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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MDPI AG
2018-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/19/11/3554 |
| _version_ | 1811208953689800704 |
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| author | Jaroslav Doležel Jana Čížková Hana Šimková Jan Bartoš |
| author_facet | Jaroslav Doležel Jana Čížková Hana Šimková Jan Bartoš |
| author_sort | Jaroslav Doležel |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-12T04:30:39Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-12T04:30:39Z |
| publishDate | 2018-11-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d57ff9eb32de4bbe806ba8cc85d286f62022-12-22T03:47:57ZengMDPI AGInternational Journal of Molecular Sciences1422-00672018-11-011911355410.3390/ijms19113554ijms19113554One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really AreJaroslav Doležel0Jana Čížková1Hana Šimková2Jan Bartoš3Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicAny 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.https://www.mdpi.com/1422-0067/19/11/3554flow cytometrygenome sizenuclear DNA contentreference genome assemblystandardization |
| spellingShingle | Jaroslav Doležel Jana Čížková Hana Šimková Jan Bartoš One Major Challenge of Sequencing Large Plant Genomes Is to Know How Big They Really Are International Journal of Molecular Sciences flow cytometry genome size nuclear DNA content reference genome assembly standardization |
| 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 | flow cytometry genome size nuclear DNA content reference genome assembly standardization |
| url | https://www.mdpi.com/1422-0067/19/11/3554 |
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