The complete mitogenome of <i>Leptestheria brevirostris</i> Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana

Emami‐Khoyi, Arsalan; Tladi, Murphy; Dalu, Tatenda; Teske, Peter R.; Vuuren, Bettine Jansen van; Rogers, D. Christopher; Nyamukondiwa, Casper; Wasserman, Ryan J.

doi:10.1080/23802359.2021.1875898

Cited by 6 publications

(3 citation statements)

References 12 publications

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“…cafer ; Table S6: Nucleotide identity (%) and number of codon substitutions for each PCG of three B. kugenumaensis mtgenomes. The references [ 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ] are cited in the Supplementary Materials.…”

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confidence: 99%

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Sun

Cheng

2022

Genes

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Thamnocephalidae, a family of Anostraca which is widely distributed on all continents of the world except Antarctica, currently consists of six genera and approximately 63 recognized species. The relationships among genera in Thamnocephalidae and the monophyly of Thamnocephalidae, determined using morphological characteristics or gene markers, remain controversial. In order to address the relationships within Thamnocephalidae, we sequenced Branchinella kugenumaensis mitogenomes and conducted a comparative analysis to reveal the divergence across mitogenomes of B. kugenumaensis. Using newly obtained mitogenomes together with available Anostracan genomic sequences, we present the most complete phylogenomic understanding of Anostraca to date. We observed high divergence across mitogenomes of B. kugenumaensis. Meanwhile, phylogenetic analyses based on both amino acids and nucleotides of the protein-coding genes (PCG) provide significant support for a non-monophyletic Thamnocephalidae within Anostraca, with Asian Branchinella more closely related to Streptocephalidae than Australian Branchinella. The phylogenetic relationships within Anostraca were recovered as follows: Branchinectidae + Chirocephalidae as the basal group of Anostraca and halophilic Artemiidae as a sister to the clade Thamnocephalidae + Streptocephalidae. Both Bayesian inference (BI)- and maximum likelihood (ML)-based analyses produced identical topologies.

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confidence: 99%

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Sun

Cheng

2022

Genes

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“…For example, the journal Mitochondrial DNA prefers such trees to be constructed using readily alignable proteome sequences, to the exclusion of previously published data from single genetic markers. In taxonomic groups for which few organelle genomes have been published, this has unavoidably resulted in the publication of phylogenies that do not include any congeners of the study species (Jooste et al 2019;Jagatap et al 2019;Tladi et al 2020;Emami-Khoyi et al 2021). However, even in comparatively well studied taxonomic groups, there is an inherent risk that the organelle genome of a species that was misidentified appears to cluster correctly because its sister species are missing from the phylogeny.…”

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confidence: 99%

Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors

Teske

2021

Conservation Genet Resour

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The reconstruction of complete mitochondrial genomes (mitogenomes) has considerable potential to clarify species relationships in cases where morphological analysis and DNA sequencing of individual genes are inconclusive. However, the trend to use only mitogenomes for the phylogenies presented in mitogenome announcements carries the inherent risk that the study species’ taxonomy is incorrect because no mitogenomes have yet been reconstructed for its sister species. Here, I illustrate this problem using the mitogenomes of two seahorses, Hippocampus capensis and H. queenslandicus. Both specimens used for mitogenome reconstruction originated from traditional Chinese medicine markets rather than native habitats. Although mitogenome phylogenies placed these specimens correctly among the seahorses from which mitogenomes were available at the time, incorporating single-marker sequence from closely related species into the phylogenies revealed that both mitogenomes are problematic. The mitogenome of the endemic South African H. capensis did not cluster among single-marker DNA sequences of seahorses from the species’ native habitat, but among sequences submitted under the names H. casscsio, H. fuscus and H. kuda that originated from all over the Indo-Pacific, including China. Phylogenetic placement of the mitogenome of H. queenslandicus within a cluster of seahorses that also included H. spinosissimus confirms an earlier finding that H. queenslandicus is a synonym of H. spinosissimus, a widespread Indo-Pacific species that also occurs in China. It is recommended that mitogenome announcements incorporate available single-marker sequences of closely related species, not only mitogenomes. The reconstruction of mitogenomes can exacerbate taxonomic confusion if existing information is ignored.

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“… 2020 ; Emami-Khoyi et al. 2021 ; Sun and He 2021 ). Two rRNA genes, 12SrRNA (827 bp) and 16SrRNA (1402 bp) are separated by a trnV-GTA.…”

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Complete mitogenome and phylogenetic analysis of the tropical rocky shore crabGrapsus albolineatus(Lamarck, 1818) (Crustacea: Grapsoidea)

Wang

Chen

et al. 2022

Mitochondrial DNA Part B

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In this study, the complete mitogenome of Grapsus albolineatus (Lamarck, 1818) (Crustacea: Grapsoidea) was sequenced. The mitogenome of G. albolineatus was a circular molecule with 15,578 bp length. Its nucleotide composition was 26.81% A, 16.37% G, 34.51% T, and 22.31% C. It comprised 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA). All PCGs were initiated by ATN codons, except for the atp8 and nad1 genes. Ten PCGs used a common stop codon of TAA or TAG, and the other three ended with a truncated stop codon (a single stop nucleotide T). Phylogenetic analysis revealed that G. albolineatus was closely related to species from the genera Pachygrapsus and Metopograpsus .

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The complete mitogenome of Leptestheria brevirostris Barnard, 1924, a rock pool clam shrimp (Branchiopoda: Spinicaudata) from Central District, Botswana

Cited by 6 publications

References 12 publications

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors

Complete mitogenome and phylogenetic analysis of the tropical rocky shore crabGrapsus albolineatus(Lamarck, 1818) (Crustacea: Grapsoidea)

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