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Abstract Detail


Genetics Section

Peery, Rhiannon [1], Kuehl, Jennifer V. [2], Boore, Jeffrey L. [2], Raubeson, Linda A. [1].

Comparisons of three Apiaceae chloroplast genomes coriander, dill and fennel.

EARLIER work by others has shown that, in Apiaceae, the extent of the large inverted repeat (IR) varies. In a few Apiaceae lineages the IR has expanded slightly, however in many lineages in the family different degrees of contraction have been detected. We have generated complete chloroplast genome sequence for Anethum graveolens (dill) and draft sequences for Foeniculum vulgare (fennel) and Coriandrum sativum (coriander). Sequences where obtained via sucrose gradient isolation of chloroplasts, RCA amplification of the cpDNA from the chloroplasts, and then shotgun sequencing of RCA template at the Joint Genome Institute. Finishing involved additional sequencing to fill quality gaps, link contigs, and verify single copy-IR boundaries. In comparison to Panax ginseng (NC_006290), in the sister family Araliaceae, the dill LSC-IR boundary at the IRB junction has contracted slightly and includes only 39 nucleotides of the 5 end of rpl2. The SSC-IR boundary in dill has expanded 237 nucleotides into the 5 end of ycf1 in comparison to Panax. Preliminary analyses indicate that the LSC-IR boundaries determined via complete genome sequencing for these three genomes are basically consistent with those determined by Plunkett and Downie [2000. Syst Bot25: 648] using Southern Hybridization. In coriander Plunkett and Downie detected a 5.7 kb insertion of unknown origin in the LSC region adjacent to IRB that we have identified as a duplication of trnH and psbA. Thus, in coriander, it appears that the IR formerly contracted to include only the rDNA region but then expanded to incorporate trnH and psbA. No other large-scale genome rearrangements have been detected in coriander, fennel, or dill. Finishing work for fennel and coriander as well as finer-scale genomic comparisons are underway.


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1 - Central Washington State University, Department of Biological Sciences, Ellensburg, Washington, 98926-7537, USA
2 - DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, California, 94598, USA

Keywords:
inverted repeat
genome rearrangements
gene duplication
comparative genomics.

Presentation Type: Oral Paper:Papers for Sections
Session: 55-3
Location: 268/Holt
Date: Tuesday, August 1st, 2006
Time: 2:30 PM
Abstract ID:650


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