Obtained sequences were screened against the SOL Genomics Network and other coffee sequences available in public databases.
The top hits of Coffee sequences with Solanaceae range from 1 to 2% (Table 3).
In addition to decreased sequence identity, there were 62 and 61 indels inferred from alignments of the Asclepias ycf1 sequence with the oleander and coffee sequences respectively, whereas there were only 16 indels inferred from an alignment of oleander and coffee.
Santa Barbara) for advice and help regarding the use of T-coffee for sequence alignments and with the construction of the phylogenetic tree.
The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta).
Finally, all proposed new genes are inspected by eye, considering their BLASTP results and a T-COFFEE multiple sequence alignment with other proteins in the pillar, for manual acceptance or rejection.
The PTHR10629 domain sequences from the Panther HMM domain database that were found in the studied genomes and other sequences from 15 ascomycetes and 8 basidiomycetes (including five and three of our study, respectively) were aligned with the T-Coffee multiple sequence alignment program [ 53] and analyzed phylogenetically with PhyML [ 54].
In response to an unexpected threat, genetically transformed plants could thus provide a satisfactory solution, all the more since in a few years, coffee genome sequencing [ 3] will enable identification of genes coding for very important agronomical traits linked to disease resistance and/or abiotic stresses.
T-coffee-aligned sequences were analysed using the neighbour-joining method (options: p-distance model, compete removal of gaps, 10,000 bootstrap replications).
That's right: They sequenced coffee.
