Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA

Abstract The macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimate...

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Autores principales:	Ina J. Andresen, Russell J. S. Orr, Anders K. Krabberød, Kamran Shalchian-Tabrizi, Jon Bråte
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e9848a2fddad42d7affa7c63b365cf4a
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spelling	oai:doaj.org-article:e9848a2fddad42d7affa7c63b365cf4a2021-12-02T17:24:00ZGenome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA10.1038/s41598-021-92092-42045-2322https://doaj.org/article/e9848a2fddad42d7affa7c63b365cf4a2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92092-4https://doaj.org/toc/2045-2322Abstract The macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7–11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.Ina J. AndresenRussell J. S. OrrAnders K. KrabberødKamran Shalchian-TabriziJon BråteNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ina J. Andresen Russell J. S. Orr Anders K. Krabberød Kamran Shalchian-Tabrizi Jon Bråte Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
description	Abstract The macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7–11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.
format	article
author	Ina J. Andresen Russell J. S. Orr Anders K. Krabberød Kamran Shalchian-Tabrizi Jon Bråte
author_facet	Ina J. Andresen Russell J. S. Orr Anders K. Krabberød Kamran Shalchian-Tabrizi Jon Bråte
author_sort	Ina J. Andresen
title	Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
title_short	Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
title_full	Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
title_fullStr	Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
title_full_unstemmed	Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA
title_sort	genome sequencing and de novo assembly of the giant unicellular alga acetabularia acetabulum using droplet mda
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e9848a2fddad42d7affa7c63b365cf4a
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Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA

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