Сибирский федеральный университет

Тип публикации: статья из журнала

Год издания: 2022

Идентификатор DOI: 10.3390/plants11152062

Ключевые слова: angiosperms, annotation, conifer, deciduous, genome, gymnosperms, microsatellites, repeats, rna-seq, seasonal senescence, siberian larch, transcriptome, transposons

Аннотация: The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies. © 2022 by the authors.

Журнал: Plants

Выпуск журнала: Vol. 11, Is. 15

Номера страниц: 2062

ISSN журнала: 22237747

Издатель: MDPI

• Bondar E.I. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center”, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation)
• Feranchuk S.I. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation)
• Miroshnikova K.A. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center”, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation)
• Sharov V.V. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center”, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation, Department of High-Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation)
• Kuzmin D.A. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Department of High-Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation)
• Oreshkova N.V. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Laboratory of Genomic Research and Biotechnology, Federal Research Center “Krasnoyarsk Science Center”, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation, Laboratory of Forest Genetics and Selection, V. N. Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation)
• Krutovsky K.V. (Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660036, Russian Federation, Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, 37077, Germany, Center for Integrated Breeding Research, Georg-August University of Göttingen, Göttingen, 37075, Germany, Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russian Federation, Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660074, Russian Federation, Scientific and Methodological Center, G. F. Morozov Voronezh State, University of Forestry and Technologies, Voronezh, 394087, Russian Federation)

• Scopus