Current MitoZoa DB: Release 10 (14-DEC-2011)

Database Aim

MitoZoa is a specialized database collecting complete and nearly-complete (longer than 7 kb) mtDNA entries of metazoan species, excluding Placozoa. One representative entry is present for those metazoan species/subspecies for which the mtDNA has been sequenced in several individuals. MitoZoa contains curated entries, whose gene annotation has been significantly improved using a semi-automatic reannotation pipeline and by manual curation of mitogenomics experts.
MitoZoa has been specifically designed to address comparative analyses of mitochondrial genomic features in a given metazoan group or in species belonging to the same genus (congeneric species). MitoZoa focuses on mitochondrial gene order, non-coding regions, gene content, and gene sequences.

Mitozoa Entry Format

MitoZoa entries are provided in two different formats: the MZ and the EMBL-like format.

The MZ (MitoZoa) format is a tabular format specifically designed for storing information on type and source of reannotations, and for emphasizing commonly hidden mitochondrial features. All fields modified or added to the original EMBL/RefSeq entries are shown in red and flagged by a "Modification Code" reported in square brackets (see Mcode in Table 2 of the online Help page). The new fields of the MZ format are described below:

1) The "MitoZoa Reannotation Summary", included in the comment field, briefly lists and comments all modifications of the original entries. It also includes a standardized message to indicate the entry AC number whose annotation was modified by MitoZoa (it can be a EMBL/Genbank/DDBJ or a RefSeq entry), and any other AC number containing exactly the same sequence.

2) The new FTkey "NCR", included in the Feature Table, is used to annotate all non-coding region sequences (NCR). This FTkey is always associated to the new FTqualifier "Code" that denotes the NCR with a code related to: species, flanking genes, and NCR length (see "NCR menu" section). By default, only NCRs with length ≥ 10 bp are shown in the MZ format, however a "NCR threshold" text box can be used to display NCRs with a length higher than a user-defined value. To show all annotated NCRs, the threshold has to be fixed to 1.

3) Genome length, molecule topology, and used genetic code are each reported in a specific field, further stressing information already present in the original entry.

4) The "MZ" field reports the date of entry creation/last update and the MitoZoa release.

5) The "ConGeneric species" field reports the count and AC number list of all MitoZoa entries belonging to a given genus.

The EMBL-like format of MitoZoa contains the following new fields/FTkeys:

MZ (MitoZoa date): date of entry creation/update and database release
GT (Genetic code Table): table number of the used genetic code, according to the NCBI Genetic Code web page
CG (ConGeneric species): list of all available mtDNAs belonging to congeneric species
CC (Comment): summary of entry reannotations
LR (Link to Resource): MitoZoa URL and intellectual copyright
NCR (Non-Coding Region): FTkey denoting the non-coding region.
prec_ORF (precursor ORF): FTkey denoting a precursor ORF with frameshift(s), recovered by RNA editing or programmed translational frameshifting.

MitoZoa Citations

If you use information from this database, please cite:

1) "MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa"
D'Onorio de Meo P, D'Antonio M, Griggio F, Lupi R, Borsani M, Pavesi G, Castrignano' T, Pesole G, Gissi C
Nucleic Acids Res. 2011. Nov 28
PMID: 22123747

2) "MitoZoa: a curated mitochondrial genome database of metazoans for comparative genomics studies"
Lupi R, de Meo PD, Picardi E, D'Antonio M, Paoletti D, Castrignano' T, Pesole G, Gissi C
Mitochondrion. 2010. 10(2):192-9
PMID: 20080208