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

Conrad, Isabelle; Craft, Abby; Thurman, Carl L.; Baeza, Juán Antonio

doi:10.1016/j.ygeno.2020.09.050

Cited by 11 publications

(7 citation statements)

References 35 publications

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“…Selective pressure in PCGs has not been studied before in any other crab belonging to the family Sesarmidae. However, a strong pattern of purifying selection has been reported for many other brachyuran crabs, crustaceans, and arthropods in general ([ 34 ] and references therein). A recent study of caridean shrimps (genus Synalpheus ) found a relationship between PCG length and the strength of purifying selection, with short genes (e.g., atp8 ) being subject to weaker purifying selection than longer PCGs [ 55 ].…”

Section: Resultsmentioning

confidence: 99%

“…A detailed characterization of the CR is not available for any other sesarmid crab. However, the presence of SSRs, tandem repeats, and numerous hairpin secondary structures are often observed in the CR of other brachyuran crabs as well as other closely or more distantly related decapod crustaceans (e.g., [ 34 ] and references therein).…”

Section: Resultsmentioning

confidence: 99%

“…Negative or purifying selection is indicated by values ω < 1, whereas positive or diversifying selection is denoted by values ω > 1. The γ-MYN model was used to account for variable mutation rates along each sequence during calculations [ 34 ].…”

Section: Methodsmentioning

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: 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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“…Selective pressure on the PCG’s was examined by comparing rates of nonsynonymous and synonymous substitutions. The values of K A (number of nonsynonymous substitutions per nonsynonymous site: K A = d N = S A /L A ), K S (number of synonymous substitutions per synonymous site: K S = d S = S S /L S ), and ω (K A /K S ) were found for each PCG using the KaKs_calculator 2.0 ( Wang et al, 2009 ; Wang et al, 2010 ; Conrad et al, 2021 ). The estimated ω values were based on a comparison between T. bairdii and its closely related species, T. indicus ( KJ417810 ).…”

Section: Methodsmentioning

confidence: 99%

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

Ennis

Ortega

Baeza

2022

PeerJ

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Baird’s tapir, or the Central American Tapir Tapirus bairdii (family Tapiridae), is one of the largest mammals native to the forests and wetlands of southern North America and Central America, and is categorized as ‘endangered’ on the 2014 IUCN Red List of Threatened Species. This study reports, for the first time, the complete mitochondrial genome of T. bairdii and examines the phylogenetic position of T. bairdii amongst closely related species in the same family and order to which it belongs using mitochondrial protein-coding genes (PCG’s). The circular, double-stranded, A-T rich mitochondrial genome of T. bairdii is 16,697 bp in length consisting of 13 protein-coding genes (PCG’s), two ribosomal RNA genes (rrnS (12s ribosomal RNA and rrnL (16s ribosomal RNA)), and 22 transfer RNA (tRNA) genes. A 33 bp long region was identified to be the origin of replication for the light strand (OL), and a 1,247 bp long control region (CR) contains the origin of replication for the heavy strand (OH). A majority of the PCG’s and tRNA genes are encoded on the positive, or heavy, strand. The gene order in T. baiirdi is identical to that of T. indicus and T. terrestris, the only two other species of extant tapirs with assembled mitochondrial genomes. An analysis of Ka/Ks ratios for all the PCG’s show values <1, suggesting that all these PCGs experience strong purifying selection. A maximum-likelihood phylogenetic analysis supports the monophyly of the genus Tapirus and the order Perissodactyla. The complete annotation and analysis of the mitochondrial genome of T. bairdii will contribute to a better understanding of the population genomic diversity and structure of this species, and it will assist in the conservation and protection of its dwindling populations.

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“…Selective pressures in mitochondrial PCGs still remains poorly studied within decapod crustaceans. However, within arthropods, including the few crustaceans in which selective pressures has been examined (Baeza, 2018;Conrad et al, 2020;Chak et al, 2020), widespread purifying selection in mitochondrial PCGs has been observed (Li et al, 2016 and references therein).…”

Section: Resultsmentioning

confidence: 99%

Characterization of the complete mitochondrial genome of the Atlantic seabob shrimpXiphopenaeus kroyeriHeller, 1862 (Decapoda: Dendrobranchiata: Penaeidae), with insights into the phylogeny of Penaeidae

Cronin

Conrad

Kerkhove

et al. 2022

Journal of Crustacean Biology

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The Atlantic seabob shrimp, Xiphopenaeus kroyeri (Heller, 1862) (Penaeidae), is commonly found on western Atlantic coasts and of high commercial importance in Brazil, Suriname, and Guyana. Current genetic resources on X. kroyeri are scarce and no genomic studies are available. This study reports the complete mitochondrial genome of X. kroyeri. Using the pipeline NOVOPlasty, we assembled and circularized the complete mitochondrial genome of X. kroyeri with an average coverage of 68x per nucleotide. The AT-rich mitochondrial genome of X. kroyeri is 15,999 bp in length and comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 1,030 bp long intergenic space is assumed to be the D-loop/Control region (CR). Selective pressure analysis indicated that the PCGs were under purifying selection. The KA/KS ratios observed for cox1, cox2, atp6, cox3, and cob were found to be much lower than the ratios observed in the other PCGs, suggesting strong purifying selection upon the former genes. The secondary structures of the tRNA genes exhibited a standard ‘cloverleaf’ structure, with the exception of trnS1. A maximum likelihood phylogenetic analysis based on all PCGs indicated that X. kroyeri is more closely related to penaeids (Penaeidae) belonging to the genera TrachypenaeusAlcock, 1901, PenaeopsisSpence Bate, 1881, and MierspenaeopsisK. Sakai & Shinomiya, 2011. This study contributes new genomic resources for this commercially important species which may aid in distinguishing cryptic species and elucidating phylogeographic patterns.

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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

Cited by 11 publications

References 35 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)

First genomic resource for an endangered neotropical mega-herbivore: the complete mitochondrial genome of the forest-dweller (Baird’s) tapir (Tapirus bairdii)

Characterization of the complete mitochondrial genome of the Atlantic seabob shrimpXiphopenaeus kroyeriHeller, 1862 (Decapoda: Dendrobranchiata: Penaeidae), with insights into the phylogeny of Penaeidae

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