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Table 6 Published plant plastome macro- and microarrays

From: A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Organism Array description Experiment Ref
tobacco nylon macroarray leaves of wild-type vs transplastomic tobacco lacking PEP [14]
tobacco cDNA microarray; 220 PCR probes (71 - 2373 bp), each corresponding to a single known gene or an intergenic region light- or dark-grown seedlings, RIP-chip analysis of MatK-bound RNAs [15, 47]
Physcomitrella patens cDNA microarray; 108 DNA fragments to detect all annotated plastid genes analysis of knockout transformant for the arginine tRNA gene, trnR-CCG [16]
Arabidopsis cDNA microarray; 79 PCR probes (88 - 1646 bp) representing protein-coding genes effects of the sig2 lesion on the global plastid gene expression [9]
Maize (used also for barley in CSH studies) cDNA microarray; 248 overlapping PCR products (73 - 1653 bp) covering the whole plastid genome identification of RNAs associated with PPR proteins in maize (CRP1, PPR4, PPR5) or whirly1 in barley, by RIP-chip [39, 48, 49]
Chlamydomonas reinhardtii cDNA microarray; PCR products (150 - 1500 bp) for 47 chloroplast, 9 mitochondrial, and 15 nuclear genes analysis of nonphotosynthetic mutants carrying mutations in the Mcd1 nuclear gene [17]
Cyanidioschyzon merolae (red algae) cDNA microarray; 193 PCR probes for protein coding genes and orfs role of nuclear-encoded sigma factors in plastid transcriptome changes during the shift from dark to light [10]
wheat (used also for barley and rice in CSH studies) nylon macroarray; 67 PCR products (200 bp - 1259 bp) representing 60 wheat plastid genes (excluding tRNAs) and 7 nuclear genes related to plastid metabolism germinating seeds and seedlings at three different
stages of development
Maize cDNA microarray; PCR probes for 887 nuclear, 62 chloroplast, and 27 mitochondrial transcripts comparison of chloroplasts and etioplasts in stage 2 semi-emerged leaf blades of one month-old plant [19]
tobacco, potato, tomato oligonucleotide microarray; 128 probes (68-71 bases) representing tobacco genes, ycfs and orfs (+ 5 probes designed for potato and tomato due to insufficient homology of tobacco probes) tomato fruit development and chloroplast-to-chromoplast conversion; potato tuber amyloplasts vs leaf chloroplasts comparison [6, 20]
Euglena gracilis nylon macroarray; 96 PCR probes (75 - 400 bp), representing all Euglena genes, pseudogenes and orfs 12 different developmental stages and stress treatments [21]
Arabidopsis nylon macroarray; 94 PCR probes for genes encoding plastid proteins, tRNAs and rRNAs; data were complemented with analysis of published data from Affymetrix 22 K ATH1 array experiments numerous nuclear Arabidopsis mutants affected in diverse chloroplast functions and wild-type plants subjected to various stresses and conditions [22]