The family of pines are part of the oldest group of trees, the gymnosperms, which arose when dinosaurs were still roaming around the Earth 290 million years ago. Pines hold several records because of this fact, since among the family are the oldest-living trees, the nearly 5,000 year old bristlecone pines of Nevada and California. Now joining that lofty group are the owners of the largest and most intricate genome fully explored to date.
The loblolly pine, also known as the southern yellow pine, is a complex species that has been around for millennia. Because of this fact, these trees have done well and are widespread, existing in many ecosystems. Having survived plague and climate alterations, the species has a very lengthy DNA sequence that is just now being studied in its entirety.
This subspecies of pine is the tree species most used in the U.S. for wood pulp production. This is because it can be farmed in many regions and climates, and because it has survived thousands of years and built up resistance to many of the bacteria and fungus that kill other tree species. Because of this resistance, however, and the trees’ long history on earth, its genome is one of the more complicated ones ever studied. As each disease is battled by the trees’ genome, the species inherits grafts of other DNA onto the strand which can be used to fight disease incursions in future.
In the past, scientists could only study an entire genome with a lot of time and massive computing power, and thus have studied only full genomes the size of the human DNA strand. The loblolly pine, however, has a genome which is seven times longer than that of humans. It is important to study the loblolly DNA, however, so that farmers and ecologists can understand the resistance these trees have to disease and the mechanisms by which they have survived for so long and in such a widespread manner.
The University of Maryland has come up with a new genome packaging method, though, which shortcuts the old method of study. This system pre-processes genomes en route to other universities, eliminating DNA sequences that are repetitive or redundant before sending them on. The loblolly genome was pre-processed in this way and then sent on to UC Davis for study.
This processing was important in that DNA has to be taken apart to be studied, and then reassembled for further research. Short sequences removed from the whole are easier to study, but putting them back together is a difficult puzzle and takes more time and computing power than studying the sequences themselves. The work done by the University of Maryland made it possible for the geneticists at UC Davis to tackle the entire massive genome of the loblolly much more quickly than expected.
Previously, studying an entire genome of that size was impossible for current computational technology. Cracking this genetic code made the pine family a record-holder yet again, producing not just the oldest known trees but the species with the longest genome ever explored thus far.
When the loblolly code was cracked, it was via a multi-university effort. Under UC Davis’ lead, many institutions lent manpower and computational resources to the endeavor. The U.S. Department of Agriculture supported the work. Johns Hopkins contributed to University of Maryland’s pre-processing efforts, while Texas A&M, Indiana University of Bloomington, Washington State University, and Children’s Hospital Research Institute in Oakland all aided in the genome study along with many independent researchers. The results of the massive undertaking were published in two journals; the scholarly Genetics, and Genome Biology, which is an open-access journal. In this way, the research was openly shared as it progressed.
It is difficult to overstate the significance of this breakthrough for industry. Understanding the loblolly pine’s resistance to disease will help farmers breed stronger strains of the species for production of wood products and for use in the new loblolly-based biofuel industry. The completed genome also offers a fuller understanding of the evolution of the species and of plants in general, of how they function in their environments over long periods of time, and how they interact with humans, animals and climates. The loblolly pine now joins fellow record-holder, the bristlecone pine tree, in superlatives, with the longest genome ever studied now standing beside the oldest tree to exist.
By Kat Turner
University of Florida