Tortula ruralis (Hedw.) Gaertn., also known as Syntrichia ruralis (Hedw.) F. Weber & D. Mohr (Pottiaceae) is a moss with a cosmopolitan distribution in relatively dry habitats. In North America the species is widespread in northern latitudes but is more common in the Western U.S., south into Mexico . Tortula ruralis has received considerable attention over the last forty years as a model for the study of vegetative desiccation tolerance, i.e., the ability to equilibrate to the water potential of dry air and survive, regaining growth and development upon rehydration. Tortula ruralis offers much as an experimental model for the study of environmental impacts on plants: it grows easily in culture, has a limited number of cell types, and, because of its morphology, experimental treatments act directly at the cellular level [2, 3]. It is the latter property that also makes it an ideal choice for an indicator species in air pollution studies [4, 5].
Tortula ruralis is among the most desiccation-tolerant of land plants and it can recover from desiccation even after at least three years in the dried state [6, 7]. Physcomitrella patens is relatively tolerant of dehydration but cannot tolerate the levels of drying that T. ruralis can survive . It is well established that the chloroplast plays a central role in the recovery of vegetative plants cells from desiccation  and it is possible that differences between the chloroplast genomes of T. ruralis and P. patens may relate to this fundamental difference between the two mosses.
The rapid recovery of photosynthesis is critical in order to recover and re-establish growth when water is available, thus maximizing the time available to the moss for carbon fixation and productivity . Following slow drying to -100 Mpa, photosystem II (PSII) activity in T. ruralis recovers within minutes after rewetting , with normal rates of carbon fixation returning within an hour . Photosynthesis is essential for the production of the energy required for repair and protein synthesis following the desiccation event. Obviously, the integrity and metabolic capacity of the chloroplast is central to the speed of recovery of photosynthesis. It is clear from electron microscopic observation of freeze-fracture preparations that chloroplast membranes, both the envelope and thylakoid membranes, in T. ruralis are unaltered by desiccation , which supports the idea that desiccation does not damage the photosynthetic apparatus. Such protection of chloroplast structure has also been demonstrated for gametophytes of Polytrichum formosum, which also appear to be unaltered by the imposition of desiccation and the rigors of rehydration . Thus it is clear that the chloroplast holds a central role in the response of T. ruralis to desiccation and rehydration and it is important to study the nature of its genome in this plant, the first vegetatively desiccation-tolerant plant to have its chloroplast genome sequenced. The genome sequence of T. ruralis, and its comparison to other chloroplast genomes, is critical if we want to understand how the interplay between the nuclear and chloroplast genomes plays a role in desiccation tolerance.
In addition to the relevance of the T. ruralis chloroplast genome to the important trait of desiccation tolerance, the genome sequence has considerable relevance to our current understanding of evolutionary history of the land plants. Current evidence suggests that mosses are the sister group of hornworts plus tracheophytes, diverging at least 450 million years ago [13, 14]. As an early diverging lineage, mosses hold a place in the phylogeny of land plants that is important for comparative purposes to seed plants , although comparisons are currently hampered because only one published chloroplast genome is available for mosses, while hundreds are available for its sister group. Several chloroplast genome sequences will be required to estimate the ancestral genome sequence for mosses, which will in turn allow comparisons with tracheophyte genomes.
The interest in Tortula ruralis as a model desiccation-tolerant organism has increased as our need to understand how plants survive dehydration stress grows and the global impact of climate change becomes more critical. This impetus and the need for increasing sampling within the mosses for phylogenetic comparative purposes led to the choice of T. ruralis for chloroplast genome sequencing. The assembly and annotation of the T. ruralis chloroplast genome sequence is presented here, only the second chloroplast genome sequenced for a moss and the first for a desiccation tolerant plant. The first chloroplast genome for a moss, Physcomitrella patens, was completed in 2003 . Because P. patens was found to have a major rearrangement in the chloroplast compared to what PCR-based methods show for most other moss lineages , the T. ruralis chloroplast genome will serve as an important point of comparison and will assist in ongoing efforts to utilize whole-genomic sequences and structural characters in a comparative phylogenetic framework [13, 18].