Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
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URI (для ссылок/цитирований):
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2570-yhttps://elib.sfu-kras.ru/handle/2311/129305
Автор:
Dmitry A. Kuzmin
Sergey I. Feranchuk
Vadim V. Sharov
Alexander N. Cybin
Stepan V. Makolov
Yuliya A. Putintseva
Natalya V. Oreshkova
Konstantin V. Krutovsky
Коллективный автор:
Институт космических и информационных технологий
Институт фундаментальной биологии и биотехнологии
Кафедра высокопроизводительных вычислений
Базовая кафедра защиты и современных технологии мониторинга лесов
Дата:
2019-02Журнал:
BMC BioinformaticsКвартиль журнала в Scopus:
Q1Квартиль журнала в Web of Science:
Q1Библиографическое описание:
Dmitry A. Kuzmin. Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb) [Текст] / Dmitry A. Kuzmin, Sergey I. Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Natalya V. Oreshkova, Konstantin V. Krutovsky // BMC Bioinformatics. — 2019. — Т. 20.Аннотация:
Background
De novo assembling of large genomes, such as in conifers (~ 12–30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.
Results
An original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.
Conclusion
Using the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.