Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers : материалы временных коллективов

Тип публикации: доклад, тезисы доклада, статья из сборника материалов конференций

Конференция: 11th International Multiconference on Bioinformatics of Genome Regulation and Structure\Systems Biology (BDRS\SB); Novosibirsk, RUSSIA; Novosibirsk, RUSSIA

Год издания: 2019

Идентификатор DOI: 10.1186/s12859-018-2571-x

Ключевые слова: Chloroplast genome, Larix sibirica, Sequencing, Siberian larch, SNPs, SSRs, Cell proliferation, DNA sequences, Forestry, Plants (botany), Program assemblers, Proteins, RNA, Genes, SSRsGenetic Markers

Аннотация: 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 thedata of the whole genome sequencing of three Siberian larch trees from different regions - theUrals, 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 ofthe 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 122,561bp, which is similar to 122,474bp in the closely related European larch (Larix decidua Mill.). As a result of annotation and comparison of the data with theexisting data available only for three larch species - L. decidua, L. potaninii var. chinensis (complete genome 122,492bp), and L. occidentalis (partial genome of 119,680bp), 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.

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Издание

Журнал: BMC BIOINFORMATICS

Выпуск журнала: Vol. 20

Номера страниц: 38

ISSN журнала: 14712105

Место издания: LONDON

Издатель: BMC

Авторы

  • Bondar Eugeniya I. (Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia)
  • Putintseva Yuliya A. (Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia)
  • Oreshkova Nataliya V. (Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia; Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia)
  • Krutovsky Konstantin V. (Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia; Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany; Russian Acad Sci, Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia; Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USAArticleProceedings Paper)

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