Improvements in the sequencing and assembly of plant genomes

Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produ...

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Autores principales:	Priyanka Sharma, Othman Al-Dossary, Bader Alsubaie, Ibrahim Al-Mssallem, Onkar Nath, Neena Mitter, Gabriel Rodrigues Alves Margarido, Bruce Topp, Valentine Murigneux, Ardashir Kharabian Masouleh, Agnelo Furtado, Robert J. Henry
Formato:	article
Lenguaje:	EN
Publicado:	GigaScience Press 2021
Materias:	Electronic computers. Computer science QA75.5-76.95
Acceso en línea:	https://doaj.org/article/12622dc17ceb4147b148133ea16b35c1
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spelling	oai:doaj.org-article:12622dc17ceb4147b148133ea16b35c12021-12-02T15:38:11ZImprovements in the sequencing and assembly of plant genomes10.46471/gigabyte.242709-4715https://doaj.org/article/12622dc17ceb4147b148133ea16b35c12021-06-01T00:00:00Zhttps://gigabytejournal.com/articles/24https://doaj.org/toc/2709-4715 Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, Macadamia jansenii, was also compared with three other Macadamia species, as well as avocado (Persea americana) and jojoba (Simmondsia chinensis). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent. Priyanka SharmaOthman Al-DossaryBader AlsubaieIbrahim Al-MssallemOnkar NathNeena MitterGabriel Rodrigues Alves MargaridoBruce ToppValentine MurigneuxArdashir Kharabian MasoulehAgnelo FurtadoRobert J. HenryGigaScience PressarticleElectronic computers. Computer scienceQA75.5-76.95ENGigaByte (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Electronic computers. Computer science QA75.5-76.95
spellingShingle	Electronic computers. Computer science QA75.5-76.95 Priyanka Sharma Othman Al-Dossary Bader Alsubaie Ibrahim Al-Mssallem Onkar Nath Neena Mitter Gabriel Rodrigues Alves Margarido Bruce Topp Valentine Murigneux Ardashir Kharabian Masouleh Agnelo Furtado Robert J. Henry Improvements in the sequencing and assembly of plant genomes
description	Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, Macadamia jansenii, was also compared with three other Macadamia species, as well as avocado (Persea americana) and jojoba (Simmondsia chinensis). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent.
format	article
author	Priyanka Sharma Othman Al-Dossary Bader Alsubaie Ibrahim Al-Mssallem Onkar Nath Neena Mitter Gabriel Rodrigues Alves Margarido Bruce Topp Valentine Murigneux Ardashir Kharabian Masouleh Agnelo Furtado Robert J. Henry
author_facet	Priyanka Sharma Othman Al-Dossary Bader Alsubaie Ibrahim Al-Mssallem Onkar Nath Neena Mitter Gabriel Rodrigues Alves Margarido Bruce Topp Valentine Murigneux Ardashir Kharabian Masouleh Agnelo Furtado Robert J. Henry
author_sort	Priyanka Sharma
title	Improvements in the sequencing and assembly of plant genomes
title_short	Improvements in the sequencing and assembly of plant genomes
title_full	Improvements in the sequencing and assembly of plant genomes
title_fullStr	Improvements in the sequencing and assembly of plant genomes
title_full_unstemmed	Improvements in the sequencing and assembly of plant genomes
title_sort	improvements in the sequencing and assembly of plant genomes
publisher	GigaScience Press
publishDate	2021
url	https://doaj.org/article/12622dc17ceb4147b148133ea16b35c1
work_keys_str_mv	AT priyankasharma improvementsinthesequencingandassemblyofplantgenomes AT othmanaldossary improvementsinthesequencingandassemblyofplantgenomes AT baderalsubaie improvementsinthesequencingandassemblyofplantgenomes AT ibrahimalmssallem improvementsinthesequencingandassemblyofplantgenomes AT onkarnath improvementsinthesequencingandassemblyofplantgenomes AT neenamitter improvementsinthesequencingandassemblyofplantgenomes AT gabrielrodriguesalvesmargarido improvementsinthesequencingandassemblyofplantgenomes AT brucetopp improvementsinthesequencingandassemblyofplantgenomes AT valentinemurigneux improvementsinthesequencingandassemblyofplantgenomes AT ardashirkharabianmasouleh improvementsinthesequencingandassemblyofplantgenomes AT agnelofurtado improvementsinthesequencingandassemblyofplantgenomes AT robertjhenry improvementsinthesequencingandassemblyofplantgenomes
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Improvements in the sequencing and assembly of plant genomes

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