EZmito: a simple and fast tool for multiple mitogenome analyses

Cucini, Claudio; Leo, Chiara; Iannotti, Nicola; Boschi, Sara; Brunetti, Claudia; Pons, Joan; Fanciulli, Pietro Paolo; Frati, Francesco; Carapelli, Antonio; Nardi, Francesco

doi:10.1080/23802359.2021.1899865

Cited by 33 publications

(10 citation statements)

References 27 publications

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“…and conforms with the general molecular features observed for insects, in having 13 protein-encoding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) (encoding for rrnL and rrnS ), and a putative A + T-rich “control” region (Cucini et al. 2021 ). The gene order is identical to that considered ancestral for Pancrustacea, with a set of tRNA-encoding genes that can be folded in the canonical cloverleaf secondary structure, except that for Serine ( trnSgcu ) that lack the DHU arm as observed in most Metazoa’s mtDNA (Comandi et al.…”

supporting

confidence: 80%

The mitogenome of the true bug Nysius cymoides (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

Carapelli

Brunetti

Cucini

et al. 2021

Mitochondrial DNA Part B

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The complete mitochondrial genome of the true bug (Homoptera) Nysius cymoides (Spinola, 1837) is herein described and used for phylogenetic comparison with other species of Lygaeoidea. The mtDNA has a gene order and other molecular features typically observed in hexapods, and a long A þ T-rich region, due to the occurrence of several repeat units. The phylogenetic analyses support the monophyly of all families except Rhyparochromidae.

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supporting

confidence: 80%

The mitogenome of the true bug Nysius cymoides (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

Carapelli

Brunetti

Cucini

et al. 2021

Mitochondrial DNA Part B

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“…The codon usage and open reading frames of the protein-coding genes (PCG) were analyzed. The codon usage of the 13 PCG’s was predicted using the Codon Usage web server ( https://www.bioinformatics.org/sms2 ) ( Stothard, 2000 ) and visualized using the EZcodon tool in the web server EZmito ( http://ezmito.unisi.it/ezcodon ) ( Cucini et al, 2021 ), both set to the vertebrate genetic code. tRNA genes were identified by MITOS and MITOS2, and the secondary structures were visualized in the Forna web server ( http://rna.tbi.univie.ac.at/forna/ ) ( Kerpedjiev, Hammer & Hofacker, 2015 ).…”

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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“…The complete mitogenomes of eight closely related species of octopus, as well as an outgroup species, Tremoctopus violaceus , were retrieved for phylogenetic analysis. The Ezsplit tool [ 20 ] was used to extract the sequences of all 13 protein coding genes (PCG) from the NCBI database, each of which was aligned separately using the codon alignment option in ClustalW with default setting [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

The complete mitochondrial genome of Octopus vulgaris

Fee,

Roura,

Emami-Khoyi

et al. 2023

Mol Biol Rep

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Background The Octopus vulgaris species complex consists of numerous morphologically similar but genetically distinct species. The current publicly available mitogenome of this species has been generated from a specimen collected from Tsukiji Fish Market, Tokyo, Japan. Octopus from the northwestern Pacific Ocean are now considered to be a separate species, Octopus sinensis. For this reason, we hypothesised that the current record of O. vulgaris was sequenced from a specimen of O. sinensis. Here, we sequenced the first complete mitogenome of a specimen of Octopus vulgaris sensu stricto that was collected from the species’ confirmed distribution areas in northeastern Atlantic. Methods and results The complete mitogenome was assembled de novo and annotated using 250 bp paired-end sequences. A single circular contig 15,655 bp in length with a mean read coverage of 1089 reads was reconstructed. The annotation pipeline identified 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA) and two ribosomal RNAs. A maximum likelihood phylogenetic tree recovered the assembled mitogenome as the sister taxon of a monophyletic group comprising O. sinensis and the previously published mitogenome of “O. vulgaris” from Japan. This confirms that the latter was a Japanese specimen of O. sinensis. Conclusion The mitogenome sequenced here is the first to be published for Octopus vulgaris sensu stricto. It represents an important first step in genetics-informed research on the evolution, conservation, and management of this commercially important species.

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EZmito: a simple and fast tool for multiple mitogenome analyses

Cited by 33 publications

References 27 publications

The mitogenome of the true bug Nysius cymoides (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

The mitogenome of the true bug Nysius cymoides (Insecta, Heteroptera) and the phylogeny of Lygaeoidea

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

The complete mitochondrial genome of Octopus vulgaris

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