Сибирский федеральный университет

Тип публикации: статья из журнала

Год издания: 2021

Идентификатор DOI: 10.3390/life11111234

Ключевые слова: gymnosperms, principal component analysis, repetitive elements

Аннотация: Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The “repeatome” information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs. Here, raw genomic NGS reads of 10 gymnosperm species were studied for the content and abundance patterns of their “repeatome”. We utilized a combi-nation of alignment on databases of repetitive elements and de novo assembly of highly repetitive sequences from genomic sequencing reads to characterize and calculate the abundance of known and putative repetitive elements in the genomes of 10 conifer plants: Pinus taeda, Pinus sylvestris, Pinus sibirica, Picea glauca, Picea abies, Abies sibirica, Larix sibirica, Juniperus communis, Taxus baccata, and Gnetum gnemon. We found that genome abundances of known and newly discovered putative repeats are specific to phylogenetically close groups of species and match biological taxa. The grouping of species based on abundances of known repeats closely matches the grouping based on abundances of newly discovered putative repeats (kChains) and matches the known taxonomic relations. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Журнал: Life

Выпуск журнала: Vol. 11, Is. 11

Номера страниц: 1234

ISSN журнала: 20751729

Издатель: MDPI

• Titievsky Avi (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel)
• Putintseva Yuliya A. (Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia)
• Taranenko Elizaveta A. (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel; Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia)
• Baskin Sofya (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel)
• Oreshkova Natalia V. (Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia; Russian Acad Sci, Fed Res Ctr Krasnoyarsk Sci Ctr Siberian Branch, Lab Genom Res & Biotechnol, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Dept Genom & Bioinformat, Krasnoyarsk 660074, Russia; GF Morozov Voronezh State Univ Forestry & Techno, Sci & Methodol Ctr, Voronezh 394087, Russia)
• Brodsky Elia (Pine Biotech Inc, New Orleans, LA 70112 USA)
• Sharova Alexandra V. (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel; Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia)
• Sharov Vadim V. (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel; Russian Acad Sci, Fed Res Ctr Krasnoyarsk Sci Ctr Siberian Branch, Lab Genom Res & Biotechnol, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia)
• Panov Julia (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel)
• Kuzmin Dmitry A. (Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia)
• Brodsky Leonid (Univ Haifa, Tauber Bioinformat Res Ctr, IL-3498838 Haifa, Israel)
• Krutovsky Konstantin V. (Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Inst Fundamental Biol & Biotechnol, Dept Genom & Bioinformat, Krasnoyarsk 660074, Russia; GF Morozov Voronezh State Univ Forestry & Techno, Sci & Methodol Ctr, Voronezh 394087, Russia; Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany)

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