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] |