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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


Array description




nylon macroarray

leaves of wild-type vs transplastomic tobacco lacking PEP



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



cDNA microarray; 79 PCR probes (88 - 1646 bp) representing protein-coding genes

effects of the sig2 lesion on the global plastid gene expression


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


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


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



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


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



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