microrobert
03-21-2014, 01:46 PM
Newly sequenced tree genome is seven times larger than human genome
The researchers found that 82 percent of the loblolly genome is made up of invasive DNA elements and other DNA pieces that copied themselves around the genome.
A team led by a UC-Davis scientist has successfully (http://news.ucdavis.edu/search/news_detail.lasso?id=10859) sequenced the genome of the loblolly pine; no small feat, as the newly sequenced tree genome is seven times bigger than the human genome. The findings were published in both Genome Biology and GENETICS.
The significance of this achievement is that the loblolly pine is the most commercially useful forest species in the United States and the information revealed by the successful genome sequencing could help researchers learn more about disease resistance in pines.
“It’s a huge genome. But the challenge isn’t just collecting all the sequence data. The problem is assembling that sequence into order,” said David Neale, a professor of plant sciences at UC-Davis.
Researchers completed the sequencing by using a faster and more efficient analytical process, developed by researchers at the University of Maryland, which pre-processes the sequence data, eliminates redundancies and generates a lower quantity of sequence data.
The researchers described the process in GENETICS:
“Applied to our data, the MaSuRCA assembler can be conceptually divided into four major phases. The first phase corrects errors in the Illumina reads, using the QuORUM error corrector. The second phase reduces the short and highly redundant Illumina paired-end reads to a concise set of super-reads [...] The third phase of assembly uses an adapted overlap-based assembler, CABOG, to assemble the super-reads together with filtered read pairs from the longer diploid libraries. The final phase further increases contiguity by using a local assembly algorithm to fill gaps in the scaffolds.”
The researchers found that 82 percent of the loblolly genome is made up of invasive DNA elements and other DNA pieces that copied themselves around the genome. The effort also revealed the location of genes that may be involved in fighting off pathogens.
“In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied,” wrote the researchers in Genome Biology.
Newly sequenced tree genome is seven times larger than human genome | The State Column (http://www.statecolumn.com/2014/03/newly-sequenced-tree-genome-is-seven-times-bigger-than-human-genome/)
The researchers found that 82 percent of the loblolly genome is made up of invasive DNA elements and other DNA pieces that copied themselves around the genome.
A team led by a UC-Davis scientist has successfully (http://news.ucdavis.edu/search/news_detail.lasso?id=10859) sequenced the genome of the loblolly pine; no small feat, as the newly sequenced tree genome is seven times bigger than the human genome. The findings were published in both Genome Biology and GENETICS.
The significance of this achievement is that the loblolly pine is the most commercially useful forest species in the United States and the information revealed by the successful genome sequencing could help researchers learn more about disease resistance in pines.
“It’s a huge genome. But the challenge isn’t just collecting all the sequence data. The problem is assembling that sequence into order,” said David Neale, a professor of plant sciences at UC-Davis.
Researchers completed the sequencing by using a faster and more efficient analytical process, developed by researchers at the University of Maryland, which pre-processes the sequence data, eliminates redundancies and generates a lower quantity of sequence data.
The researchers described the process in GENETICS:
“Applied to our data, the MaSuRCA assembler can be conceptually divided into four major phases. The first phase corrects errors in the Illumina reads, using the QuORUM error corrector. The second phase reduces the short and highly redundant Illumina paired-end reads to a concise set of super-reads [...] The third phase of assembly uses an adapted overlap-based assembler, CABOG, to assemble the super-reads together with filtered read pairs from the longer diploid libraries. The final phase further increases contiguity by using a local assembly algorithm to fill gaps in the scaffolds.”
The researchers found that 82 percent of the loblolly genome is made up of invasive DNA elements and other DNA pieces that copied themselves around the genome. The effort also revealed the location of genes that may be involved in fighting off pathogens.
“In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied,” wrote the researchers in Genome Biology.
Newly sequenced tree genome is seven times larger than human genome | The State Column (http://www.statecolumn.com/2014/03/newly-sequenced-tree-genome-is-seven-times-bigger-than-human-genome/)