MITOS: Improved de novo metazoan mitochondrial genome annotation

doi:10.1016/J.YMPEV.2012.08.023

Home
/
Papers
/
MITOS: Improved de novo metazoan mitochondrial genome annotation

Journal Article•DOI•

MITOS: Improved de novo metazoan mitochondrial genome annotation

Matthias Bernt¹, Alexander Donath¹, Frank Jühling², Frank Jühling¹, Fabian Externbrink¹, Catherine Florentz², Guido Fritzsch¹, Joern Pütz², Martin Middendorf¹, Peter F. Stadler - Show less +6 more•Institutions (2)

Leipzig University¹, University of Strasbourg²

01 Nov 2013-Molecular Phylogenetics and Evolution (Mol Phylogenet Evol)-Vol. 69, Iss: 2, pp 313-319

TL;DR: The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences and it is shown that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality.

read less

About: This article is published in Molecular Phylogenetics and Evolution.The article was published on 2013-11-01. It has received 3323 citations till now. The article focuses on the topics: RefSeq.

...read moreread less

Citations

PDF

Open Access

More filters

Journal Article•DOI•

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

[...]

Christoph Hahn¹, Lutz Bachmann¹, Bastien Chevreux¹•Institutions (1)

American Museum of Natural History¹

01 Jul 2013-Nucleic Acids Research

TL;DR: The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR.

...read moreread less

Abstract: We present an in silico approach for the reconstruction of complete mitochondrial genomes of nonmodel organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/ chrishah/MITObim.

...read moreread less

1,604 citations

Journal Article•DOI•

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.

[...]

Stephan Greiner¹, Pascal Lehwark, Ralph Bock¹•Institutions (1)

Max Planck Society¹

02 Jul 2019-Nucleic Acids Research

TL;DR: A new version of OGDRAW equipped with a new front end enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades.

...read moreread less

Abstract: Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

...read moreread less

888 citations

Cites methods from "MITOS: Improved de novo metazoan mi..."

...These range from specialized applications such as MITOS (11), that were designed for a subset of organellar genomes and whose output requires little to no quality control or manual curation, to GeSeq, a flexible tool that allows the annotation of essentially any organellar genome (15)....
[...]

Journal Article•DOI•

MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

[...]

Wataru Iwasaki¹, Tsukasa Fukunaga¹, Ryota Isagozawa¹, Koichiro Yamada, Yasunobu Maeda¹, Takashi P. Satoh, Tetsuya Sado², Kohji Mabuchi¹, Hirohiko Takeshima¹, Masaki Miya², Mutsumi Nishida¹ - Show less +7 more•Institutions (2)

University of Tokyo¹, American Museum of Natural History²

01 Nov 2013-Molecular Biology and Evolution

TL;DR: MitoFish contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses.

...read moreread less

Abstract: Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface.

...read moreread less

590 citations

Cites background or methods from "MITOS: Improved de novo metazoan mi..."

...2012), the most comprehensive database for mitogenomes, is known to contain many incorrect mitogenomic annotations (Bernt et al. 2013), which can lead to inaccurate research results....
[...]
...MITOS (Bernt et al. 2013) is an automated pipeline for the de novo annotation of metazoan mitogenomes and comes closest to what MitoAnnotator achieves....
[...]
...In addition, RefSeq (Pruitt et al. 2012), the most comprehensive database for mitogenomes, is known to contain many incorrect mitogenomic annotations (Bernt et al. 2013), which can lead to inaccurate research results....
[...]

Journal Article•DOI•

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

[...]

Jelmer W. Poelstra¹, Nagarjun Vijay¹, Christen M. Bossu¹, Henrik Lantz¹, Henrik Lantz², Bettina Ryll², Inge Müller³, Inge Müller⁴, Vittorio Baglione⁵, Per Unneberg¹, Martin Wikelski³, Martin Wikelski⁴, Manfred Grabherr¹, Jochen B. W. Wolf¹ - Show less +10 more•Institutions (5)

Science for Life Laboratory¹, Uppsala University², Max Planck Society³, University of Konstanz⁴, University of Valladolid⁵

20 Jun 2014-Science

TL;DR: Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone, indicating localized genomic selection can cause marked heterogeneity in introgressive landscapes while maintaining phenotypic divergence.

...read moreread less

Abstract: The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

...read moreread less

495 citations

Journal Article•DOI•

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization.

[...]

Guanliang Meng, Yiyuan Li¹, Chentao Yang, Shanlin Liu²•Institutions (2)

University of Texas at Austin¹, China Agricultural University²

20 Jun 2019-Nucleic Acids Research

TL;DR: A mitogenome toolkit MitoZ is developed, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenomes assembly together with annotations and visualization results from HTS raw reads.

...read moreread less

Abstract: Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.

...read moreread less

465 citations

1
2
3
4
…
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200

Collapse

References

PDF

Open Access

More filters

Journal Article•DOI•

Basic Local Alignment Search Tool

[...]

Stephen F. Altschul¹, Warren Gish¹, Webb Miller², Eugene W. Myers³, David J. Lipman¹ - Show less +1 more•Institutions (3)

National Institutes of Health¹, Pennsylvania State University², University of Arizona³

01 Oct 1990-Journal of Molecular Biology

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.

...read moreread less

88,255 citations

"MITOS: Improved de novo metazoan mi..." refers methods in this paper

...Systematic semi-automatic error screening using a list of rules based on tRNAscan-SE (Lowe and Eddy, 1997), ARWEN (Laslett and Canback, 2008), and BLAST (Altschul et al., 1990) searches as well as expert knowledge is used for MitoZoa (Lupi et al., 2010), a recently released new data base....
[...]
...Furthermore all raw data of BLAST and Infernal, a graphical representation of the structure of the ncRNAs predicted by the covariance models, and a file containing the gene order are available (lacking the anticodon information for tRNA-encoding genes)....
[...]
...It uses a novel strategy based on aggregating BLAST searches with previously annotated protein sequences to identify protein coding genes (Section 2.1), thereby avoiding the need for a built-in data base of specifically curated protein models....
[...]
...BLAST is used by MOSAS to search for open reading frames and rRNAs based on a local data base of query sequences (currently from insects only)....
[...]
...Protein coding genes are annotated by means of a sophisticated aggregation procedure based on BLAST searches, which allows for the detection of frameshifts, duplication events, and split genes....
[...]

Journal Article•DOI•

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

[...]

Todd M. Lowe¹, Sean R. Eddy¹•Institutions (1)

Washington University in St. Louis¹

01 Mar 1997-Nucleic Acids Research

TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.

...read moreread less

Abstract: We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

...read moreread less

9,629 citations

"MITOS: Improved de novo metazoan mi..." refers methods in this paper

...Systematic semi-automatic error screening using a list of rules based on tRNAscan-SE (Lowe and Eddy, 1997), ARWEN (Laslett and Canback, 2008), and BLAST (Altschul et al., 1990) searches as well as expert knowledge is used for MitoZoa (Lupi et al., 2010), a recently released new data base....
[...]

Journal Article•DOI•

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

[...]

Kim D. Pruitt¹, Tatiana Tatusova¹, Donna Maglott¹•Institutions (1)

National Institutes of Health¹

17 Dec 2004-Nucleic Acids Research

TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.

...read moreread less

Abstract: The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff.

...read moreread less

4,229 citations

"MITOS: Improved de novo metazoan mi..." refers background in this paper

...The most comprehensive and up-to-date resource for mitochondrial genomes and their annotation is NCBI RefSeq (Pruitt et al., 2007)....
[...]
...About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs....
[...]

Journal Article•DOI•

Biopython: freely available Python tools for computational molecular biology and bioinformatics

[...]

Peter J. A. Cock¹, Tiago Antao², Jeffrey T. Chang³, Brad Chapman⁴, Cymon J. Cox⁵, Andrew Dalke, Iddo Friedberg⁶, Thomas Hamelryck⁷, Frank Kauff⁸, Bartosz Wilczyński⁹, Michiel J. L. de Hoon - Show less +7 more•Institutions (9)

University of Dundee¹, Liverpool School of Tropical Medicine², Duke University³, Harvard University⁴, University of the Algarve⁵, University of California, San Diego⁶, University of Copenhagen⁷, Kaiserslautern University of Technology⁸, University of Warsaw⁹

01 Jun 2009-Bioinformatics

TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.

...read moreread less

Abstract: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence. le formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.

...read moreread less

3,855 citations

"MITOS: Improved de novo metazoan mi..." refers methods in this paper

...We implemented specialised parser for mitogenome annotations based on biopython (Cock et al., 2009) for this task....
[...]
...In the following we provide a detailed description of the individual components of MITOS....
[...]

Journal Article•DOI•

Automatic annotation of organellar genomes with DOGMA

[...]

Stacia K. Wyman, Robert K. Jansen¹, Jeffrey L. Boore²•Institutions (2)

University of Texas at Austin¹, Joint Genome Institute²

22 Nov 2004-Bioinformatics

TL;DR: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar genomes and allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.

...read moreread less

Abstract: Summary: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar (plant chloroplast and animal mitochondrial) genomes. It is a Web-based package that allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. DOGMA provides a graphical user interface for viewing and editing annotations. Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank. Availability: http://phylocluster.biosci.utexas.edu/dogma/ Supplementary information: Detailed documentation and tutorials for annotating both animal mitochondrial and plant chloroplast genomes can be found on the DOGMA home page.

...read moreread less

2,754 citations

"MITOS: Improved de novo metazoan mi..." refers methods in this paper

...DOGMA (Wyman et al., 2004) is a semi-automated pipeline of methods dealing with both mitochondrial and chloroplast genomes....
[...]
...Automatic annotation of organellar genomes with DOGMA....
[...]
...COVE (Eddy and Durbin, 1994) is employed by DOGMA to identify tRNAs candidates based on secondary structure....
[...]