Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

ABSTRACT Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we ass...

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Autores principales:	Luigi Faino, Michael F. Seidl, Erwin Datema, Grardy C. M. van den Berg, Antoine Janssen, Alexander H. J. Wittenberg, Bart P. H. J. Thomma
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c0098a1c6acc4ca29c45e5de5b84d93d
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spelling	oai:doaj.org-article:c0098a1c6acc4ca29c45e5de5b84d93d2021-11-15T15:41:26ZSingle-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome10.1128/mBio.00936-152150-7511https://doaj.org/article/c0098a1c6acc4ca29c45e5de5b84d93d2015-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00936-15https://doaj.org/toc/2150-7511ABSTRACT Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism's biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism's biology.Luigi FainoMichael F. SeidlErwin DatemaGrardy C. M. van den BergAntoine JanssenAlexander H. J. WittenbergBart P. H. J. ThommaAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 4 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Luigi Faino Michael F. Seidl Erwin Datema Grardy C. M. van den Berg Antoine Janssen Alexander H. J. Wittenberg Bart P. H. J. Thomma Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
description	ABSTRACT Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism's biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism's biology.
format	article
author	Luigi Faino Michael F. Seidl Erwin Datema Grardy C. M. van den Berg Antoine Janssen Alexander H. J. Wittenberg Bart P. H. J. Thomma
author_facet	Luigi Faino Michael F. Seidl Erwin Datema Grardy C. M. van den Berg Antoine Janssen Alexander H. J. Wittenberg Bart P. H. J. Thomma
author_sort	Luigi Faino
title	Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
title_short	Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
title_full	Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
title_fullStr	Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
title_full_unstemmed	Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome
title_sort	single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/c0098a1c6acc4ca29c45e5de5b84d93d
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Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

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