The complete mitochondrial genome of Africa's largest freshwater copepod, <i>Lovenula raynerae</i>

Jooste, Candice M.; Emami‐Khoyi, Arsalan; Gan, Han Ming; Wasserman, Ryan J.; Dalu, Tatenda; Teske, Peter R.

doi:10.1080/23802359.2018.1555013

Cited by 5 publications

(10 citation statements)

References 15 publications

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“…Due to its large size and abundance, it has a strong effect on phytoplankton and it therefore plays an important role in tropical freshwater food webs. Complete mitochondrial genome data of such keystone species provide useful information for understanding its own phylogeny and the ecology of the order Calanoida (Jooste et al 2019). Here, we sequence and annotate the mitochondrial genome of P. tunguidus and compare it to that of other copepods.…”

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confidence: 99%

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The mitochondrial genome of Phyllodiaptomus tunguidus Shen & Tai, 1964 (Copepoda, Calanoida) and its phylogeny

Zhang

Liu

et al. 2020

Mitochondrial DNA Part B

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The mitochondrial genome of Phyllodiaptomus diaptomus was sequenced and assembled via Next-Generation Sequencing (NGS) and iterative assembly with a reference seed. The genome is 16446 bp long, A þ T biased (69.4%), with 13 protein-coding genes, 22 tRNAs, and 2 rRNA. All protein-coding genes are initiated by a typical "ATN" codon. ND1, ND2, ATP6 genes are terminated with "TAG", the other 10 genes are terminated with "TAA". This is the first complete mitogenome published in the Diaptomidae. It provides molecular information useful to a better understanding of the phylogeny of calanoids.

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confidence: 99%

“…Complete mitochondrial genome data of such keystone species provide useful information for understanding its own phylogeny and the ecology of the order Calanoida (Jooste et al. 2019 ). Here, we sequence and annotate the mitochondrial genome of P. tunguidus and compare it to that of other copepods.…”

mentioning

confidence: 99%

The mitochondrial genome of Phyllodiaptomus tunguidus Shen & Tai, 1964 (Copepoda, Calanoida) and its phylogeny

Zhang

Liu

et al. 2020

Mitochondrial DNA Part B

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“…In conclusion, while the generation of mitogenomic data for seahorses can be expected to clarify taxonomic relationships between problematic species, it is important that such resources are compared with as many previously generated sequences as possible prior to publication. In this particular case, the fact that the phylogenetic trees presented in mitogenome announcements typically only include previously published complete mitogenomes (Jooste et al 2019), to the exclusion of shorter fragments from more closely related species, prevented the discovery of the misidentification of the specimen on which the problematic H. capensis mitogenome was based. Moreoever, while the incorporation of genetic data into the species description of H. casscsio is commendable, the fact that the new species was only compared with Chinese seahorses, while published data from more closely related species were ignored, likely resulted in nothing more than the description of yet another synonym.…”

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Mitogenome reconstruction of an endangered African seahorse from a Traditional Chinese Medicine market was based on a misidentification

Teske

2020

Preprint

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The recently published complete mitochondrial genome of the endangered Knysna seahorse, Hippocampus capensis Boulenger, 1900, was based on a specimen obtained from a Traditional Chinese Medicine market. As H. capensis is endemic to temperate South Africa and exceptionally rare, illegal trade to supply Asian markets would constitute a considerable extinction risk. I investigated the phylogenetic placement of the Chinese specimen using mitochondrial DNA control region and cytochrome b sequences from the H. capensis mitogenome among corresponding published sequences of H. capensis and a number of closely related seahorse species. The Chinese specimen was distinct from H. capensis and instead clustered with H. casscsio, a seahorse that was recently described from the South China Sea. The sequences of H. casscsio clustered randomly among those of specimens identified as H. fuscus, a species whose taxonomic validity is disputed, and which is considered to be a synonym of the widespread Indo-Pacific seahorse H. kuda. Given that the morphological identification of seahorses is difficult, it is recommended that the publication of new species descriptions and genomic resources be preceded by a comprehensive comparison with the available molecular data. The taxonomy of seahorses is far from resolved, and cutting-edge molecular studies will not improve this situation if they do not take existing information into consideration.

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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.…”

Section: Introductionmentioning

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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The complete mitochondrial genome of Africa's largest freshwater copepod, Lovenula raynerae

Cited by 5 publications

References 15 publications

The mitochondrial genome of Phyllodiaptomus tunguidus Shen & Tai, 1964 (Copepoda, Calanoida) and its phylogeny

The mitochondrial genome of Phyllodiaptomus tunguidus Shen & Tai, 1964 (Copepoda, Calanoida) and its phylogeny

Mitogenome reconstruction of an endangered African seahorse from a Traditional Chinese Medicine market was based on a misidentification

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

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