Research article
Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale – A wild ancestor of cultivated buckwheat
-
* Corresponding author: Maria D Logacheva maria.log@gmail.com
1 Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
2 Department of Evolutionary Biochemistry, A.N. Belozersky Institute, M.V. Lomonosov Moscow State University, Moscow, Russia
3 Department of Horticulture and Landscape Architecture, Washington State University, Pullman, USA
4 Department of Genetics, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
BMC Plant Biology 2008, 8:59 doi:10.1186/1471-2229-8-59
Published: 20 May 2008Additional files
Additional file 1:
Conserved primers developed for amplification and sequencing of buckwheat chloroplast genome. Table.
Format: DOC Size: 200KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 2:
Taxon-specific primers. Contains the list of buckwheat-specific primers. Primers are named according their position in buckwheat chloroplast genome. For example, for the primers 4080F and 4621R 4080 and 4621 are the starts of the primer sequences on forward and reverse strands, respectively. Primers annealing at the IR region have double name according their position on both IRa and IRb.
Format: DOC Size: 173KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 3:
Alignment of rpl23 homologs in angiosperms and gymnosperms, illustrating the mutations in rpl23 in Caryophyllales. Beta and Spinacia have 14 bp deletion (alignment positions 131–145), Silene has a substitution in 17 alignment position. This substitution (G instead of T or C) creates a stop codon TAG. Fagopyrum has and insertion of 4 bp (alignment positions 49–53).
Format: TXT Size: 18KB Download file
Additional file 4:
Details of the PCR assay of IR expansion, including primer locations and expected amplicon lengths. Table.
Format: DOC Size: 27KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 5:
Distribution of potential RNA editing site in rpl2, psbL and ndhD in angiosperms. Filled squares denote the presence of ACG initiation codon, thin squares – the presence of typical ATG initiation codon. Blue color is for rpl2, red for psbL and black for ndhD. Question marks denote ambiguous character state (due to the loss of gene or the lack of sequence data). Phylogenetic tree is inferred from maximum parsimony analysis of nucleotide data set.
Format: JPEG Size: 844KB Download file
