Accurate annotation of protein-coding genes in mitochondrial genomes

Arab, Marwa Al; Siederdissen, Christian Höner zu; Tout, Kifah; Sahyoun, Abdullah H.; Stadler, Peter F.; Bernt, Matthias

doi:10.1016/j.ympev.2016.09.024

Cited by 28 publications

(21 citation statements)

References 33 publications

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“…A primer pair (c1-mt14781 5 0 -AGAAGCGGCTATTTTATGAGATTTGGAAG-3 0 and c1-mt1385 5 0 -TGCTCATACGATGAATCCTAATACTCCGA-3 0 ) was designed for both terminal ends, and the produce was sequenced by Sanger's sequencing method. Finally, the draft mitochondrial genome was annotated using the MITOS web server (Bernt et al 2013) with the protein prediction method of AL Arab et al (2017), and deposited in GenBank under accession number MK847519.…”

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confidence: 99%

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The first mitochondrial genome of scale insects (Hemiptera: Coccoidea)

Deng

Huang

2019

Mitochondrial DNA Part B

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Here, we report the first mitochondrial genome of scale insects sequenced from Ceroplastes japonicus (Hemiptera: Coccidae). The genome has a circular genome of 14,979 bp in length, with a high A þ T content of 85.15%. Twelve protein-coding genes (excluding atp8), 13 tRNA, and 2 rRNA genes were detected and annotated using the MITOS web server. The absence of atp8 and some tRNAs might indicate possible novel structures or loss of genes.

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confidence: 99%

“…The absence of atp8 is observed in the current annotation. The atp8 gene has a very short and poorly conserved sequence and tends to be missed by BLAST-based approaches (Al Arab et al 2017). However, some cases of loss of atp8 have been reported in nematodes, cnidarians, and flatworms (Okimoto et al 1991;Beagley et al 1996;Le et al 2002).…”

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confidence: 99%

The first mitochondrial genome of scale insects (Hemiptera: Coccoidea)

Deng

Huang

2019

Mitochondrial DNA Part B

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“…In all, 3.02 Gb of raw data were retrieved, and were used for mitochondrial genome assembly using MITObim v1.9 (Hahn et al 2013) with a previously published sequence (JQ692071) (Qiu et al 2012) as the initial reference. Mitogenome annotation was done by aligning against those of closely related taxa available from GenBank, and adjusted if necessary according to the prediction of the MITOS web server (Bernt et al 2013;Al Arab et al 2017).…”

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Characterization of the complete mitochondrial genome of the Tianjun yak (Bos grunniens)

Guo

Bao

et al. 2019

Mitochondrial DNA Part B

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Tianjun yak (Bos grunniens) is a yak breed with strong adaptation to the high-elevation, cold and anoxic environments. Its complete mitochondrial genome is 16,323 bp long with an asymmetric base composition, and harbors the 37 typical mitochondrial genes and one noncoding control region. The PCGs are initiated with the typical ATA or ATG codons, and are terminated with TAA, TAG or the incomplete stop codon T--. Phylogenetic analysis suggests that Tianjun yak is most closely related to the polled yak. ARTICLE HISTORY

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“…Mitogenome annotation was done using MITOS2 that includes the latest protein identification model 54 , 55 . We used two references in MITOS2, RefSeq63 Metazoa and RefSeq81 Metazoa, to annotate the mitogenomes for verification and confirmation, especially if one version did not predict all genes.…”

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confidence: 99%

Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human-infecting blood fluke, Schistosoma mansoni

Zhang

Laidemitt

et al. 2018

Sci Rep

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Using high throughput Illumina sequencing technology, we determined complete sequences for the mitochondrial genome (mitogenome) and nuclear ribosomal DNA (rDNA) complex for three African freshwater snail taxa within the genus Biomphalaria, B. pfeifferi, B. sudanica and B. choanomphala, and for two laboratory strains of B. glabrata originating from the Neotropics. Biomphalaria snails are obligate vectors of the blood fluke Schistosoma mansoni, a major etiologic agent of human intestinal schistosomiasis. Our data show that mitogenomes from African and Neotropical Biomphalaria are highly conserved. With respect to rDNA, the two internal transcribed spacers (ITS1 and 2) were found to be highly variable whereas the three ribosomal RNA genes (28S, 5.8S and 18S rRNA) exhibited no or very limited variation. Our analyses reveal that the two taxa inhabiting Lake Victoria, B. sudanica and B. choanomphala, are very similar to one another relative to the similarity either shows to B. pfeifferi or B. glabrata. This new sequence information may prove useful for developing new markers for snail identification, environmental detection/monitoring purposes or for tracking epidemiology and snail dependencies of S. mansoni in endemic areas. It also provides new information pertinent to still unresolved questions in Biomphalaria systematics and nomenclature.

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Accurate annotation of protein-coding genes in mitochondrial genomes

Cited by 28 publications

References 33 publications

The first mitochondrial genome of scale insects (Hemiptera: Coccoidea)

The first mitochondrial genome of scale insects (Hemiptera: Coccoidea)

Characterization of the complete mitochondrial genome of the Tianjun yak (Bos grunniens)

Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human-infecting blood fluke, Schistosoma mansoni

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