Dr Kanae Nishii, Senior Laboratory Technician
As Senior Laboratory Technician, Kanae has multiple roles, and she is
-working behind the scene to maintain the laboratories functional and productive. She is the microscopist in the STS team and responsible for the maintenance and updating of equipment.
-providing training in various laboratory methods, from plant observation with stereo microscopes to high-molecular DNA extraction for next generation long read sequencing.
-developing protocols for the research teams and collaborators, and her own developmental studies.
-carrying out Evo-Devo and genetic studies in the family Gesneriaceae and supervises research projects for MSc and PhD students.
Research Projects
Genome sequencing and high-molecular weight DNA extraction
Kanae used to be involved 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 often 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
HMW DNA extraction protocol for PacBio HiFi sequencing
https://plantmethods.biomedcentral.com/articles/10.1186/s13007-023-01009-x
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 currently study the genetic mechanism underlying this variation and how the novel forms evolved.
Utilizing next generation sequencing methods, we generate the genomic foundation to carry out genetic studies in this non-model genus. We 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 for revealing genetic functionality through mutagenesis.
For our first model species, Streptocarpus rexii, the genome is deposited in: https://plantgarden.jp/en/list/t121488. Dr Yun-Yu Chen enormously contributed to the core genomic resources for Streptocarpus.
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.
See also Hannah Atkins and Michael Möller's biography
Gesneriaceae Resource Centre https://padme.rbge.org.uk/grc/welcome
Highlight 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 https://www.protocols.io/view/r-editing-of-hmmsearch-output-heatmap-with-associa-bkqwkvxe