Conifers div. Pinophyta include approximately 6-8 families, 65-70 genera and 600-700 species worldwide. Pinaceae is the largest extant family with approximately 220-250 species mostly dominating the temperate regions of the northern hemisphere. Its distribution ranges from sub arctic to tropical. Conifers represent the largest terrestrial carbon sink and have immense economic and ecological importance. Conifer plantations for wood production account for 60% of worldwide reforestation and cover nearly 800 000 square kilometres (FAO, 2007 State of the World's Forests).
The problems raised by global warming in different ecosystems and depletion by certain diseases and pests, fires, as well as harvesting at a faster rate than regeneration either naturally or artificially, are all important reasons to investigate and enhance our knowledge about the mechanisms controlling the expression of important adaptive and productive traits. This knowledge will allow the exploitation of natural genetic resources and the use of new forest reproductive materials for adaptation to climatic change. This will facilitate the maintainance of high quality standards of European forests as sustainable production tools.
Conifers have a large genome size (20-30 Gigabase pairs) and high frequency of repetitive sequences. These pose considerable limitation to structural and functional genomic studies. Conifer gene sequences are highly conserved and gene order is frequently collinear. Thus, comparative genomic methods and approaches would be highly useful for the rapid transfer of concepts and findings from one species to another. Conifers evolve very slowly and have relatively slow nucleotide substitution rate per year compared to other species. Some recently diverged species show a surprisingly high level of shared polymorphism. Thus, species such as the Mediterranean Pinus pinaster and the boreal Pinus sylvestris have adapted to rather different environments using very similar genomic resources.
Knowledge about genetically controlled plasticity and adaptation under various environmental conditions will improve both short and long term performance predictions under current and prognosed climate change scenarios, which is highly significant for conifer breeding, not only within but also beyond European boundaries. Recent advances in microarray and high-throughput sequencing techniques facilitate the study of epigenomics, which elucidates how cells decipher and execute the information stored and encoded in the genome. Next-generation sequencing can radically change our ability to sequence conifer genomes in a very short span of time. This is the key to unlocking conifer mega-genomes.