John Muir declared the sugar pine to be “king of the conifers” more than a century ago. Now scientists have sequenced its genome.
At 10 times the size of the human genome, the sugar pine genome is the largest ever sequenced for any organism. The findings are expected to provide valuable information that may help preserve the iconic but endangered tree.
“Having the genome sequence allows us to discover the underlying genetic determinants of disease resistance, which will greatly facilitate reforestation efforts,” says David Neale, a forest tree geneticist at the University of California, Davis. “We can now give forest managers modern, rapid genetic tools to identify resistant trees.”
The genome has been publicly released and is available through open access at the Pine Reference Sequences website.
The sugar pine (Pinus lambertiana) is one of the tallest tree species in the world. It is endemic primarily to California, stretching south into parts of Baja Mexico and north into Oregon. The tree’s pinecones, averaging 10 to 20 inches in length, are among the longest of any conifer species.
“The sugar pine has important environmental value as a key component of California forests, ecological and recreational value throughout the Sierra Nevada, and economic value as a source of timber,” Neale says.
Around 1930, white pine blister rust was introduced into California. The fungal pathogen is a significant threat to sugar pines and other species of “white pines.” In fact, of the commercially important white pines in North America, sugar pine is most susceptible to white pine blister rust.
In addition, sugar pine survival is threatened by damage from bark beetles, and the ongoing drought and lack of snowpack in the Sierra.
Pine trees and other ancient conifers are dominant species in forests found in temperate regions of the world. The genus Pinus includes over 100 species of pine trees, which fall into two major subgroups—yellow pines and white pines. The loblolly pine, a member of the yellow pine subgroup, was sequenced by Neale, Langley and colleagues last year. The newly sequenced sugar pine has a genome 1.5 times larger than the loblolly pine, which itself was considered large when it was sequenced. These two new reference sequences serve as foundations for future studies and applications in pine trees.
“The sequencing and assembly of these two pine genomes reaches the present-day limits of genomic technologies and methods,” says geneticist Charles Langley. “Like the human genome reference sequence, they are not yet complete, but they do provide an almost complete ‘parts list’ and a draft of the ‘instructions.'”
Bohun Kinloch, an emeritus research geneticist with the US Forest Service, used traditional breeding methods and progeny testing over many years, before sequencing existed, to detect a rare blister rust resistance gene in sugar pine “parent trees” in 1970.
“The US Forest Service plants seedlings from resistant parent trees into forests, so the new diagnostic tools derived from the reference sequences will speed the finding of disease-resistant parent trees directly, bypassing costly progeny testing. Seeds planted from these parents will help protect new generations of sugar pine trees from the devastating blister rust pathogen,” Kinloch says.
A report of the sequencing and analyses of the sugar pine genome is pending publication in a scientific journal. The scientific reports of the loblolly genome sequencing appeared last year in the journals Genetics and Genome Biology.
Researchers at Johns Hopkins University and the University of Connecticut contributed to the work.
Source: UC Davis