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Isolating Linum usitatissimum L. Nuclear DNA Enabled Assembling High-Quality Genomeстатья
Статья опубликована в высокорейтинговом журнале
Статья опубликована в журнале из списка Web of Science и/или Scopus- Авторы: Dvorianinova Ekaterina M., Bolsheva Nadezhda L., Pushkova Elena N., Rozhmina Tatiana A., Zhuchenko Alexander A., Novakovskiy Roman O., Povkhova Liubov V., Sigova Elizaveta A., Zhernova Daiana A., Borkhert Elena V., Kaluzhny Dmitry N., Melnikova Nataliya V., Dmitriev Alexey A.
- Журнал: International Journal of Molecular Sciences
- Том: 23
- Номер: 21
- Год издания: 2022
- Издательство: MDPI
- Местоположение издательства: Basel, Switzerland
- Первая страница: 13244
- DOI: 10.3390/ijms232113244
- Аннотация: High-quality genome sequences help to elucidate the genetic basis of numerous biological processes and track species evolution. For flax (Linum usitatissimum L.)—a multifunctional crop, high-quality assemblies from Oxford Nanopore Technologies (ONT) data were unavailable, largely due to the difficulty of isolating pure high-molecular-weight DNA. This article proposes a scheme for gaining a contiguous L. usitatissimum assembly using Nanopore data. We developed a protocol for flax nuclei isolation with subsequent DNA extraction, which allows obtaining about 5 μg of pure high-molecular-weight DNA from 0.5 g of leaves. Such an amount of material can be collected even from a single plant and yields more than 30 Gb of ONT data in two MinION runs. We performed a comparative analysis of different genome assemblers and polishers on the gained data and obtained the final 447.1-Mb assembly of L. usitatissimum line 3896 genome using the Canu—Racon (two iterations)—Medaka combination. The genome comprised 1695 contigs and had an N50 of 6.2 Mb and a completeness of 93.8% of BUSCOs from eudicots_odb10. Our study highlights the impact of the chosen genome construction strategy on the resulting assembly parameters and its eligibility for future genomic studies.
- Добавил в систему: Жернова Даяна Александровна