KN's main interest lies in unravelling the evolutionary history of plants. More specifically, KN focuses on plant development and morphology and their underlying physiological and genetic mechanisms in a phylogenetic setting, using the family Gesneriaceae as study material.

 

Genome sequencing and high molecular weight DNA extraction

I am currently working as a laboratory technician on the Darwin Tree of Life project. The project aims to develop high molecular weight (HMW) DNA extraction protocols for long read sequencing. Plants are diverse in their secondary metabolite contents, and these sometimes hamper pure DNA extraction.

Darwin Tree of Life Project: https://www.darwintreeoflife.org/rbge-2/
HMW DNA extraction protocol for Oxford Nanopore Technologies sequencing: https://stories.rbge.org.uk/archives/30792

 

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

The meristem is an important part in the organogenesis during a plant’s life. In the family Gesneriaceae, the ordinary meristem function diversified during the evolution and diversification of the species and has shifted to lateral organs, like the leaf, rather than in the shoot apex. This shift is most notable in the genus Streptocarpus that includes species with ordinary shoot apical meristems and those with only leaf meristems. We are currently working to establish genetic resources for our model species Streptocarpus rexii, such as genome sequences and transcriptomes. Former PhD student Yun-Yu Chen contributed greatly in generating the first genetic map in this genus using an experimental cross generated at RBGE. In collaboration with Michelle Hart and Michael Möller, we are working on a genome-wide association study (GWAS) to identify the core developmental genes in this genus. The functions of those genes are being examined in collaboration with Prof. Tomoko Abe (RIKEN, Japan). In the RBGE horticulture department, Nathan Kelso and Sadie Barber contribute significantly to the projects, growing important plant materials for our research.

 

Streptocarpus rexii genome browser https://plantgarden.jp/en/list/t121488 (under construction)

 

Morphological diversity observed in the genus 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 the PADME platform for the website.

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

KN is also contributing in the supervision of international visitors to RBGE laboratories and/or generates sequencing data for collaborative projects.

See also Hannah Atkins and Michael Möller's biography

 

Gesneriaceae Resource Centre https://padme.rbge.org.uk/grc/welcome

 

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 https://www.protocols.io/view/r-editing-of-hmmsearch-output-heatmap-with-associa-bkqwkvxe

 

Memberships

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

 

Selected Publications

 

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

 

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

 

Degrees

 

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)