Mind the<i>numt</i>: Finding informative mitochondrial markers in a giant grasshopper genome

Pereira, Ricardo José Garcia; Ruiz‐Ruano, Francisco J.; Thomas, Callum J. E.; Pérez-Ruiz, Mar; Jiménez‐Bartolomé, Miguel; Liu, Shanlin; Torre, J. de la; Bella, José L.

doi:10.1111/jzs.12446

Cited by 16 publications

(12 citation statements)

References 68 publications

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“…Similarly, the finding of COI-like sequences was not surprising, since they are increasingly reported in major clades characterized by large genomes, which contain a high frequency of nuclear pseudogenes originating from the mitochondrial genome (nuclear DNA of mitochondrial origin, nuMTs). In some crustaceans, the COI gene, typically used in DNA barcoding, was found in disproportionally higher diversity and coverage in the nuclear DNA than the rest of the mitogenome, consistent with multiple insertions of that region into the nuclear genome [ 54 ]. In the future, different markers (less likely to be duplicated as nuMTs) or species-specific primers should be used to further characterize Tremoctopus specimens from Sardinia, in order to additionally check for the genetic variability of T. violaceus within the Mediterranean Basin.…”

Section: Discussionmentioning

confidence: 99%

First Integrative Morphological and Genetic Characterization of Tremoctopus violaceussensu stricto in the Mediterranean Sea

Agus

Carbonara

Melis

et al. 2021

Animals

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An integrative approach based on morphological and genetic analyses was undertaken for the first time to confirm the species identification of Mediterranean samples belonging to the genus Tremoctopus. Sequences of two mtDNA genes (cytochrome c oxidase subunit (COI) and 16S) were generated for the first time from Mediterranean samples. Both the similarity-based identifications and tree-based methods indicated that three females can be identified as Tremoctopus violaceus sensu stricto in agreement with their morphological classifications. All Mediterranean sequences clustered with the sequences of Tremoctopus violaceus from the Gulf of Mexico and were clearly differentiated from the sequences attributed to T. gracilis and T. robsoni. The chromatic pattern of the web and some features of gill filaments, arms formula, stylets, radulae, beaks, and stomach contents were given for all the samples; 105,758, 20,140, and 11,237 oocytes were estimated in the mature, immature, and developing samples, respectively. The presence of four spermatangia inside the cavity of the maturing female suggested the ability of this species to mate before reaching full maturity with more partners. Age investigation using beaks, performed for the first time in T. violaceus and within the genus gave results consistent with the different sizes and maturity conditions of the samples.

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Section: Discussionmentioning

confidence: 99%

First Integrative Morphological and Genetic Characterization of Tremoctopus violaceussensu stricto in the Mediterranean Sea

Agus

Carbonara

Melis

et al. 2021

Animals

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“…Among the 668 HC species, 126 lacked COI NUMTs (≥ 100 bp), but the others averaged 15.6 with counts ranging from 1 to 443. Pereira et al (2021) suggested that some mitochondrial segments might be incorporated less frequently into the nuclear genome than the COI barcode region, but our mitogenome-wide scan did not support this hypothesis. In accord with expectations (Hazkani-Covo et al 2010), NUMT counts were positively correlated with genome size, and R 2 rose from 34% to 56% when analysis extended from the COI barcode to the entire mitogenome.…”

Section: Variation In Numt Countsmentioning

confidence: 60%

Interrogating 1000 Insect Genomes for NUMTs: A Risk Assessment for Species Scans

Bock

Prosser

2022

Preprint

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The nuclear genomes of most animal species include segments of the mitogenome, but the count of these NUMTs varies greatly. This study examines the incidence of NUMTs derived from a 658 bp region of the cytochrome c oxidase I (COI) gene as a proxy for other coding regions of the mitochondrial genome. Analysis focuses on the most diverse group of terrestrial organisms, insects, because COI-based identification systems play a key role in clarifying their diversity, an essential antecedent to genome sequencing. Nearly 10,000 COI NUMTs ≥ 100 bp were detected in the genomes of 1,002 insect species with a range from 0–443. NUMT counts were similar among congeners, but differences among genera in a family were often large with genome size explaining 56% of the mitogenome-wide variation in counts. While many of these NUMTs possessed an indel or premature stop codon allowing their exclusion, the others could complicate species diagnosis as they averaged 10.1% divergence from their mitochondrial homologue. The count of NUMTs varies widely among insect lineages, peaking in groups that employ direct development or incomplete metamorphosis. They can raise the apparent species count by up to 22% when the 658 bp barcode region is examined while shorter targets (300 bp, 150 bp) elevate exposure (58–111%) to “ghost” species. As a result, NUMTs represent a particular complication for protocols (e.g., eDNA, metabarcoding) which employ short amplicons for biodiversity assessments.

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“…In organisms with large genomes and that are, therefore, more tolerant to the presence of NUMTs, these are likely to be amplified even when species-specific primers are used. For example, a recent study showed that DNA barcoding in Orthoptera is particularly challenging due to the widespread presence of NUMTs, and other mitochondrial markers may have to be employed to infer species diversity correctly [ 44 ].…”

Section: Resultsmentioning

confidence: 99%

Species Diversity and Phylogenetic Relationships of Olive Lace Bugs (Hemiptera: Tingidae) Found in South Africa

Hlaka

Guilbert

Smit

et al. 2021

Insects

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Olive lace bugs (Hemiptera: Tingidae) are small sap-sucking insects that feed on wild and cultivated Olea europaea. The diversity of olive lace bug species in South Africa, the most important olive producer on the continent, has been incompletely surveyed. Adult specimens were collected in the Western Cape province for morphological and DNA-based species identification, and sequencing of complete mitogenomes. Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. were found at 12 sites. Intra- and interspecific genetic divergences and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed high levels of congruity between taxonomic and genetic data. The phylogenetic position of the four species found in South Africa was inferred using new and available mitogenomes of Tingidae. Notably, olive lace bugs formed a cluster of closely related species. However, Cysteochila was non-monophyletic as C. lineata was recovered as a sister species to P. australis whereas Cysteochila chiniana, the other representative of the genus, was grouped with Trachypeplus jacobsoni and Tingis cardui in a different cluster. This result suggests that feeding on O. europaea may have a common origin in Tingidae and warrants future research on potential evolutionary adaptations of olive lace bugs to this plant host.

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Mind thenumt: Finding informative mitochondrial markers in a giant grasshopper genome

Abstract: This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 16 publications

References 68 publications

First Integrative Morphological and Genetic Characterization of Tremoctopus violaceussensu stricto in the Mediterranean Sea

First Integrative Morphological and Genetic Characterization of Tremoctopus violaceussensu stricto in the Mediterranean Sea

Interrogating 1000 Insect Genomes for NUMTs: A Risk Assessment for Species Scans

Species Diversity and Phylogenetic Relationships of Olive Lace Bugs (Hemiptera: Tingidae) Found in South Africa

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