title: Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica.
abstract: Allopolyploidization combines parental genomes and often confers broader species distribution. However, little is known about parentally transmitted gene expression underlying quantitative traits following allopolyploidization because of the complexity of polyploid genomes. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the zinc hyperaccumulator Arabidopsis halleri and of the nonaccumulator Arabidopsis lyrata We found that A. kamchatica retained the ability to hyperaccumulate zinc from A. halleri and grows in soils with both low and high metal content. Hyperaccumulation of zinc by A. kamchatica was reduced to about half of A. halleri, but is 10-fold greater than A. lyrata Homeologs derived from A. halleri had significantly higher levels of expression of genes such as HEAVY METAL ATPASE4 (HMA4), METAL TRANSPORTER PROTEIN1 and other metal ion transporters than those derived from A. lyrata, which suggests cis-regulatory differences. A. kamchatica has on average about half the expression of these genes compared with A. halleri due to fixed heterozygosity inherent in allopolyploids. Zinc treatment significantly changed the ratios of expression of 1% of homeologous pairs, including genes putatively involved in metal homeostasis. Resequencing data showed a significant reduction in genetic diversity over a large genomic region (290 kb) surrounding the HMA4 locus derived from the A. halleri parent compared with the syntenic A. lyrata-derived region, which suggests different evolutionary histories. We also estimated that three A. halleri-derived HMA4 copies are present in A. kamchatica Our findings support a transcriptomic model in which environment-related transcriptional patterns of both parents are conserved but attenuated in the allopolyploids.
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, CH 8057, Switzerland.
authors.forename: Timothy
authors.initials: T
authors.lastname: Paape
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, CH 8057, Switzerland Functional Genomics Center Zurich, Winterthurerstrasse 190, Zurich, CH 8057, Switzerland.
authors.forename: Masaomi
authors.initials: M
authors.lastname: Hatakeyama
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, CH 8057, Switzerland.
authors.forename: Rie
authors.initials: R
authors.lastname: Shimizu-Inatsugi
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, CH 8057, Switzerland.
authors.forename: Teo
authors.initials: T
authors.lastname: Cereghetti
authors.affiliation: Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Sugadaira Montane Research Center, University of Tsukuba, Ueda, Nagano, Japan.
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Onda
authors.affiliation: Sugadaira Montane Research Center, University of Tsukuba, Ueda, Nagano, Japan.
authors.forename: Tanaka
authors.initials: T
authors.lastname: Kenta
authors.affiliation: Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Sese
authors.affiliation: Department of Evolutionary Biology and Environmental Studies and Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, CH 8057, Switzerland Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan kentaro.shimizu@ieu.uzh.ch.
authors.forename: Kentaro K
authors.initials: KK
authors.lastname: Shimizu
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000096:biosynthesis / Q000235:genetics; D018628:Gene Dosage; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D006706:Homeostasis; D011123:Polyploidy; D059467:Transcriptome; D015032:Zinc / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D015032:Zinc
keywords: allopolyploid; heavy metal; homeolog; hyperaccumulation; selective sweep; transcriptomics