title: Identification and characterization of genes on a single subgenome in the hexaploid wheat (Triticum aestivum L.) genotype 'Chinese Spring'.
abstract: Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the 'Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat. Unexpectedly, no bias in expression breadth or in the distribution patterns of GO (gene ontology) terms for these genes was detected among the high-confidence genes. Further, network and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses indicated that most of these genes were not functionally related to each other. Interestingly, 30.7% of these SSG genes were most highly expressed in root, showing biased distribution given the distribution of the whole high-confidence genes. Collectively, these results facilitate our understanding of the loss of the genes that were retained in a SSG during the formation of hexaploid wheat.
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.affiliation: b CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD 4067, Australia.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Zheng
authors.affiliation: c National Foxtail Millet Improvement Centre, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
authors.forename: Jiri
authors.initials: J
authors.lastname: Stiller
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Xiu-Jin
authors.initials: XJ
authors.lastname: Lan
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Yaxi
authors.initials: Y
authors.lastname: Liu
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Mei
authors.initials: M
authors.lastname: Deng
authors.affiliation: d School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, USA.
authors.forename: Penghao
authors.initials: P
authors.lastname: Wang
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.|e College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China.
authors.forename: Zhien
authors.initials: Z
authors.lastname: Pu
authors.affiliation: f Institute of Ecological and Environmental Sciences, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Guangdeng
authors.initials: G
authors.lastname: Chen
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Qian-Tao
authors.initials: QT
authors.lastname: Jiang
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: Yuming
authors.initials: Y
authors.lastname: Wei
authors.affiliation: a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
authors.forename: You-Liang
authors.initials: YL
authors.lastname: Zheng
mesh_terms: D000465:Algorithms; D002681:China; D032461:Chromosomes, Plant / Q000235:genetics*; D004171:Diploidy; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D018515:Plant Leaves / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D018547:Plant Stems / Q000378:metabolism; D011123:Polyploidy; D017423:Sequence Analysis, RNA; D057891:Tetraploidy; D059467:Transcriptome; D014908:Triticum / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: Chinese Spring; evolution; gene loss; génome du blé; perte de gènes; wheat genome; évolution