01951nas a2200265   4500008004100000245009000041210006900131300001200200490000800212520099700220653008201217653001201299653011301311100001501424700001501439700001601454700001401470700001601484700001501500700001501515700001901530700001501549700001501564856010601579       2007                        eng d00aTranscriptional response of Citrus aurantifolia to infection by Citrus tristeza virus0 aTranscriptional response of Citrus aurantifolia to infection by   a298-3060 v3673 aChanges in gene expression of Mexican lime plants in response to infection with a severe (T305) or a mild (T385) isolate of Citrus tristeza virus (CTV) were analyzed using a cDNA microarray containing 12,672 probes to 6875 different citrus genes. Statistically significant (P<0.01) expression changes of 334 genes were detected in response to infection with isolate T305, whereas infection with T385 induced no significant change. Induced genes included 145 without significant similarity with known sequences and 189 that were classified in seven functional categories. Genes related with response to stress and defense were the main category and included 28% of the genes induced. Selected transcription changes detected by microarray analysis were confirmed by quantitative real-time RT-PCR. Changes detected in the transcriptome upon infecting lime with T305 may be associated either with symptom expression, with a strain-specific defense mechanism, or with a general response to stress.10aCitrus/*genetics/physiology/virology Closterovirus/genetics/*physiology Genes10aGenetic10aPlant Oligonucleotide Array Sequence Analysis Reverse Transcriptase Polymerase Chain Reaction *Transcription1 aGandia, M.1 aConesa, A.1 aAncillo, G.1 aGadea, J.1 aForment, J.1 aPallas, V.1 aFlores, R.1 aDuran-Vila, N.1 aMoreno, P.1 aGuerri, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1761743101950nas a2200229   4500008004100000245009500041210006900136300001000205490000700215520116100222653001401383653005301397653002801450653003701478100001801515700001501533700001901548700001501567700001901582700001301601856010601614       2001                        eng d00aPhylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment0 aPhylogenetic analysis of viroid and viroidlike satellite RNAs fr  a155-90 v533 aThe proposed monophyletic origin of a group of subviral plant pathogens (viroids and viroid-like satellite RNAs), as well as the phylogenetic relationships and the resulting taxonomy of these entities, has been recently questioned. The criticism comes from the (apparent) lack of sequence similarity among these RNAs necessary to reliably infer a phylogeny. Here we show that, despite their low overall sequence similarity, a sequence alignment manually adjusted to take into account all the local similarities and the insertions/deletions and duplications/rearrangements described in the literature for viroids and viroid-like satellite RNA, along with the use of an appropriate estimator of genetic distances, constitutes a data set suitable for a phylogenetic reconstruction. When the likelihood-mapping method was applied to this data set, the tree-likeness obtained was higher than that corresponding to a sequence alignment that does not take into consideration the local similarities. In addition, bootstrap analysis also supports the major groups previously proposed and the reconstruction is consistent with the biological properties of this RNAs.10aEvolution10aMolecular *Phylogeny Plant Viruses/*genetics RNA10aSatellite/*genetics RNA10aViral/genetics Viroids/*genetics1 aElena, S., F.1 aDopazo, J.1 ade la Pena, M.1 aFlores, R.1 aDiener, T., O.1 aMoya, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11479686