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One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are

Any project seeking to deliver a plant or animal reference genome sequence must address the question as to the completeness of the assembly. Given the complexity introduced particularly by the presence of sequence redundancy, a problem which is especially acute in polyploid genomes, this question is...

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Autores principales: Doležel, Jaroslav, Čížková, Jana, Šimková, Hana, Bartoš, Jan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274785/
https://www.ncbi.nlm.nih.gov/pubmed/30423889
http://dx.doi.org/10.3390/ijms19113554
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author Doležel, Jaroslav
Čížková, Jana
Šimková, Hana
Bartoš, Jan
author_facet Doležel, Jaroslav
Čížková, Jana
Šimková, Hana
Bartoš, Jan
author_sort Doležel, Jaroslav
collection PubMed
description Any project seeking to deliver a plant or animal reference genome sequence must address the question as to the completeness of the assembly. Given the complexity introduced particularly by the presence of sequence redundancy, a problem which is especially acute in polyploid genomes, this question is not an easy one to answer. One approach is to use the sequence data, along with the appropriate computational tools, the other is to compare the estimate of genome size with an experimentally measured mass of nuclear DNA. The latter requires a reference standard in order to provide a robust relationship between the two independent measurements of genome size. Here, the proposal is to choose the human male leucocyte genome for this standard: its 1C DNA amount (the amount of DNA contained within unreplicated haploid chromosome set) of 3.50 pg is equivalent to a genome length of 3.423 Gbp, a size which is just 5% longer than predicted by the most current human genome assembly. Adopting this standard, this paper assesses the completeness of the reference genome assemblies of the leading cereal crops species wheat, barley and rye.
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spelling pubmed-62747852018-12-15 One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are Doležel, Jaroslav Čížková, Jana Šimková, Hana Bartoš, Jan Int J Mol Sci Brief Report Any project seeking to deliver a plant or animal reference genome sequence must address the question as to the completeness of the assembly. Given the complexity introduced particularly by the presence of sequence redundancy, a problem which is especially acute in polyploid genomes, this question is not an easy one to answer. One approach is to use the sequence data, along with the appropriate computational tools, the other is to compare the estimate of genome size with an experimentally measured mass of nuclear DNA. The latter requires a reference standard in order to provide a robust relationship between the two independent measurements of genome size. Here, the proposal is to choose the human male leucocyte genome for this standard: its 1C DNA amount (the amount of DNA contained within unreplicated haploid chromosome set) of 3.50 pg is equivalent to a genome length of 3.423 Gbp, a size which is just 5% longer than predicted by the most current human genome assembly. Adopting this standard, this paper assesses the completeness of the reference genome assemblies of the leading cereal crops species wheat, barley and rye. MDPI 2018-11-11 /pmc/articles/PMC6274785/ /pubmed/30423889 http://dx.doi.org/10.3390/ijms19113554 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Brief Report
Doležel, Jaroslav
Čížková, Jana
Šimková, Hana
Bartoš, Jan
One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are
title One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are
title_full One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are
title_fullStr One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are
title_full_unstemmed One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are
title_short One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are
title_sort one major challenge of sequencing large plant genomes is to know how big they really are
topic Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274785/
https://www.ncbi.nlm.nih.gov/pubmed/30423889
http://dx.doi.org/10.3390/ijms19113554
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