title: Transcriptome asymmetry in synthetic and natural allotetraploid wheats, revealed by RNA-sequencing.
abstract: Allopolyploidization has occurred frequently within the Triticum-Aegilops complex which provides a suitable system to investigate how allopolyploidization shapes the expression patterns of duplicated homeologs. We have conducted transcriptome-profiling of leaves and young inflorescences in wild and domesticated tetraploid wheats, Triticum turgidum ssp. dicoccoides (BBAA) and ssp. durum (BBAA), an extracted tetraploid (BBAA), and a synthetic tetraploid (S(l) S(l) AA) wheat together with its diploid parents, Aegilops longissima (S(l) S(l) ) and Triticum urartu (AA). The two diploid species showed tissue-specific differences in genome-wide ortholog expression, which plays an important role in transcriptome shock-mediated homeolog expression rewiring and hence transcriptome asymmetry in the synthetic tetraploid. Further changes of homeolog expression apparently occurred in natural tetraploid wheats, which led to novel transcriptome asymmetry between the two subgenomes. In particular, our results showed that extremely biased homeolog expression can occur rapidly upon the allotetraploidzation and this trend is further enhanced in the course of domestication and evolution of polyploid wheats. Our results suggest that allopolyploidization is accompanied by distinct phases of homeolog expression changes, with parental legacy playing major roles in the immediate rewiring of homeolog expression upon allopolyploidization, while evolution and domestication under allotetraploidy drive further homeolog-expression changes toward re-established subgenome expression asymmetry.
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Xutong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Huakun
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Yaling
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.|Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA.
authors.forename: Linfeng
authors.initials: L
authors.lastname: Li
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Bao
authors.initials: B
authors.lastname: Liu
mesh_terms: D005075:Biological Evolution; D004171:Diploidy; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056626:Inflorescence / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D057891:Tetraploidy; D059467:Transcriptome / Q000235:genetics*; D014908:Triticum / Q000235:genetics*
chemical_list: D012333:RNA, Messenger
keywords: Triticum-Aegilops complex; allopolyploidization; homeolog expression bias; transcriptome asymmetry; wheat