.2 | −0.009 | −0.256 |
| M. longicarpus | 15,548 | 32.4 | 36.6 | 19.2 | 11.8 | 69 | −0.06 | −0.236 |
| M. longipes | 16,424 | 37.5 | 34.2 | 18 | 10.4 | 71.7 | 0.046 | −0.266 |
| C. bimaculata | 15,712 | 33.9 | 37.6 | 16.9 | 11.5 | 71.5 | −0.052 | −0.192 |
| T. thungwa | 16,156 | 37.2 | 36 | 9.1 | 17.6 | 73.2 | 0.017 | 0.318 |
| P. trituberculatus | 16,026 | 33.3 | 36.9 | 18.5 | 11.3 | 70.2 | −0.051 | −0.241 |
| C. sapidus | 16,263 | 34.2 | 34.9 | 19.8 | 11.1 | 69.1 | −0.011 | −0.279 |
| P. gigas | 15,515 | 35 | 35.5 | 18.7 | 10.8 | 70.5 | −0.006 | −0.268 |
| S. serrata | 15,775 | 34.6 | 38 | 17.1 | 10.4 | 72.6 | −0.047 | −0.242 |
| S. tranquebarica | 15,833 | 35 | 38.7 | 16.5 | 9.7 | 73.7 | −0.05 | −0.258 |
| S. olivacea | 15,723 | 33.5 | 35.9 | 19.4 | 11.2 | 69.4 | −0.035 | −0.267 |
| C. japonica | 15,738 | 33.8 | 35.4 | 18.9 | 11.9 | 69.2 | −0.024 | −0.228 |
| X. testudinatus | 15,798 | 36.7 | 37.2 | 16.8 | 9.3 | 73.9 | −0.007 | −0.286 |
| G. yunohana | 15,567 | 34.3 | 35.7 | 19.3 | 10.8 | 70 | −0.019 | −0.281 |
| A. distinguendus | 15,700 | 32.3 | 27.9 | 25.5 | 14.4 | 60.2 | 0.073 | −0.278 |
| A. rodriguezensis | 15,611 | 35.3 | 33.5 | 20.9 | 10.3 | 68.8 | 0.025 | −0.341 |
| P. crassipes | 15,652 | 30.5 | 35.8 | 21 | 12.7 | 66.3 | −0.08 | −0.245 |
| R. ranina | 15,557 | 30.3 | 36.3 | 21.1 | 12.2 | 66.6 | −0.09 | −0.266 |
| T. crenata | 15,787 | 34.4 | 35.3 | 18.8 | 11.5 | 69.7 | −0.013 | −0.24 |
| C. feriata | 15,660 | 34.1 | 36.1 | 18.6 | 11.3 | 70.2 | −0.028 | −0.246 |
| H. malayensis | 15,793 | 37.3 | 34.4 | 18.3 | 10 | 71.7 | 0.04 | −0.292 |
| P. pelagicus | 16,157 | 33.7 | 35 | 19.1 | 12.2 | 68.7 | −0.019 | −0.219 |
| M. gladiator | 15,878 | 33.3 | 35.7 | 19.2 | 11.8 | 69 | −0.034 | −0.242 |
| N. minutum | 15,637 | 38 | 39.7 | 13.4 | 8.9 | 77.7 | −0.022 | −0.201 |
| C. haematocheir | 15,899 | 37.3 | 38.3 | 15 | 9.4 | 75.6 | −0.013 | −0.226 |
| E. anaglyptus | 16,435 | 33.2 | 34.8 | 21 | 11.1 | 68 | −0.023 | −0.309 |
| A. lactea | 15,659 | 34.8 | 34.6 | 18.5 | 12 | 69.4 | 0.003 | −0.214 |
| P. subquadrata | 16,898 | 34.2 | 33.5 | 21.7 | 10.5 | 67.7 | 0.01 | −0.347 |
| O. punctatus | 16,084 | 32.6 | 35.5 | 19.4 | 12.5 | 68.1 | −0.042 | −0.218 |
| L. depressum | 16,537 | 35.4 | 37.9 | 17.3 | 9.3 | 73.3 | −0.034 | −0.302 |
Table 4.
Codon number and relative synonymous codon usage (RSCU) in Grapsus albolineatus. * represents the termination codon.
Table 4.
Codon number and relative synonymous codon usage (RSCU) in Grapsus albolineatus. * represents the termination codon.
| Codon | Count | RSCU | Codon | Count | RSCU | Codon | Count | RSCU | Codon | Count | RSCU |
|---|---|---|---|---|---|---|---|---|---|---|---|
| UUU (F) | 233 | 1.43 | UCU (S) | 108 | 2.26 | UAU (Y) | 87 | 1.25 | UGU (C) | 25 | 1.61 |
| UUC (F) | 93 | 0.57 | UCC (S) | 37 | 0.77 | UAC (Y) | 52 | 0.75 | UGC (C) | 6 | 0.39 |
| UUA (L) | 229 | 2.42 | UCA (S) | 69 | 1.44 | UAA (*) | 8 | 1.6 | UGA (W) | 71 | 1.45 |
| UUG (L) | 80 | 0.85 | UCG (S) | 15 | 0.31 | UAG (*) | 2 | 0.4 | UGG (W) | 27 | 0.55 |
| CUU (L) | 102 | 1.08 | CCU (P) | 67 | 1.82 | CAU (H) | 45 | 1.08 | CGU (R) | 15 | 1.07 |
| CUC (L) | 36 | 0.38 | CCC (P) | 27 | 0.73 | CAC (H) | 38 | 0.92 | CGC (R) | 5 | 0.36 |
| CUA (L) | 96 | 1.01 | CCA (P) | 44 | 1.2 | CAA (Q) | 48 | 1.41 | CGA (R) | 29 | 2.07 |
| CUG (L) | 25 | 0.26 | CCG (P) | 9 | 0.24 | CAG (Q) | 20 | 0.59 | CGG (R) | 7 | 0.5 |
| AUU (I) | 201 | 1.32 | ACU (T) | 93 | 1.84 | AAU (N) | 76 | 1.2 | AGU (S) | 42 | 0.88 |
| AUC (I) | 103 | 0.68 | ACC (T) | 28 | 0.55 | AAC (N) | 51 | 0.8 | AGC (S) | 10 | 0.21 |
| AUA (M) | 163 | 1.5 | ACA (T) | 73 | 1.45 | AAA (K) | 67 | 1.51 | AGA (S) | 68 | 1.42 |
| AUG (M) | 54 | 0.5 | ACG (T) | 8 | 0.16 | AAG (K) | 22 | 0.49 | AGG (S) | 34 | 0.71 |
| GUU (V) | 107 | 1.57 | GCU (A) | 101 | 1.82 | GAU (D) | 44 | 1.19 | GGU (G) | 51 | 0.88 |
| GUC (V) | 17 | 0.25 | GCC (A) | 46 | 0.83 | GAC (D) | 30 | 0.81 | GGC (G) | 33 | 0.57 |
| GUA (V) | 116 | 1.7 | GCA (A) | 63 | 1.14 | GAA (E) | 53 | 1.36 | GGA (G) | 95 | 1.63 |
| GUG (V) | 33 | 0.48 | GCG (A) | 12 | 0.22 | GAG (E) | 25 | 0.64 | GGG (G) | 54 | 0.93 |
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Zhang, X.; Tang, S.; Chen, Y.; Liu, Q.; Tang, B. Mitochondrial Genome of Grapsus albolineatus and Insights into the Phylogeny of Brachyura. Animals 2025, 15, 679. https://doi.org/10.3390/ani15050679
AMA Style
Zhang X, Tang S, Chen Y, Liu Q, Tang B. Mitochondrial Genome of Grapsus albolineatus and Insights into the Phylogeny of Brachyura. Animals. 2025; 15(5):679. https://doi.org/10.3390/ani15050679
Chicago/Turabian StyleZhang, Xue, Sheng Tang, Yaohui Chen, Qiuning Liu, and Boping Tang. 2025. "Mitochondrial Genome of Grapsus albolineatus and Insights into the Phylogeny of Brachyura" Animals 15, no. 5: 679. https://doi.org/10.3390/ani15050679
APA StyleZhang, X., Tang, S., Chen, Y., Liu, Q., & Tang, B. (2025). Mitochondrial Genome of Grapsus albolineatus and Insights into the Phylogeny of Brachyura. Animals, 15(5), 679. https://doi.org/10.3390/ani15050679
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