MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for species- or genus-level identification, but also the large subunit (LSU; 23S/28S) rRNA gene is employed in taxonomic assignment. The METAXA software tool is a popular utility for extracting partial rRNA sequences from large sequencing data sets and assigning them to an archaeal, bacterial, nuclear eukaryote, mitochondrial or chloroplast origin. This study describes a comprehensive update to METAXA - METAXA2 - that extends the capabilities of the tool, introducing support for the LSU rRNA gene, a greatly improved classifier allowing classification down to genus or species level, as well as enhanced support for short-read (100 bp) and paired-end sequences, among other changes. The performance of METAXA2 was compared to other commonly used taxonomic classifiers, showing that METAXA2 often outperforms previous methods in terms of making correct predictions while maintaining a low misclassification rate. METAXA2 is freely available from http://microbiology.se/software/metaxa2/.

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“…) and mitozoa (version 2.0; release 10; D'Onorio de Meo et al . ), cross‐checked with data from Greengenes (DeSantis et al . ; McDonald et al .…”

Section: Methodsmentioning

confidence: 99%

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

Bengtsson‐Palme

Hartmann

Eriksson

et al. 2015

Molecular Ecology Resources

376

307

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“…Therefore, tRNAs were initially re‐detected using two computer programs: tRNAscan‐SE version 1.21 (Lowe & Eddy, 1997) and ARWEN 1.2.3.c (Laslett & Canback, 2008). Confirmation was performed by blast searches of all tRNAs in MitoZoa 2.0 (de Meo et al., 2012). …”

Section: Methodsmentioning

confidence: 99%

The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

Shen

Kou

Zhong

et al. 2017

Ecology and Evolution

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In this study, the complete mitochondrial (mt) genome sequence of the South China deep‐sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep‐sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep‐sea benthic environment; based on their large size, Bathynomus is included in the “supergiant group” of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein‐coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date. Although the overall genome organization is typical for metazoans, the mt genome of Bathynomus sp. shows a number of derived characters, such as an inversion of 10 genes when compared to the pancrustacean ground pattern. Rearrangements in some genes (e.g., cob, trnT, nad5, and trnF) are shared by nearly all isopod mt genomes analyzed thus far, and when compared to the putative isopod ground pattern, five rearrangements were found in Bathynomus sp. Two tRNAs exhibit modified secondary structures: The TΨC arm is absent from trnQ, and trnC lacks the DHU. Within the class Malacostraca, trnC arm loss is only found in other isopods. Phylogenetic analysis revealed that Bathynomus sp. (Cymothoida) and Sphaeroma serratum (Sphaeromatidea) form a single clade, although it is unclear whether Cymothoida is monophyletic or paraphyletic. Moreover, the evolutionary rate of Bathynomus sp. (dN/dS [nonsynonymous mutational rate/synonymous mutational rate] = 0.0705) is the slowest measured to date among Cymothoida, which may be associated with its relatively constant deep‐sea environment. Overall, our results may provide useful information for understanding the evolution of deep‐sea Isopoda species.

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“…Sequences were extracted from revised entries of complete mitochondrial genomes collected in the MitoZoa database (D’Onorio de Meo et al, 2012) The analyzed taxon sample consists of 66 species, that is, all available species of Tunicata, Cephalochordata and Xenoturbellida; almost all available species of Hemichordata and Echinodermata; few representatives of Vertebrata; and two outgroup species (the arthropod Drosophila melanogaster and the mollusk Aplysia californica ) (Supplementary file 1). Outgroups were selected among taxa closely related to deuterostomes, in order to ensure the analysis of the largest possible set of unambiguously aligned sites.…”

Section: Methodsmentioning

confidence: 99%

The genome sequence of the colonial chordate, Botryllus schlosseri

Voskoboynik

Neff

Sahoo

et al. 2013

eLife

Self Cite

223

213

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Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration.DOI: http://dx.doi.org/10.7554/eLife.00569.001

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MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

Cited by 49 publications

References 35 publications

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods

The genome sequence of the colonial chordate, Botryllus schlosseri

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