Assembly of cucumber (Cucumis sativus L.) somaclones

Agnieszka Skarzyńska; Wiktor Kuśmirek; Magdalena Pawełkowicz; Wojciech Pląder; Robert M. Nowak

doi:10.1117/12.2280630

7 August 2017 Assembly of cucumber (Cucumis sativus L.) somaclones

Agnieszka Skarzyńska, Wiktor Kuśmirek, Magdalena Pawełkowicz, Wojciech Pląder, Robert M. Nowak

Proceedings Volume 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017; 1044534 (2017) https://doi.org/10.1117/12.2280630
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2017, 2017, Wilga, Poland

Abstract

The development of next generation sequencing opens the possibility of using sequencing in various plant studies, such as finding structural changes and small polymorphisms between species and within them. Most analyzes rely on genomic sequences and it is crucial to use well-assembled genomes of high quality and completeness. Herein we compare commonly available programs for genomic assembling and newly developed software - dnaasm. Assemblies were tested on cucumber (Cucumis sativus L.) lines obtained by in vitro regeneration (somaclones), showing different phenotypes. Obtained results shows that dnaasm assembler is a good tool for short read assembly, which allows obtaining genomes of high quality and completeness.

Citation Download Citation

Agnieszka Skarzyńska, Wiktor Kuśmirek, Magdalena Pawełkowicz, Wojciech Pląder, and Robert M. Nowak "Assembly of cucumber (Cucumis sativus L.) somaclones", Proc. SPIE 10445, Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017, 1044534 (7 August 2017); https://doi.org/10.1117/12.2280630

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