Requirements and standards for organelle genome databases

Journal Article · Mon Jan 09 04:00:00 EST 2006 · Journal of Integrative Biology

DOI:https://doi.org/10.1089/omi.2006.10.119· OSTI ID:919820

Boore, Jeffrey L

Mitochondria and plastids (collectively called organelles)descended from prokaryotes that adopted an intracellular, endosymbioticlifestyle within early eukaryotes. Comparisons of their remnant genomesaddress a wide variety of biological questions, especially when includingthe genomes of their prokaryotic relatives and the many genes transferredto the eukaryotic nucleus during the transitions from endosymbiont toorganelle. The pace of producing complete organellar genome sequences nowmakes it unfeasible to do broad comparisons using the primary literatureand, even if it were feasible, it is now becoming uncommon for journalsto accept detailed descriptions of genome-level features. Unfortunatelyno database is currently useful for this task, since they have littlestandardization and are riddled with error. Here I outline what iscurrently wrong and what must be done to make this data useful to thescientific community.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director, Office of Science. Office of Biological andEnvironmental Research; National Science Foundation
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 919820
• Report Number(s): LBNL--59357; BnR: 600305000
• Journal Information: Journal of Integrative Biology, Journal Name: Journal of Integrative Biology Journal Issue: 2 Vol. 10
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
CELL CONSTITUENTS
DATA BASE MANAGEMENT
GENES
MITOCHONDRIA
STANDARDIZATION
database organelle plastid chloroplast mitochondria prokaryoteeukaroyte evolution endosymbiont