title: The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri.
abstract: Polyploidization, or genome duplication, has played a critical role in the diversification of animals, fungi and plants. Little is known about the population structure and multiple origins of polyploid species because of the difficulty in identifying multiple homeologous nuclear genes. The allotetraploid species Arabidopsis kamchatica is closely related to the model species Arabidopsis thaliana and is distributed in a broader climatic niche than its parental species. Here, we performed direct sequencing of homeologous pairs of the low-copy nuclear genes WER and CHS by designing homeolog-specific primers, and obtained also chloroplast and ribosomal internal transcribed spacer sequences. Phylogenetic analysis showed that 50 individuals covering the distribution range including North America are allopolyploids derived from Arabidopsis lyrata and Arabidopsis halleri. Three major clusters within A. kamchatica were detected using Bayesian clustering. One cluster has widespread distribution. The other two are restricted to the southern part of the distribution range including Japan, where the parent A. lyrata is not currently distributed. This suggests that the mountains in Central Honshu and surrounding areas in Japan served as refugia during glacial-interglacial cycles and retained this diversity. We also found that multiple haplotypes of nuclear and chloroplast sequences of A. kamchatica are identical to those of their parental species. This indicates that multiple diploid individuals contributed to the origin of A. kamchatica. The haplotypes of low-copy nuclear genes in Japan suggest independent polyploidization events rather than introgression. Our findings suggest that self-compatibility and gene silencing occurred independently in different origins.
authors.affiliation: Institute of Plant Biology, University of Zurich, Zurich CH-8008, Switzerland.
authors.forename: Rie
authors.initials: R
authors.lastname: Shimizu-Inatsugi
authors.forename: Judita
authors.initials: J
authors.lastname: Lihová
authors.forename: Hiroko
authors.initials: H
authors.lastname: Iwanaga
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kudoh
authors.forename: Karol
authors.initials: K
authors.lastname: Marhold
authors.forename: Outi
authors.initials: O
authors.lastname: Savolainen
authors.forename: Kuniaki
authors.initials: K
authors.lastname: Watanabe
authors.forename: Valentin V
authors.initials: VV
authors.lastname: Yakubov
authors.forename: Kentaro K
authors.initials: KK
authors.lastname: Shimizu
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000145:classification / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D032461:Chromosomes, Plant; D016000:Cluster Analysis; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D005828:Genetics, Population; D006239:Haplotypes; D010802:Phylogeny; D011123:Polyploidy
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer