Pisum sativum JI2822 Assembly and Gene Annotation

About Pisum sativum

Pea is a pulse or fodder crop, but the word often refers to the seed or sometimes the pod of this flowering plant species. Peas are eaten as a vegetable. Carl Linnaeus gave the species the scientific name Pisum sativum in 1753. Some sources now treat it as Lathyrus oleraceus; however the need and justification for the change is disputed. Each pod contains several seeds (peas), which can have green or yellow cotyledons when mature. Botanically, pea pods are fruit, since they contain seeds and develop from the ovary of a (pea) flower. The name is also used to describe other edible seeds from the Fabaceae such as the pigeon pea, the cowpea, the seeds from several species of Lathyrus and is used as a compound form for example Sturt's desert pea.

Picture credit: Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons (Image source)

Assembly

The assembly presented here has been imported from INSDC and is linked to the assembly accession [GCA_964186695.1]. The total length and structure of the assembly are supported by raw data available under Study ID PRJEB75659 at EMBL-EBI. Additional associated genome data have been deposited in the Zenodo repository. Chromosomes are oriented according to cytogenetic convention, with the short arm uppermost, as noted in a supplementary file of Rayner et al. (2024) [1].

The total length of the assembly is 3842015444 bp contained within 170 scaffolds. The scaffold N50 value is 535013209, the scaffold L50 value is 4. The GC% content of the assembly is 38.0%.

Annotation

The annotation presented is derived from genes imported from the community GFF3 with the assembly accession GCA_964186695.1. Genomic annotation was deposited along with initial assembly submission by "John Innes Centre".

The JI2822 genome annotation includes repeat annotation, as detailed in the supplementary materials of Rayner et al. (2024) [1]. A suite of fast neutron (FN) mutants derived from JI2822 was developed and sequenced to identify mutations driving significant variation in seed proteome and predicted seed quality. This analysis was based on sequencing a quintuple mutant in reference to the parental JI2822 genome.

Supporting this work, mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE repository. The dataset identifiers are: - PXD048561 (TMT labelling) - PXD048566 (iTRAQ labelling)

These datasets provide a proteomic characterisation of seed quality traits in the JI2822 mutant population.

Protein features, BLAST hits and cross-references have been computed by Ensembl Plants.

References

1. Rayner, T. et al. (2024). A reference-grade genome for pea (Pisum sativum) cultivar JI2822 and functional insights from fast neutron mutants. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erae518

2. Rayner, T. et al. (2025). Mutant tools for improving seed quality in pea. International Journal of Molecular Sciences. https://www.mdpi.com/1422-0067/26/6/2612