Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome...

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Main Authors:	Liu, Miao, Stiller, Jiri, Holušová, Kateřina, Vrána, Jan, Liu, Dengcai, Doležel, Jaroslav, Liu, Chunji
Format:	Online
Language:	English
Published:	Nature Publishing Group 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099574/

id	pubmed-5099574
recordtype	oai_dc
spelling	pubmed-50995742016-11-10 Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat Liu, Miao Stiller, Jiri Holušová, Kateřina Vrána, Jan Liu, Dengcai Doležel, Jaroslav Liu, Chunji Article The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence indicating that they could be associated with adaptation in wheat. Nature Publishing Group 2016-11-08 /pmc/articles/PMC5099574/ /pubmed/27821854 http://dx.doi.org/10.1038/srep36398 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Liu, Miao Stiller, Jiri Holušová, Kateřina Vrána, Jan Liu, Dengcai Doležel, Jaroslav Liu, Chunji
spellingShingle	Liu, Miao Stiller, Jiri Holušová, Kateřina Vrána, Jan Liu, Dengcai Doležel, Jaroslav Liu, Chunji Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
author_facet	Liu, Miao Stiller, Jiri Holušová, Kateřina Vrána, Jan Liu, Dengcai Doležel, Jaroslav Liu, Chunji
author_sort	Liu, Miao
title	Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
title_short	Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
title_full	Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
title_fullStr	Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
title_full_unstemmed	Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
title_sort	chromosome-specific sequencing reveals an extensive dispensable genome component in wheat
description	The hexaploid wheat genotype Chinese Spring (CS) has been used worldwide as the reference base for wheat genetics and genomics, and significant resources have been used by the international community to generate a reference wheat genome based on this genotype. By sequencing flow-sorted 3B chromosome from a hexaploid wheat genotype CRNIL1A and comparing the obtained sequences with those available for CS, we detected that a large number of sequences in the former were missing in the latter. If the distribution of such sequences in the hexaploid wheat genome is random, CRNILA sequences missing in CS could be as much as 159.3 Mb even if only fragments of 50 bp or longer were considered. Analysing RNA sequences available in the public domains also revealed that dispensable genes are common in hexaploid wheat. Together with those extensive intra- and interchromosomal rearrangements in CS, the existence of such dispensable genes is another factor highlighting potential issues with the use of reference genomes in various studies. Strong deviation in distributions of these dispensable sequences among genotypes with different geographical origins provided the first evidence indicating that they could be associated with adaptation in wheat.
publisher	Nature Publishing Group
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099574/
_version_	1613717154975186944

Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

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