The complete mitochondrial genome of <i>Anomaloglossus baeobatrachus</i> (Amphibia: Anura: Aromobatidae)

Vacher, Jean‐Pierre; Fouquet, Antoine; Holota, Hélène; Thébaud, Christophe

doi:10.1080/23802359.2016.1172053

Cited by 6 publications

(9 citation statements)

References 11 publications

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“…Machado, Lyra, and Grant validated the efficiency of this strategy as a means of assembling organelle genomes as bycatch from short genomic sequence reads sequenced using high‐throughput sequencing technology even when the total number of reads is low, and the reference belongs to distantly related taxa (i.e., different species, family, or even order). Subsequently, several authors have incorporated both the strategy and the partial mitogenomes provided by Machado, Lyra, and Grant into their methods and body of evidence (e.g., Anmarkrud & Lifjeld, ; Vacher, Fouquet, Holota, & Thébaud, ; Yuan, Xia, Zheng, & Zeng, ), highlighting the need to develop and improve the methods used to assemble and analyze mitogenome sequences.…”

Section: Introductionmentioning

confidence: 99%

“…A quick survey of the recent specialized literature (searching https://www.scopus.com and https://scholar.google.com.br for "complete mitochondrial genome" within the last 3 years) shows that many authors infer circularity through visual inspection of either reads at the ends of the assembly (e.g., Gan, Schultz, & Austin, 2014;Grau, Nuñez, Plötner, & Poustka, 2015;Vacher et al, 2016) or other more complicated methods (Cong & Grishin, 2016). However, we have observed that MITObim assemblies often produce sequences flanked by erroneous sequences that seem to have resulted from the spurious assembly of repetitive fragments.…”

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confidence: 99%

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A new strategy to infer circularity applied to four new complete frog mitogenomes

Machado

Janies

Brouwer

et al. 2018

Ecology and Evolution

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We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae (Melanophryniscus moreirae), Dendrobatidae (Hyloxalus subpunctatus and Phyllobates terribilis), and Scaphiopodidae (Scaphiopus holbrookii). These are the first complete mitogenomes of these four genera and Scaphiopodidae. We assembled mitogenomes from short genomic sequence reads using a baiting and iterative mapping strategy followed by a new ad hoc mapping strategy developed to test for assembly circularization. To assess the quality of the inferred circularization, we used Bowtie2 alignment scores and a new per‐position sequence coverage value (which we named “connectivity”). Permutation tests with 400 iterations per specimen and 1% or 5% chance of mutation at the ends of the putative circular sequences showed that the proposed method is highly sensitive, with a single nucleotide insertion or deletion being sufficient for circularity to be rejected. False positives comprised only 2% of all observations and possessed significantly lower alignment scores. The size, gene content, and gene arrangement of each mitogenome differed among the species but matched the expectations for their clades. We argue that basic studies on circular sequences can benefit from the results and bioinformatics procedures introduced here, especially when closely related references are lacking.

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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

A new strategy to infer circularity applied to four new complete frog mitogenomes

Machado

Janies

Brouwer

et al. 2018

Ecology and Evolution

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“…DNA was isolated from liver tissue using the Wizard Genomic extraction protocol (Promega; Madison, WI, USA). Mitogenomes were sequenced and assembled following the method described in Vacher et al (2016). We used 200 ng of DNA to create a DNA sequencing library that was hybridized and sequenced on a 1/24th of lane of an Illumina HiSeq 2500 flow cell (Illumina Inc., San Diego, CA).…”

Section: Methodsmentioning

confidence: 99%

On the brink of extinction: two new species of Anomaloglossus from French Guiana and amended definitions of Anomaloglossus degranvillei and A. surinamensis (Anura: Aromobatidae)

Fouquet

Vacher

Courtois

et al. 2018

Zootaxa

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A large portion of the amphibian species occurring in Amazonia remains undescribed. A recent study on species delineation in Anomaloglossus, a genus endemic to the Guiana Shield, demonstrated the existence of two undescribed species previously identified as A. degranvillei, which we describe herein. In addition to divergence at the molecular level, these two new taxa are also distinguished by subtle morphological characters and substantial differences in the advertisement calls (note length, dominant frequency, note structure). One species occurs in the hilly lowlands of north-eastern French Guiana and is mainly distinguished from its closest relatives by a small body size (15.9-18.8 mm in males) and by vocalisations characterized by the emission of short notes of 0.09 s on average. The other species is only known from the Itoupé Massif in southern French Guiana and is mainly distinguished from its closest relatives by a moderate body size (19.4-20.4 mm in males) and by vocalisations characterized by the emission of long notes of 0.23 s on average. We also provide amended definitions for two previously described species in the A. degranvillei species group: A. degranvillei, which is endemic to a few massifs in central French Guiana, and A. surinamensis, which is distributed throughout Suriname and French Guiana. The new species described here and A. degranvillei have very narrow ranges within French Guiana and seem to have rapidly declined during the last decade. Therefore, we suggest A. degranvillei and A. dewynteri to be considered as "Critically Endangered" and A. blanci as "Vulnerable" according to the IUCN standards.

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“… 2016 ; Vacher et al. 2016 ) with MAFFT v.7 (Katoh and Standley 2013 ). The mitogenome sequence of Bufo tibetanus was used as outgroup.…”

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confidence: 99%

“…New sequences were submitted to GenBank (accession numbers MF069434-MF069441). Sequences were aligned to published complete or near-complete mitochondrial genomes of dendrobatid and aromobatid frogs (Zhang et al 2013;Machado et al 2016;Vacher et al 2016) with MAFFT v.7 (Katoh and Standley 2013). The mitogenome sequence of Bufo tibetanus was used as outgroup.…”

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confidence: 99%

The mitochondrial genomes of three species of poison frogs (Anura: Dendrobates)

Lyra

Sanchez

Kuenzel

et al. 2017

Mitochondrial DNA Part B

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We reconstructed nearly complete mitogenomes for three species of poison frogs, Dendrobates auratus, D. leucomelas , and D. tinctorius, from RNAseq data. We recovered the 13 protein-coding genes, 22 tRNA genes (except tRNA-Val for D. leucomelas ), and two rRNA genes for all three species, plus partial sequences of the control region. The order of genes agrees with that known from a previously sequenced D. auratus , being the most commonly found for neobatrachian frogs. Based on full-sibling comparisons we estimate the probable error rate of Illumina-RNAseq reconstructed mitogenomes of up to 0.15%.

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The complete mitochondrial genome of Anomaloglossus baeobatrachus (Amphibia: Anura: Aromobatidae)

Cited by 6 publications

References 11 publications

A new strategy to infer circularity applied to four new complete frog mitogenomes

A new strategy to infer circularity applied to four new complete frog mitogenomes

On the brink of extinction: two new species of Anomaloglossus from French Guiana and amended definitions of Anomaloglossus degranvillei and A. surinamensis (Anura: Aromobatidae)

The mitochondrial genomes of three species of poison frogs (Anura: Dendrobates)

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