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Putintseva Yuliya A.
Bondar Eugeniya I.
Simonov Evgeniy P.
Sharov Vadim V.
Oreshkova Natalya V.
Kuzmin Dmitry A.
Konstantinov Yuri M.
Shmakov Vladimir N.
Belkov Vadim I.
Sadovsky Michael G.
Keech Olivier
Krutovsky Konstantin V.
2021-02-15T12:29:13Z
2021-02-15T12:29:13Z
2020
14712164
http://elib.sfu-kras.ru/handle/2311/137952
Статья из журнала. Научное издание.
Background: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from similar to 222 Kbp inBrassica napusto 11.3 Mbp inSilene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibiricaLedeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results: Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions: Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plantSilene conica(11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.
BMC
Vol. 21, Is. 1
http://apps.webofknowledge.com/InboundService.do?SID=X1HogM8pCtTkhgkuprQ&product=WOS&UT=WOS%3A000576214200001&SrcApp=Alerting&DestFail=http%3A%2F%2Fwww.webofknowledge.com&Init=Yes&action=retrieve&SrcAuth=Alerting&Func=Frame&customersID=Alerting&IsProductCode=Yes&mode=FullRecord
larix sibirica
long reads
mitochondrial genome
mtdna
nucleotide sequence
rna editing
Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome : научное издание
Journal Article
Putintseva Yuliya A.: Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia
Bondar Eugeniya I.: Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia; Russian Acad Sci, Lab Genom Res & Biotechnol, Fed Res Ctr, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia
Simonov Evgeniy P.: Univ Tyumen, Inst Environm & Agr Biol XBIO, Tyumen 625003, Russia
Sharov Vadim V.: Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia; Russian Acad Sci, Lab Genom Res & Biotechnol, Fed Res Ctr, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia
Oreshkova Natalya V.: Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia; Russian Acad Sci, Lab Genom Res & Biotechnol, Fed Res Ctr, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia; Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia
Kuzmin Dmitry A.: Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia
Konstantinov Yuri M.: Russian Acad Sci, Siberian Inst Plant Physiol & Biochem, Lab Plant Genet Engn, Siberian Branch, Irkutsk 664033, Russia
Shmakov Vladimir N.: Russian Acad Sci, Siberian Inst Plant Physiol & Biochem, Lab Plant Genet Engn, Siberian Branch, Irkutsk 664033, Russia
Belkov Vadim I.: Russian Acad Sci, Siberian Inst Plant Physiol & Biochem, Lab Plant Genet Engn, Siberian Branch, Irkutsk 664033, Russia
Sadovsky Michael G.: Russian Acad Sci, Inst Computat Modeling, Siberian Branch, Krasnoyarsk 660036, Russia
Keech Olivier: Umea Univ, Dept Plant Physiol, UPSC, S-90187 Umea, Sweden
Krutovsky Konstantin V.: Siberian Fed Univ, Lab Forest Genom, Genome Res & Educ Ctr, Inst Fundamental Biol & Biotechnol, Krasnoyarsk 660036, Russia; August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany; George August Univ Gottingen, Ctr Integrated Breeding Res, D-37075 Gottingen, Germany; Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia
654
LONDON
10.1186/s12864-020-07061-4
BMC GENOMICS
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541822362-496042376


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