Plant genomics & bioinformatics · Helsinki, Finland

Single-cell and spatial insight into plant biology

Phytonex Genomics turns your plant sequencing data into publication-ready results, from genome assembly and population genomics to single-cell and spatial transcriptomics.

Discuss your projectView services
Plant-specificPolyploid and non-model species
Peer-reviewedMethods published in Genome Biology
End to endDesign, analysis and manuscript figures
MesophyllEpidermisGuard cellsPhloemXylemBundle sheathMeristemUMAP 1UMAP 2
Illustrative UMAP of plant single-cell transcriptomes, coloured by annotated cell type.
Core technologies

From genomes to single cells in tissue

We work with data from Illumina, PacBio, Oxford Nanopore, 10x Genomics Chromium and Visium, and comparable platforms.

01

Genomics

Genome assembly and annotation, whole-genome resequencing, variant calling, population and comparative genomics for species identification and trait mapping.

02

Transcriptomics

Bulk RNA-seq for expression profiling, differential expression, pathway enrichment and functional annotation across treatments and conditions.

03

Single-cell

scRNA-seq and snRNA-seq for cell-type identification, developmental trajectories, stress responses and cellular heterogeneity in plant tissues.

04

Spatial

Spatially resolved gene expression, tissue architecture mapping and integration with single-cell data to place cell types in their native context.

Applications

Who we work with

Genomic analysis for research, breeding and environmental decision-making.

Academic research

Bioinformatics support for plant research groups, from experimental design to publication.

  • Study design and grant support
  • Complete analysis and interpretation
  • Manuscript figures and methods text

Agricultural breeding

Genomic tools that help breeders develop improved, climate-resilient crop varieties.

  • Marker and candidate gene discovery
  • GWAS and genomic selection
  • Expression of traits across tissues

Invasive species & biosecurity

Genomic identification and monitoring of invasive plants to support environmental authorities.

  • Species and lineage identification
  • Hybridisation and ploidy analysis
  • Population origin and spread
How we work

A clear, four-step process

01

Consultation

We discuss your research question, samples and platform, and agree on a fixed written quote.

02

Data processing

Quality control, alignment and preprocessing with reproducible, version-controlled pipelines.

03

Analysis

Tailored downstream analysis, with regular check-ins so the results answer your question.

04

Delivery

A report with figures, interpretation, methods text and all code and processed data.

Dr. Cui Wang, founder of Phytonex Genomics Oy
Our team

Dr. Cui Wang

Founder & Lead Bioinformatician

Dr. Wang received a PhD in Ecology and Evolutionary Biology from the University of Helsinki in 2018 and has since worked as a postdoctoral researcher at Shandong University and the University of Helsinki. The research combines genome assembly, population genomics and single-cell and spatial transcriptomics to understand how plants adapt, hybridise and invade new environments.

Dr. Wang led the first integrated single-cell and spatial transcriptomic study of the invasive common reed (Phragmites australis), published in Genome Biology in 2026, generated chromosome-level genome assemblies of this polyploid grass, and contributed to the Nature Genetics genome of Coffea arabica. Every Phytonex project is analysed with the same methods and care used in peer-reviewed research.

Plant scRNA-seq & snRNA-seqSpatial transcriptomicsChromosome-level genome assemblyPolyploid & non-model genomesPopulation genomics & introgressionInvasive species genomics
Google Scholar profile →
Selected publications

Our methods, in peer-reviewed research

Full publication list on Google Scholar →

Service packages

What we deliver

Analysis of your existing sequencing data, from raw reads to publication-ready figures. Every project starts with a free consultation and a fixed written quote tailored to your samples and goals.

Bulk RNA-seq

QC, alignment and quantification, differential expression, GO/KEGG enrichment, report and publication-ready figures.

Single-cell RNA-seq

QC, clustering, plant cell-type annotation, marker genes and differential expression. Advanced modules: multi-sample integration, trajectories, gene regulatory networks, cell–cell communication.

Spatial transcriptomics

Preprocessing, spatial clustering, spatially variable genes and tissue maps, with optional deconvolution and integration with single-cell data.

Genomes & population genomics

Genome assembly and annotation, variant calling, population structure, introgression and selection scans, GWAS.

Consulting & custom analysis

Experimental design, grant support, reanalysis of public data, manuscript figures and methods.

Free first consultation and letters of support for grant applications Discounted rates for multi-sample projects and long-term collaborations Request a quote →
Contact

Let's discuss your project

Tell us about your species, samples and research question. We usually reply within two working days.