Gene Arrangement and Adaptive Evolution in the Mitochondrial Genomes of Terrestrial Sesarmid Crabs Geosesarma faustum and Geosesarma penangensis

Lau, Nyok-Sean; Sam, Ka-Kei; Ahmad, Amirrudin; Siti, K. Daud; Zafir, Abdul Wahab Ahmad; Shu‐Chien, Alexander Chong

doi:10.3389/fevo.2021.778570

Cited by 4 publications

(10 citation statements)

References 41 publications

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“…Most of the PCGs and tRNA genes are encoded on the L-strand, whereas only four PCGs ( nad5 , nad4 , nad4l , and nad1 ), the two ribosomal RNA genes, and eight tRNA genes (trnH, trnF, trnP, trnL2, trnQ, trnV, trnC, and trnY) are encoded in the H-strand ( Table 1 ) ( Figure 1 ). Gene order and strand arrangement in M. depressus is identical to that reported before in all co-familiar species (except G. penangense [ 46 ]) with mitochondrial genomes deposited in GenBank (i.e., O. neglectum, O. sinense, P. bidens, and P. tripectinis , among others [ 47 , 48 , 49 , 50 ]). In contrast to the gene arrangement observed in all sesarmid crabs, with a trnQ - trnI - trnM , G. penangense exhibits a trnI - trnQ - trnM gene arrangement [ 46 ].…”

Section: Resultssupporting

confidence: 75%

“…Gene order and strand arrangement in M. depressus is identical to that reported before in all co-familiar species (except G. penangense [ 46 ]) with mitochondrial genomes deposited in GenBank (i.e., O. neglectum, O. sinense, P. bidens, and P. tripectinis , among others [ 47 , 48 , 49 , 50 ]). In contrast to the gene arrangement observed in all sesarmid crabs, with a trnQ - trnI - trnM , G. penangense exhibits a trnI - trnQ - trnM gene arrangement [ 46 ]. Compared to other decapod infraorders, brachyuran crabs (infraorder Brachyura) contain a translocation of the trnH gene between the trnE and trnF genes, rather than between the nad5 and nad4 genes [ 5 ].…”

Section: Resultssupporting

confidence: 75%

“…In addition to M. depressus , codons for Met are frequently used in P. pictum [ 6 ]. All the codons coding for the aforementioned amino acids are AT-rich, in line with the observed overrepresentation of A and T nucleotides in the mitogenome of M. depressus and other co-familiar crabs [ 5 , 46 ].…”

Section: Resultsmentioning

confidence: 72%

“…This nucleotide usage is within the range reported for other sesarmid crab species ( Supplementary Table S1 ). The highest AT-content value has been reported for Geosesarma penangense (78.44%) [ 46 ], whereas the lowest reported AT-content value belongs to Parasesarma tripectinis (74.22%) [ 50 ]. AT-skewed mitochondrial genomes are often reported across metazoan clades, including crustaceans and brachyuran crabs [ 48 , 52 , 53 ].…”

Section: Resultsmentioning

confidence: 99%

“…The trnS1 gene exhibited a deletion of the dihydroxyuridine (DHU) arm, having only its loop. Other co-familiar crabs, including O. sinense , P. pictum , P. affine , P. bidens , G. faustum , G. penangense , C. sinense , and C. haematocheir , presented the same deletion of the DHU arm in the trnS1 gene [ 5 , 6 , 46 , 48 , 49 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 ], with the exception of O. neglectum [ 47 ], in which all tRNAs exhibited the typical cloverleaf secondary structure. A truncated trnS1 gene represents a conserved mitochondrial feature in eumetazoans, including crabs and other decapod crustaceans [ 6 , 49 , 56 ].…”

Section: Resultsmentioning

confidence: 99%

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Characterization of the Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae)

Rodriguez-Pilco

Lesný

Podsiadłowski

et al. 2022

Genes

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Metopaulias depressus is a non-marine crab endemic to Jamaica that dwells in rainforest bromeliads and exhibits elaborate active parental care behavior. Current genomic resources on M. depressus are rare, limiting the understanding of its adaptation to terrestrial life in species that evolved from marine ancestors. This study reports the complete mitochondrial genome of M. depressus assembled using Sanger sequencing. The AT-rich mitochondrial genome of M. depressus is 15,765 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 691 bp-long intergenic space is assumed to be the control region (CR) or D-loop. A set of selective pressure analyses indicate that the entirety of the PCGs experience purifying selection. Cox1, cox2, nad5, cox3, and atp6 experience strong purifying selection, and atp8 experiences weak purifying selection compared to the rest of the PCGs. The secondary structures of most tRNA genes exhibit a standard ‘cloverleaf’ structure, with the exception of trnS1, which lacks the dihydroxyuridine (DHU) arm but not the loop, the trnH gene, which lacks the thymine pseudouracil cytosine (T) loop but not the arm, and trnM, which exhibits an overly developed T loop. A maximum likelihood phylogenetic analysis based on all PCGs indicated that M. depressus is more closely related to the genera Clistocoeloma, Nanosesarma, and Parasesarma than to Chiromantes, Cristarma, Geosesarma, and Orisarma. This study contributes to deciphering the phylogenetic relationships within the family Sesarmidae and represents a new genomic resource for this iconic crab species.

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Section: Resultssupporting

confidence: 75%

Section: Resultssupporting

confidence: 75%

Section: Resultsmentioning

confidence: 72%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Characterization of the Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae)

Rodriguez-Pilco

Lesný

Podsiadłowski

et al. 2022

Genes

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Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

Wolfe

Ballou

Luque

et al. 2022

Preprint

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For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 species spanning 88 of 104 families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least five and up to 15 times convergently, and returned to the sea from non-marine environments three or four times. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and newly compiled fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

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Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon

Zhang,

Tian

et al. 2024

Animals

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As indicator organisms for water pollution detection, Pseudogasteromyzon species play a vital role in aquatic environment monitoring. We have successfully sequenced the mitogenomes of P. fasciatus jiulongjiangensis and P. myersi and downloaded the mitogenomes of nine other Pseudogastromyzon fish on GenBank to conduct a detailed comparative analysis of their phylogenetic relationships and evolutionary history. The findings revealed a conservation in both gene composition and gene order. Except for the trnS1 gene lacking dihydrouracil arms, the other 21 tRNAs showed the typical clover-leaf secondary structure. According to the ΔRSCU method, we identified the seven most abundant optimal codons: CUA, GUA, CCA, CAA, GAA, AGC, and GGC. The construction of maximum parsimony, maximum likelihood, and Bayes trees yielded congruent topologies, and the 11 Pseudogastromyzon species were clustered into two major clusters. Among them, one of which was composed of P. fangi, P. changtingensis changtingensis, and P. changtingensis tungpeiensis, while the remaining eight species formed another cluster, further subdivided into five smaller clusters. Distinct clusters formed between P. fasciatus jiulongjiangensis and P. meihuashanensis, P. cheni and P. peristictus, and P. laticeps and P. lianjiangensis, and the remaining two species were clustered separately, thereby enhancing our understanding of them. Furthermore, our analysis results of divergence times revealed that these 11 Pseudogasteromyzon species underwent rapid differentiation in the Pleistocene epochs. Overall, our study sheds light on the phylogenetic relationship and evolutionary history of Pseudogasteromyzon species, providing a necessary knowledge foundation for further understanding the intricacies of an ecosystem health assessment.

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Gene Arrangement and Adaptive Evolution in the Mitochondrial Genomes of Terrestrial Sesarmid Crabs Geosesarma faustum and Geosesarma penangensis

Cited by 4 publications

References 41 publications

Characterization of the Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae)

Characterization of the Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae)

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon

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