bioRxivGenomicsPreprint
A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume
Peter M. F. EmmrichiD, Abhimanyu SarkariD, Isaac NjaciiD, Gemy KaithakottiliD, Noel EllisiD, Christopher Moore, Anne EdwardsiD, Darren HeavensiD, Darren Waite, Jitender CheemaiD, Martin TrickiD, Jonathan D. MooreiD, Anne WebbiD, Rosa CaiazzoiD, Jane E. Thomas, Janet A. HigginsiD, David SwarbreckiD, Shiv KumariD, Sagadevan MundreeiD, Matthew LooseiD, Levi J YantiD, Cathie R. MartiniD, Trevor L. WangiD
Abstract
We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp. We generated two assemblies of this genome, i) EIv1 using Illumina PCR-free paired-end sequencing and assembly followed by long-mate-pair scaffolding and ii) Rbp using Oxford Nanopore Technologies long-read sequencing and assembly followed by polishing with Illumina paired-end data. EIv1 has a total length of 8.12 Gbp (including 1.9 billion Ns) and scaffold N50 59,7 kbp. Annotation has identified 33,819 high confidence genes in the assembly. Rbp has a total length of 6.2 Gbp (with no Ns) and a contig N50 of 155.7 kbp. Gene space assessment using the eukaryote BUSCO database showed completeness scores of 82.8 % and 89.8%, respectively.
- organism: plant (other)
- assay: whole-genome sequencing
- research focus: genome assembly
- approach: statistical model
Abstract summary
Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract
Grass pea, a diploid legume with a 6.3 Gbp genome, gets two draft assemblies, one short-read and one Nanopore, plus 33,819 annotated genes.
Grass pea (Lathyrus sativus) is a resilient diploid legume closely related to pea, with a genome measured at 6.3 Gbp. The work reports two drafts of it, one from PCR-free Illumina reads with long-mate-pair scaffolding and one from Oxford Nanopore long reads, as a genomic resource for the crop.
Key results
ShownThe Nanopore-based assembly (Rbp) is more contiguous and gap-free than the Illumina-based one (EIv1).
Rbp: 6.2 Gbp total with no Ns and contig N50 155.7 kbp. EIv1: 8.12 Gbp total including 1.9 billion Ns and scaffold N50 given as 59,7 kbp. Measured genome size of accession LS007 is 6.3 Gbp. · Abstract
ShownGene-space recovery is incomplete in both drafts, and better in the long-read assembly.
BUSCO completeness against the eukaryote set: 82.8% for EIv1 and 89.8% for Rbp. · Abstract
ShownAnnotation of the assembly yields a high-confidence gene set.
33,819 high-confidence genes called in the assembly; the abstract names neither the annotation method nor which of the two drafts was annotated. · Abstract
Methods, data and reproducibility
The genome of a European grass pea accession was sequenced twice over: PCR-free Illumina paired-end reads assembled and then scaffolded with long-mate-pair libraries (EIv1), and Oxford Nanopore long reads assembled and polished with Illumina paired-end data (Rbp). Both drafts were assessed with BUSCO, and an annotation of the assembly called 33,819 high-confidence genes.
- Whole-genome sequencing of grass pea European accession LS007 (2n=14), genome size 6.3 Gbp · Lathyrus sativus (grass pea)
- Methods & tools
- Illumina PCR-free paired-end sequencing, long-mate-pair scaffolding, Oxford Nanopore Technologies long-read sequencing, BUSCO
Limitations (2)
- Both drafts fall short of complete gene space (BUSCO 82.8% and 89.8%), and EIv1 carries 1.9 billion Ns, so neither is a finished reference. · noted in this summary
- The two assemblies are reported side by side rather than merged, the abstract names no assembler or annotation software, and only one accession of one species was sequenced. · noted in this summary
Read this if you work on legume comparative genomics or need a starting reference for grass pea, and want to know how contiguous and complete the available drafts are.
- Citations
- 42
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