Products & Services
Applications

Applications

Nanopore sequencing offers advantages in all areas of research. Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins.

Learn about applications
View all Applications
Resources
News Explore
Contact

Peter Emmrich

Beware of Ogres: grass pea and the challenges of assembling large legume genomes

Grass pea (Lathyrus sativus) is exceptionally resilient to drought, flooding, and salinity. However, it contains a toxin which, when a lot of the plant is consumed over months, can cause paralysis from the waist down.

The problem of the presence of the toxin can be tackled through plant breeding; this requires an understanding of e.g. the genetics of toxin synthesis, for which a genome assembly is needed.

The grass pea genome is 6.3 Gb and highly repetitive, featuring ‘Ogre elements’, spanning up to 25 kbp.

Short-read assembly of grass pea produced a 6.2 Gb assembly across 1.6 million contigs.

Scaffolding the assembly with paired-end short reads increased contiguity, but introduced 2 billion Ns into the assembly.

Long-read nanopore sequencing on PromethION to 36x coverage + polishing with short reads produced a 6.2 Gb assembly ‘with no Ns’ in 163 contigs, with almost 3-fold improvement in contig N50 vs the scaffolded short-read assembly.

Gene annotation revealed 45k protein-coding genes & >75k transcripts. BUSCO completeness was 82-90%.

Open a chat to talk to our sales team
FAQs

FAQs

Search