May 23, 2013
Researchers Map Genome Of Two Important Spruce Tree Species
April Flowers for redOrbit.com - Your Universe Online
The genomes of two of the most economically important forest trees in the world were released by Canadian and Swedish scientists. In Canada, the conifers supply raw materials for the forest industry, accounting for $23.7 billion of the nation´s economy in 2011, while the gross output of the Swedish forest industry was $29.7 billion in 2009.Between them, the white spruce and the Norway spruce genomes have 20-30 billion base-pairs and are up to 10 times larger than the human genome, making these sequence assemblies the largest to date.
THE WHITE SPRUCE
A group of Canadian scientists, led by Professor Steven Jones, Head of Bioinformatics at the BC Cancer Agency Genome Sciences Centre (BCGSC) and a professor at both the University of British Columbia (UBC) and Simon Fraser University (SFU), sequenced the white spruce genome as part of the SMarTForests Project.
SMarTForests builds upon previous discoveries of the past decade to break new ground in spruce genome sequencing in order to represent Canada in international conifer genome initiatives and to achieve efficient translation of results toward end-users from across Canada.
"Attempting the sequencing of such a large genome was an incredibly ambitious task and required the development of novel software and innovative use of DNA sequence technology to piece together short DNA sequences to form this massive genome, much like a large jigsaw puzzle," said Jones. The findings of this study were published in the journal Bioinformatics.
"Many projects are now attempting to decipher genomes of economically important plants," Inanc Birol, a scientist with BCGSC and a professor with both UBC and SFU, said in a statement. "We demonstrated a superior and less expensive method to do the job."
"These genome sequences allow us to develop innovative tools for tree breeding, addressing economically and ecologically important targets such as insect resistance, wood quality, growth rates and adaptation to changing climate" added UBC Prof. Joerg Bohlmann, a collaborator on both studies.
"A genome-based marker system could serve to reduce the time of a spruce breeding cycle from currently 25 to as short as five years, and will contribute directly to the competitiveness of the Canadian and Scandinavian forest industry," said Prof. John MacKay of UniversitÃ© Laval, who also participated in both studies.
THE NORWAY SPRUCE
The Norway spruce, or the Christmas tree, is a species with a huge economic and ecological impact. The research project to map the genome of this important tree was led by the UmeÃ¥ Plant Science Centre (UPSC) in UmeÃ¥ and the Science for Life Laboratory (SciLifeLab) in Stockholm. The findings of their study were published in the journal Nature.
The knowledge gained from this study is expected to have immense importance to the forestry industry in many countries.
"Forest tree breeding is now entering a new era, and Sweden has the potential to be in the forefront of development," UPSC Professor Ove Nilsson, said in a UmeÃ¥ University statement. "Newer and more effective methods can begin to be used to ensure that the over 200 million tree seedlings planted each year in Sweden are as strong, healthy and well-adapted as possible for both poor and rich soil areas in different parts of the country."
Approximately 29,000 functional genes were identified for the Norway spruce, which is marginally more than humans have. This leaves the question of why the genome is seven times larger than the human genome? The researchers say the answer is “genome obesity” caused by extensive repetitive DNA sequences, which have accumulated for several hundred million years of evolutionary history. Although other plant and animal species have efficient mechanisms to eliminate repetitive DNA, this mechanism doesn´t seem to operate well in conifers.
"It is remarkable that the spruce is doing so well despite this unnecessary genetic load," said Professor PÃ¤r Ingvarsson at UPSC. "Of course, some of this DNA has a function but it seems strange that it would be beneficial to have so very much. This appears to be something special for conifers."
Getting the nearly 20 billion “letters” found in the tree´s genetic code into the correct order was the biggest challenge for the research team, rather than obtaining the actual DNA sequences.
"Imagine a library with ten thousand books as thick as the bible, written in a language with only four letters," explained Professor Stefan Jansson at UPSC. "If someone took one hundred identical copies of each of the ten thousand titles, passed them all through a document shredder and mixed all the shreds, and you then were asked to piece together an accurate copy of each title, you can realize that it can be a bit problematic."
"We had to customize computers and rewrite many of the computer programs used in similar studies in order to handle the large amount of DNA sequences," said Professor Joakim Lundeberg from SciLifeLab. There were many other practical problems that had to be solved along the way to pull through the project, including that the national data storage system was stretched to the limit.
"But the timing was optimal; when the new DNA sequencing machines were unpacked at our newly established laboratory, DNA arrived from our model spruce tree. By sequencing and analyzing the largest genome in the world so far, we have shown that SciLifeLab has both technical and scientific capacity for research at the highest international level," concluded Lundeberg.