Krutovsky K. V., Oreshkova N. V., Putintseva Yu. A., Ibe A. A., Deych K. O., Shilkina E. A. Preliminary Results of De Novo Whole Genome Sequencing of the Siberian Larch (Larix sibirica Ledeb.) and the Siberian Stone Pine (Pinus sibirica Du Tour)
Gubkin str., 3, Moscow, 119333 Russian Federation
2 University of Göttingen
Büsgenweg, 2, Göttingen, D-37077 Germany
3 Siberian Federal University, Genome Research and Education Center
Akademgorodok, 50a/2, Krasnoyarsk, 660036 Russian Federation
4 Texas A&M University
HFSB 305, 2138 TAMU, College Station, Texas, 77843 USA
5 V. N. Sukachev Institute of Forest, Russian Academy of Sciences, Siberian Branch
Abstract
How to cite: Krutovsky K. V.1, 2, 3, 4, Oreshkova N. V.3, 5, Putintseva Yu. A.3, Ibe A. A.3, 6, Deych K. O.3, 6, Shilkina E. A.3, 6 Preliminary results of de novo whole genome sequencing of the Siberian larch (Larix sibirica Ledeb.) and the Siberian stone pine (Pinus sibirica Du Tour) // Sibirskij Lesnoj Zurnal (Siberian Journal of Forest Science). 2014. N. 4: 79–83 (in Russian with English abstract)
© Krutovsky K. V., Oreshkova N. V., Putintseva Yu. A., Ibe A. A., Deych K. O., Shilkina E. A., 2014
The Illumina HiSeq2000 DNA sequencing generated 2 906 977 265 high quality paired-end nucleotide sequences (reads) and 576 Gbp for Siberian larch (Larix sibirica Ledeb.) that corresponds to 48X coverage of the larch genome (12.03 Gbp), and 3 427 566 813 reads and 679 Gbp for Siberian stone pine (Pinus sibirica Du Tour.) that corresponds to 29X coverage of its genome (23.6 Gbp). These data are not enough to assemble and annotate whole genomes, but the obtained nucleotide sequences have allowed us to discover and develop effective highly polymorphic molecular genetic markers, such as microsatellite loci that are required for population genetic studies and identification of the timber origin. Sequence data can be used also to discover single nucleotide polymorphisms (SNPs). The chloroplast genomes of Larix sibirica (122561 bp) and Pinus sibirica (116704 bp) were completely assembled and annotated. First working draft assemblies of mitochondrial genome were also obtained for these two species. In addition, genome studies of high and low pathogenic forms or strains of major pathogens of the Russian boreal forests as Heterobasidion annosum s.l. and Armillaria mellea s.l. have been carried out. Genomic studies of Russian boreal forests and major phytopathogens associated with them will allow us to identify biomarkers that can be used for solving important scientific and economic problems related to the conservation of forest genetic resources and breeding more resilient and fast growing trees with improved wood quality and resistance to diseases and adverse environmental factors.
