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 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.
CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia.|Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
Miao
M
Liu
CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia.
Jiri
J
Stiller
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
Kateřina
K
Holušová
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
Jan
J
Vrána
Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
Dengcai
D
Liu
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
Jaroslav
J
Doležel
CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD 4067, Australia.|School of Plant Biology, The University of Western Australia, Perth, WA 6009, Australia.
Chunji
C
Liu
D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D018745:Genome, Plant; D011123:Polyploidy; D017422:Sequence Analysis, DNA / Q000379:methods*; D014908:Triticum / Q000235:genetics*