Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers

BMC Bioinformatics

  ^{1    1    2    3} 

[1] 0000 0001 0940 9855, grid.412592.9, Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;0000 0001 0940 9855, grid.412592.9, Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;0000 0001 2254 1834, grid.415877.8, Laboratory of Forest Genetics and Selection, V.N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, 660036, Krasnoyarsk, Russian Federation;0000 0001 0940 9855, grid.412592.9, Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;0000 0001 2364 4210, grid.7450.6, Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, D-37077, Göttingen, Germany;0000 0001 2192 9124, grid.4886.2, Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333, Moscow, Russia;0000 0004 4687 2082, grid.264756.4, Department of Ecosystem Science and Management, Texas A&M University, 77843-2138, College Station, TX, USA;

关键词: Chloroplast genome;    Larix sibirica;    Sequencing;    Siberian larch;    SNPs;    SSRs;   

DOI  :  10.1186/s12859-018-2571-x

来源: publisher

【 摘 要 】

BackgroundThe main objectives of this study were sequencing, assembling, and annotation of chloroplast genome of one of the main Siberian boreal forest tree conifer species Siberian larch (Larix sibirica Ledeb.) and detection of polymorphic genetic markers – microsatellite loci or simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs).ResultsWe used the data of the whole genome sequencing of three Siberian larch trees from different regions - the Urals, Krasnoyarsk, and Khakassia, respectively. Sequence reads were obtained using the Illumina HiSeq2000 in the Laboratory of Forest Genomics at the Genome Research and Education Center of the Siberian Federal University. The assembling was done using the Bowtie2 mapping program and the SPAdes genomic assembler. The genome annotation was performed using the RAST service. We used the GMATo program for the SSRs search, and the Bowtie2 and UGENE programs for the SNPs detection. Length of the assembled chloroplast genome was 122,561 bp, which is similar to 122,474 bp in the closely related European larch (Larix decidua Mill.). As a result of annotation and comparison of the data with the existing data available only for three larch species - L. decidua, L. potaninii var. chinensis (complete genome 122,492 bp), and L. occidentalis (partial genome of 119,680 bp), we identified 110 genes, 34 of which represented tRNA, 4 rRNA, and 72 protein-coding genes. In total, 13 SNPs were detected; two of them were in the tRNA-Arg and Cell division protein FtsH genes, respectively. In addition, 23 SSR loci were identified.ConclusionsThe complete chloroplast genome sequence was obtained for Siberian larch for the first time. The reference complete chloroplast genomes, such as one described here, would greatly help in the chloroplast resequencing and search for additional genetic markers using population samples. The results of this research will be useful for further phylogenetic and gene flow studies in conifers.

【 授权许可】

CC BY