Table 6.

Published plant plastome macro- and microarrays

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	[18]
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]