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

Plastids form a large family of cellular organelles that occur in plants and algae. The most prominent members of the plastid family are chloroplasts. Chloroplasts use light energy to convert carbon dioxide into organic compounds in a process called photosynthesis. Depending on tissue localization and environmental conditions, other types of plastids may develop. Plastids are also involved in various aspects of plant cell metabolism, e.g., they can store starch, lipids or proteins. Certain factors can induce mature plastids to transform from one type to another, as well as to revert back [1]. The process of plastid biogenesis and interconversion is coupled with large structural and biochemical changes. This huge transformation potential of plastids is partly a result of the presence of their own genetic material (plastome) and inherent transcriptional and translation machinery. The first complete sequences of plastid genomes (from Nicotiana tabacum and Marchantia polymorpha) were determined in 1986. Currently, more than 200 plastome sequences are available in GenBank. Most of them (more than 170) are derived from flowering plants. The majority of plastomes were sequenced after 2006, when high throughput sequencing methods became more widely available and less expensive [2,3]. The sequences of plastid genomes and their organization are highly conserved. Plastomes range in length from 120 to 200 Mbp. They usually contain two large inverted repeats (IR), namely IRA and IRB, separated by single copy regions. However, in some plants, such as Medicago truncatula, the plastomes lack one IR region. Genes encoded in the plastome can be divided into two categories: protein coding (about 70-100 genes, mostly coding for proteins related to the light-phase of photosynthesis or coding for ribosomal proteins), and RNA coding (about 30-50 rRNA and tRNA genes). There are also some conserved open reading frames (conserved ORFs), which have undefined or poorly defined functions. Some