The complete chloroplast genome sequence of Pelargonium xhortorum: Or ganization and evolution of the largest and most highlyrearranged chloroplast genome of land plants

Journal Article · Fri Jan 20 04:00:00 EST 2006 · Molecular Biology and Evolution, Oxford Press - ifaccepted

OSTI ID:919822

Chumley, Timothy W; Palmer, Jeffrey D; Mower, Jeffrey P; Fourcade, H Matthew; Calie, Patrick J; Boore, Jeffrey L; Jansen, Robert K

The chloroplast genome of Pelargonium e hortorum has beencompletely sequenced. It maps as a circular molecule of 217,942 bp, andis both the largest and most rearranged land plant chloroplast genome yetsequenced. It features two copies of a greatly expanded inverted repeat(IR) of 75,741 bp each, and consequently diminished single copy regionsof 59,710 bp and 6,750 bp. It also contains two different associations ofrepeated elements that contribute about 10 percent to the overall sizeand account for the majority of repeats found in the genome. Theyrepresent hotspots for rearrangements and gene duplications and include alarge number of pseudogenes. We propose simple models that account forthe major rearrangements with a minimum of eight IR boundary changes and12 inversions in addition to a several insertions of duplicated sequence.The major processes at work (duplication, IR expansion, and inversion)have disrupted at least one and possibly two or three transcriptionaloperons, and the genes involved in these disruptions form the core of thetwo major repeat associations. Despite the vast increase in size andcomplexity of the genome, the gene content is similar to that of otherangiosperms, with the exceptions of a large number of pseudogenes as partof the repeat associations, the recognition of two open reading frames(ORF56 and ORF42) in the trnA intron with similarities to previouslyidentified mitochondrial products (ACRS and pvs-trnA), the loss of accDand trnT-GGU, and in particular, the lack of a recognizably functionalrpoA. One or all of three similar open reading frames may possibly encodethe latter, however.

• Research Organization: COLLABORATION - U.Texas
• Sponsoring Organization: USDOE
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 919822
• Report Number(s): LBNL--59384; BnR: WN0219080
• Journal Information: Molecular Biology and Evolution, Oxford Press - ifaccepted, Journal Name: Molecular Biology and Evolution, Oxford Press - ifaccepted Journal Issue: 11 Vol. 23
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
CHLOROPLASTS
Chloroplast genome evolution gene rearrangement duplicationrecombination repeats
FUNCTIONALS
GENES
INTRONS
MAGNOLIOPHYTA