rapid evolution; breeding system; genome-wide association study; Arabidopsis
Akiyama Reiko, Sun Jianqiang, Hatakeyama Masaomi, Lischer Heidi E. L., Briskine Roman V., Hay Angela, Gan Xiangchao, Tsiantis Miltos, Kudoh Hiroshi, Kanaoka Masahiro M., Sese Jun, Shimizu Kentaro K., Shimizu‐Inatsugi Rie (2020), Fine‐scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species, in New Phytologist
Tsuchimatsu Takashi, Kakui Hiroyuki, Yamazaki Misako, Marona Cindy, Tsutsui Hiroki, Hedhly Afif, Meng Dazhe, Sato Yutaka, Städler Thomas, Grossniklaus Ueli, Kanaoka Masahiro M., Lenhard Michael, Nordborg Magnus, Shimizu Kentaro K. (2020), Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana, in Nature Communications
, 11(1), 2885-2885.
Kakui Hiroyuki, Yamazaki Misako, Hamaya Naoto-Benjamin, Shimizu Kentaro K. (2020), Pollen Grain Counting Using a Cell Counter, in Geitmann Anja (ed.), Springer US, New York, NY, 1-11.
Song Young Hun, Kubota Akane, Kwon Michael S., Covington Michael F., Lee Nayoung, Taagen Ella R., Laboy Cintrón Dianne, Hwang Dae Yeon, Akiyama Reiko, Hodge Sarah K., Huang He, Nguyen Nhu H., Nusinow Dmitri A., Millar Andrew J., Shimizu Kentaro K., Imaizumi Takato (2018), Molecular basis of flowering under natural long-day conditions in Arabidopsis, in Nature Plants
, 4(10), 824-835.
Yew Chow-Lih, Kakui Hiroyuki, Shimizu Kentaro K. (2018), Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica, in Journal of Plant Research
, 131(2), 349-358.
Kuo Tony, Hatakeyama Masaomi, Tameshige Toshiaki, Shimizu Kentaro K., Sese Jun (2018), Homeolog expression quantification methods for allopolyploids, in -
Paape Timothy, Briskine Roman V., Halstead-Nussloch Gwyneth, Lischer Heidi E. L., Shimizu-Inatsugi Rie, Hatakeyama Masaomi, Tanaka Kenta, Nishiyama Tomoaki, Sabirov Renat, Sese Jun, Shimizu Kentaro K. (2018), Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica, in Nature Communications
, 9(1), 3909-3909.
Briskine Roman V., Shimizu Kentaro K. (2017), Positional bias in variant calls against draft reference assemblies, in BMC Genomics
, 18(1), 263-263.
Lischer Heidi E. L., Shimizu Kentaro K. (2017), Reference-guided de novo assembly approach improves genome reconstruction for related species, in BMC Bioinformatics
, 18(1), 474-474.
Yamasaki Eri, Altermatt Florian, Cavender-Bares Jeannine, Schuman Meredith C, Zuppinger-Dingley Debra, Garonna Irene, Schneider Fabian D, Guillén-Escribà Carla, van Moorsel Sofia J, Hahl Terhi, Schmid Bernhard, Schaepman-Strub Gabriela, Schaepman Michael E, Shimizu Kentaro K (2017), Genomics meets remote sensing in global change studies: monitoring and predicting phenology, evolution and biodiversity, in Current Opinion in Environmental Sustainability
, 29, 177-186.
Briskine Roman V., Paape Timothy, Shimizu-Inatsugi Rie, Nishiyama Tomoaki, Akama Satoru, Sese Jun, Shimizu Kentaro K. (2017), Genome assembly and annotation of Arabidopsis halleri , a model for heavy metal hyperaccumulation and evolutionary ecology, in Molecular Ecology Resources
, 17(5), 1025-1036.
Takada Yoshinobu, Murase Kohji, Shimosato-Asano Hiroko, Sato Takahiro, Nakanishi Honoka, Suwabe Keita, Shimizu Kentaro K., Lim Yong Pyo, Takayama Seiji, Suzuki Go, Watanabe Masao (2017), Duplicated pollen–pistil recognition loci control intraspecific unilateral incompatibility in Brassica rapa, in Nature Plants
, 3(7), 17096-17096.
Izuno Ayako, Kitayama Kanehiro, Onoda Yusuke, Tsujii Yuki, Hatakeyama Masaomi, Nagano Atsushi J., Honjo Mie N., Shimizu-Inatsugi Rie, Kudoh Hiroshi, Shimizu Kentaro K., Isagi Yuji (2017), The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae), in Molecular Ecology
, 26(6), 1515-1532.
Hirao Akira S., Onda Yoshihiko, Shimizu-Inatsugi Rie, Sese Jun, K. Shimizu Kentaro, Kenta Tanaka (2017), Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq, in American Journal of Molecular Biology
, 07(04), 1031-1046.
Paape Timothy, Hatakeyama Masaomi, Shimizu-Inatsugi Rie, Cereghetti Teo, Onda Yoshihiko, Kenta Tanaka, Sese Jun, Shimizu Kentaro K. (2016), Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica, in Molecular Biology and Evolution
, 33(11), 2781-2800.
Izuno Ayako, Hatakeyama Masaomi, Nishiyama Tomoaki, Tamaki Ichiro, Shimizu-Inatsugi Rie, Sasaki Ryuta, Shimizu Kentaro K., Isagi Yuji (2016), Genome sequencing of Metrosideros polymorpha (Myrtaceae), a dominant species in various habitats in the Hawaiian Islands with remarkable phenotypic variations, in Journal of Plant Research
, (4), 727-736.
Shimizu-Inatsugi Rie, Terada Aika, Hirose Kyosuke, Kudoh Hiroshi, Sese Jun, Shimizu Kentaro K. (2016), Plant adaptive radiation mediated by polyploid plasticity in transcriptomes, in Molecular Ecology
, 26(1), 193-207.
Novikova Polina Yu, Hohmann Nora, Nizhynska Viktoria, Tsuchimatsu Takashi, Ali Jamshaid, Muir Graham, Guggisberg Alessia, Paape Tim, Schmid Karl, Fedorenko Olga M, Holm Svante, Säll Torbjörn, Schlötterer Christian, Marhold Karol, Widmer Alex, Sese Jun, Shimizu Kentaro K, Weigel Detlef, Krämer Ute, Koch Marcus A, Nordborg Magnus (2016), Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism, in Nature Genetics
, (9), 1077-1082.
Gan Xiangchao, Hay Angela, Kwantes Michiel, Haberer Georg, Hallab Asis, Ioio Raffaele Dello, Hofhuis Hugo, Pieper Bjorn, Cartolano Maria, Neumann Ulla, Nikolov Lachezar A., Song Baoxing, Hajheidari Mohsen, Briskine Roman, Kougioumoutzi Evangelia, Vlad Daniela, Broholm Suvi, Hein Jotun, Meksem Khalid, Lightfoot David, Shimizu Kentaro K., Shimizu-Inatsugi Rie, Imprialou Martha, Kudrna David, et al. (2016), The Cardamine hirsuta genome offers insight into the evolution of morphological diversity, in Nature Plants
, (11), 16167-16167.
Shimizu Kentaro, Tsuchimatsu Takashi (2015), Evolution of selfing: recurrent patterns in molecular adaptation, in Annual Reviews
, 46, 593-622.
The breeding system of plants, animals and fungi is a major selective force on various reproductive traits. This fact makes it a highly interesting study object for diverse disciplines, such as behavioral biology, breeding science or medical science as well as evolutionary biology. In plants, the evolution of autogamy or self-fertilization is considered a very frequent evolutionary transition of breeding systems. The establishment of autogamy is typically characterized by the loss of self-incompatibility, accompanied by small floral size and a reduced pollen to ovule ratio. Interestingly, the evolutionary shift to autogamy causes changes in genomic patterns, including a reduction in genome size, more exactly in the number of transposable elements. We have studied the molecular basis of the evolution of self-compatibility using relatives to the model species Arabidopsis thaliana. We discovered the disruption of the gene SCR/SP11, which is the male self-incompatibility locus, which was responsible for the evolutionary loss of self-incompatibility. Furthermore, we identified that this loss-of function in SCR is a recurrent pattern. These findings support the hypothesis of sexual conflict. With the advance of the 1001 genome project of Arabidopsis thaliana, in which more than 1000 different ecotypes were sequenced, genome-wide association studies (GWAS) and genome scans became feasible approaches to study selection on quantitative traits. We propose the use of GWAS of study the evolution of breeding systems in Arabidopsis relatives.