Dr Kanae Nishii

Image: Morphological diversity observed in the genus Streptocarpus.

Genetic and Evo-Devo studies in the genus Streptocarpus (Gesneriaceae)

Streptocarpus (Gesneriaceae) species exhibit prominent variation in plant form linked to the location and behaviour of their meristems. We study the genetic mechanism underlying this variation and how novel forms evolved.

Utilizing next generation sequencing methods, we provide the genomic foundation to carry out genetic studies in this non-model genus. We have generated experimental populations in collaboration with the Horticulture team, specifically Sadie Barber and Nathan Kelso, to unravel genotype-phenotype correlations as well as the physiological regulatory system via plant hormones and environmental factors.

In collaboration with Prof. Tomoko Abe (RIKEN, Japan), we work on a project that aims to reveal genetic functionality through mutagenesis.

The genome sequence of our first model species, Streptocarpus rexii, is deposited in: https://plantgarden.jp/en/list/t121488 . Dr Yun-Yu Chen contributed greatly to developing core genomic resources for Streptocarpus.

Systematic research in Gesneriaceae

In collaboration with Hannah Atkins and Michael Möller, we are working on the systematics and taxonomy of the family Gesneriaceae. As part of this work, we are developing the Gesneriaceae Resource Centre (GRC), with Martin Pullan developing a PADME platform for the website.

In collaboration with Mathieu Perret (Conservatoire et Jardin botaniques de la Ville de Genève), we recently generated a Gesneriaceae-specific hybrid bait set for target gene capture and next generation sequencing.

(See also Hannah Atkins and Michael Möller's biography).

Gesneriaceae Resource Centre 

Highlights from previous projects

Gene evolution in angiosperms

Gene duplication and diversification is key to the evolution of organismal diversity. We study key genes for the establishment of the green plant lineage, employing omics analyses. In collaboration with Frank Wright (BioSS), we studied the cytokinin synthesis gene ISOPENTENYLTRANSFERASE (IPT), and with Prof. Hidetoshi Iida (Tokyo Gakugei University), MID1-COMPLEMENTING ACTIVITY (MCA), a plant specific calcium channel.

Commands:  

R editing of HMMSEARCH output: heatmap with associated with gene tree and protein illustration

Kanae previously worked as a laboratory technician on the Darwin Tree of Life project, to develop high molecular weight (HMW) DNA extraction protocols for long-read sequencing. Plants are diverse in their secondary metabolite contents, and these often hamper pure DNA extraction.

• Darwin Tree of Life Project
• HMW DNA extraction protocol for Oxford Nanopore Technologies sequencing
• HMW DNA extraction protocol for PacBio HiFi sequencing

Japanese Society of Plant Physiologists

The Botanical Society of Japan

ORCID ID https://orcid.org/0000-0001-8141-8908

Researchgate https://www.researchgate.net/profile/Kanae-Nishii

Researchmap https://researchmap.jp/knishii 

Visiting Researcher Kanagawa University, Japan (Prof. Akitoshi Iwamoto Lab)

BSc Agriculture

Department of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Japan (1997-2001)

MSc Science

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan (2001-2003)

PhD Science

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan (2003-2007)

*To see full publication list, please check ‘Kanae Nishii’ in Research Gate (https://www.researchgate.net/home).

Streptocarpus genetics:

Chen Y-Y, Nishii K*, Kidner CA, Hackett CA, Möller M (2020) QTL dissection of floral traits in Streptocarpus (Gesneriaceae). Euphytica 216:110. https://doi.org/10.1007/s10681-020-02647-1

Nishii K, Fei Y, Hudson A, Möller M, Attila Molnar A* (2020) Virus-induced gene silencing in Streptocarpus rexii (Gesneriaceae). Molecular Biotechnology 62:317-325. https://doi.org/10.1007/s12033-020-00248-w

 Chen YY, Nishii K*, Barber S, Hackett C, Kidner CA, Gharbi K, Nagano AJ, Iwamoto A, Möller M (2018) A first genetic map in the genus Streptocarpus generated with RAD sequencing based SNP markers. South African Journal of Botany 117: 158-168. https://doi.org/10.1016/j.sajb.2018.05.009

Gesneriaceae Evo-Devo:

Nishii K*, Spada A, Möller M (2020) Hormonal crosstalk in the regulation of meristem activity and the phyllomorph architecture in Streptocarpus (Gesneriaceae): a review. Rheedea 30: 96-115. https://dx.doi.org/10.22244/rheedea.2020.30.01.04

Huang B-H, Nishii K*, Wang C-N, Möller M (2019) Quantitative assessment of anisocotyly in Haberlea rhodopensis and Ramonda myconi. Edinburgh Journal of Botany 76:377-391. https://doi.org/10.1017/S0960428619000179

Chen YY, Nishii K, Spada A, Wang CN, Sakakibara H, Kojima M, Wright F, MacKenzie K, Möller M (2017) Cytokinin biosynthesis ISOPENTENYLTRANSFE RASE genes are differentially expressed during phyllomorph development in the acaulescent Streptocarpus rexii (Gesneriaceae). South African Journal of Botany 109: 96-111. https://doi.org/10.1016/j.sajb.2016.12.010

Nishii K, Huang BH, Wang CN, Möller M (2017) From shoot to leaf: step-wise shifts in meristem and KNOX1 activity correlate with the evolution of a unifoliate body plan in Gesneriaceae. Development, Genes and Evolution 227: 41-60. 10.1007/s00427-016-0568-x

Nishii K, Ho M-J, Chou Y-W, Gabotti D, Wang C-N, Spada A, Möller M (2014) GA2 and GA20-oxidase expressions are associated with the meristem position in Streptocarpus rexii (Gesneriaceae). Plant Growth Regulation 72: 123-140. 10.1007/s10725-013-9844-1

Nishii K, Möller M, Kidner CA, Spada A, Mantegazza R, Wang C-N, Nagata T (2010) A complex case of simple leaves: indeterminate leaves co-express ARP and KNOX1 genes. Development, Genes and Evolution 220: 25-40. 10.1007/s00427-010-0326-4

Nishii K*, Kuwabara A, Nagata T (2004) Characterization of anisocotylous leaf formation in Streptocarpus wendlandii (Gesneriaceae): Significance of plant growth regulators. Annals of Botany 94: 457-467.10.1093/aob/mch160

Gesneriaceae systematics:

Ogutcen E, CamilleChriste C, Nishii K, Salamin N, Möller M, Perret M (2021)  Phylogenomics of Gesneriaceae using targeted capture of nuclear genes. Molecular Phylogenetics and Evolution 158:107068. 10.1016/j.ympev.2021.107068

Atkins HJ, Bramley GLC, Nishii K, Möller M, Olivar JEC, Kartonegoro A, Hughes M (2021) Sectional polyphyly and morphological homoplasy in Southeast Asian Cyrtandra (Gesneriaceae): consequences for the taxonomy of a mega-diverse genus. Plant Systematics and Evolution 307: 60. https://doi.org/10.1007/s00606-021-01784-x

Atkins HA, Bramley GLC, Johnson MA, Kartonegoro A, Nishii K, Kokubugata G, Möller M, Hughes M (2020) A molecular phylogeny of Southeast Asian Cyrtandra (Gesneriaceae) supports an emerging paradigm for Malesian plant biogeography. Frontiers of Biogeography 12: e44814. https://doi.org/10.21425/F5FBG44184

Nishii K, Kokubugata, G, Möller M, Atkins HJ* (2019) Notes on Cyrtandra (Gesneriaceae) from Japan, Taiwan and Batan island (Philippines). Edinburgh Journal of Botany 76: 333-344. https://doi.org/10.1017/S0960428619000106

Nishii K, Hughes M, Briggs M, Haston E, Christie F, DeVilliers MJ, Hanekom T, Roos WG, Bellstedt DU, Möller M (2015) Streptocarpus redefined to include all Afro-Malagasy Gesneriaceae: Molecular phylogenies prove congruent with geography and cytology and uncovers remarkable morphological homoplasies. Taxon 64: 1243-1274. 10.12705/646.8

Gene evolution:

Nishii K*, Möller M, Iida H (2021) Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA. PLoS ONE 16: e0249735. https://doi.org/10.1371/journal.pone.0249735

Nishii K*, Wright F, Chen YY, Möller M (2018) Tangled history of a multigene family: the evolution of ISOPENTENYLTRANSFERASE genes. PLoS One 13: e0201198. https://doi.org/10.1371/journal.pone.0201198