Methods

Research

Methods

Monitoring ONT sequencing (MinKNOW)

ONT nanopore

High molecular weight DNA

stinging nettle in vitro cultures

stinging nettle leaf producing anthocyanins

Molecular Biology

High molecular weight DNA extraction (doi:10.17504/protocols.io.bcvyiw7w)
Numerous PCR types (long range, colony, nested, cross-over)
Recombinant DNA technology ('cloning'): bacteria transformation, plasmid extraction, plasmid analysis
Plant transformation
Long read sequencing (ONT) (doi: 10.1017/qpb.2021.18 and 10.3390/genes11030274)
RNA extraction
Extraction of metabolites
Various assays to analyze flavonoids
In vitro plant cultivation

Protocols for various methods are shared through our GitHub repository.

Phylogenetic tree of the Musa acuminata MYBs

KIPEs3 workflow

Simplified KIPEs workflow

Workflow of the MYB_annotator

bHLH_annotator workflow

https://pbb-tools.de/

Bioinformatics

de novo genome assembly (doi: 10.1101/2023.06.27.546741 and 10.1371/journal.pone.0216233)
genome sequence annotation (doi: 10.1101/2023.06.27.546741)
read mapping and variant calling (doi: 10.3390/plants9040439)
RNA-Seq analysis (doi: 10.1186/s12864-018-5360-z)
Co-expression analyses
Synteny analysis (doi: 10.1371/journal.pone.0280155)
Functional annotation of genes (doi: 10.3390/plants9091103)
Tool development (doi: 10.1186/s12864-022-08452-5 and 10.1101/2023.05.02.539087)

Protocols and access to scripts are described on GitHub. A list of helpful tools for functional genomics are available in this GitHub repository.