Requirements and standards for organelle genome databases.
Mitochondria and plastids (collectively called organelles) descended from prokaryotes that adopted an intracellular, endosymbiotic lifestyle within early eukaryotes. Comparisons of their remnant genomes address a wide variety of biological questions, especially when including the genomes of their prokaryotic relatives and the many genes transferred to the eukaryotic nucleus during the transitions from endosymbiont to organelle. The pace of producing complete organellar genome sequences now makes it unfeasible to do broad comparisons using the primary literature and, even if it were feasible, it is now becoming uncommon for journals to accept detailed descriptions of genome-level features. Unfortunately, no database is completely useful for this task, since they have little standardization and are riddled with error. Further, the descriptors necessary to make full use of these data are generally lacking. Here, I outline what is currently wrong and what must be done to make this data useful to the scientific community.
Boore
Jeffrey L
JL
Department of Energy (DOE) Joint Genome Institute and Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94598, USA. JLBoore@berkeley.edu
D000818:Animals; D002736:Chloroplasts / Q000235:genetics; D030561:Databases, Nucleic Acid / Q000592:standards*; D016678:Genome; D015894:Genome, Human; D023281:Genomics / Q000592:standards*; D006801:Humans; D008928:Mitochondria / Q000235:genetics; D015388:Organelles / Q000235:genetics*