Grasspea (Lathyrus sativus L.) is an underutilised but promising legume crop with tolerance to a wide range of abiotic and biotic stress factors, and potential for climate-resilient agriculture. Despite a long history and wide geographical distribution of cultivation, only limited breeding resources are available. This paper reports a 5.96 Gbp genome assembly of grasspea genotype LS007, of which 5.03 Gbp is scaffolded into 7 pseudo-chromosomes. The assembly has a BUSCO completeness score of 99.1% and is annotated with 31719 gene models and repeat elements. This represents the most contiguous and accurate assembly of the grasspea genome to date.

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus CB10 1SD Cambridge United Kingdom

Institute of Plant Molecular Biology Biology Centre CAS Branisovska 31 Ceske Budejovice CZ 37005 Czech Republic

Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av da República Oeiras 2780 157 Portugal

John Innes Centre Norwich Research Park Colney Lane Norwich NR4 7UH UK

Norwich Institute for Sustainable Development School of International Development University of East Anglia Norwich NR4 7TJ UK

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Dixit, G. P., Parihar, A. K., Bohra, A. & Singh, N. P. Achievements and prospects of grass pea (Lathyrus sativus L.) improvement for sustainable food production. The Crop Journal4, 407–416 (2016).

Kislev, M. E. Origins of the cultivation of Lathyrus sativus and L. cicera (Fabaceae). Economic Botany43, 262–270 (1989).

Coward, F., Shennan, S., Colledge, S., Conolly, J. & Collard, M. The spread of Neolithic plant economies from the Near East to northwest Europe: a phylogenetic analysis. Journal of Archaeological Science35, 42–56 (2008).

Lambein, F., Travella, S., Kuo, Y.-H., Van Montagu, M. & Heijde, M. Grass pea (Lathyrus sativus L.): orphan crop, nutraceutical or just plain food? Planta10.1007/s00425-018-03084-0 (2019). PubMed

Campbell, C. G. Grass Pea: Lathyrus Sativus L. Promoting the conservation and use of underutilized and neglected crops vol. 18 (International Plant Genetic Resources Institute, 1997).

Rajarammohan, S. et al. Genome sequencing and assembly of Lathyrus sativus - a nutrient-rich hardy legume crop. Sci Data10, 32 (2023). PubMed PMC

Edwards, A. et al. Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nat Commun14, 876 (2023). PubMed PMC

Neumann, P., Novák, P., Hoštáková, N. & Macas, J. Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification. Mob DNA10, 1 (2019). PubMed PMC

Macas, J., Koblízková, A. & Neumann, P. Characterization of Stowaway MITEs in pea (Pisum sativum L.) and identification of their potential master elements. Genome48, 831–839 (2005). PubMed

Macas, J., Neumann, P. & Pozárková, D. Zaba: a novel miniature transposable element present in genomes of legume plants. Mol Genet Genomics269, 624–631 (2003). PubMed

Yang, T. et al. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet54, 1553–1563 (2022). PubMed PMC

Sanches, M. et al. Grass pea (Lathyrus sativus) interesting panoply of mechanisms to cope with contrasting water stress conditions – a controlled study of sub populational differences in a worldwide collection of accessions. Agricultural Water Management292, 108664 (2024).

Jones, A. et al. High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. PLOS ONE16, e0253830 (2021). PubMed PMC

Schalamun, M. et al. Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora. Molecular Ecology Resources19, 77–89 (2019). PubMed PMC

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods18, 170–175 (2021). PubMed PMC

Laetsch, D. R. & Blaxter, M. L. BlobTools: Interrogation of genome assemblies. Preprint at 10.12688/f1000research.12232.1 (2017).

Laetsch, D. R., Koutsovoulos, G., Booth, T., Stajich, J. & Kumar, S. DRL/blobtools: BlobTools v1.0.1. Zenodo10.5281/zenodo.845347 (2017).

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio] (2013).

Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience10, giab008 (2021). PubMed PMC

Durand, N. C. et al. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Systems3, 95–98 (2016). PubMed PMC

Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science356, 92–95 (2017). PubMed PMC

Durand, N. C. et al. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Systems3, 99–101 (2016). PubMed PMC

Vondrak, T. et al. Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats. The Plant Journal101, 484–500 (2020). PubMed PMC

Aliyeva-Schnorr, L., Ma, L. & Houben, A. A Fast Air-dry Dropping Chromosome Preparation Method Suitable for FISH in Plants. J Vis Exp e53470 10.3791/53470 (2015). PubMed PMC

Macas, J. et al. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae. PLoS ONE10, e0143424 (2015). PubMed PMC

Macas, J., Neumann, P. & Navrátilová, A. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics8, 427 (2007). PubMed PMC

Macas, J. et al. Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes. PLOS Genetics19, e1010633 (2023). PubMed PMC

Neumann, P. et al. Centromeres Off the Hook: Massive Changes in Centromere Size and Structure Following Duplication of CenH3 Gene in Fabeae Species. Molecular Biology and Evolution32, 1862–1879 (2015). PubMed PMC

Neumann, P. et al. Epigenetic Histone Marks of Extended Meta-Polycentric Centromeres of Lathyrus and Pisum Chromosomes. Frontiers in Plant Science7 (2016). PubMed PMC

Macas, J. et al. Long read sequencing and centromere characterization of Fabeae species (2022).

Ávila Robledillo, L. et al. Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae. Molecular Biology and Evolution37, 2341–2356 (2020). PubMed PMC

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics30, 2114–2120 (2014). PubMed PMC

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods9, 357–359 (2012). PubMed PMC

Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: fast processing of NGS alignment formats. Bioinformatics31, 2032–2034 (2015). PubMed PMC

Stovner, E. B. & Sætrom, P. epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics35, 4392–4393 (2019). PubMed

Novak, P. kavonrtep/TideCluster: 0.0.8. Zenodo10.5281/zenodo.7885626 (2023).

Gao, Y., Liu, B., Wang, Y. & Xing, Y. TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics35, i200–i207 (2019). PubMed PMC

Novak, P. Domain based annotation of transposable elements - DANTE (2023).

Novak, P. kavonrtep/dante_ltr: 0.2.3.2. Zenodo10.5281/zenodo.8183566 (2023).

Novák, P., Neumann, P., Pech, J., Steinhaisl, J. & Macas, J. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads. Bioinformatics29, 792–793 (2013). PubMed

Novák, P., Neumann, P. & Macas, J. Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nat Protoc15, 3745–3776 (2020). PubMed

Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker (2013).

Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics26, 841–842 (2010). PubMed PMC

Novak, P. Various bioinformatics utilities (2023).

Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M. & Stanke, M. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinformatics32, 767–769 (2016). PubMed PMC

Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics3, lqaa108 (2021). PubMed PMC

Santos, C., Polanco, C., Rubiales, D. & Vaz Patto, M. C. The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high-density linkage maps in comparative mapping and synteny analysis. The Plant Genome14, 1–15 (2021). PubMed

Santos, C., Martins, D., Rubiales, D. & Vaz Patto, M. C. Partial Resistance Against Erysiphe pisi and E. trifolii Under Different Genetic Control in Lathyrus cicera: Outcomes from a Linkage Mapping Approach. Plant Disease104, 2875–2884 (2020). PubMed

Kreplak, J. et al. A reference genome for pea provides insight into legume genome evolution. Nature Genetics51, 1411–1422 (2019). PubMed

BioBam Bioinformatics. OmicsBox – Bioinformatics Made Easy (2019).

Bayer, M. et al. Comparative visualization of genetic and physical maps with Strudel. Bioinformatics27, 1307–1308 (2011). PubMed PMC

Kuznetsov, D. et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Res51, D445–D451 (2023). PubMed PMC

Vigouroux, M. et al. PRJEB70892 - Lathyrus sativus LS007 HiFi genome sequencing, PacBio raw data. European Nucleotide Archivehttps://www.ebi.ac.uk/ena/browser/view/PRJEB70892, https://identifiers.org/ena.embl:ERP155791 (2024).

Vigouroux, M. et al. PRJEB70892 - Lathyrus sativus LS007 HiFi genome sequencing, scaffolded genome assembly. NCBIhttps://www.ncbi.nlm.nih.gov/datasets/genome/GCA_963859935.3/, https://identifiers.org/ncbi/insdc.gca:GCA_963859935.3 (2024).

Vigouroux, M. et al. Supporting files for research paper ‘A chromosome-scale reference genome of Lathyrus sativus’ 10.5281/zenodo.10671532 (2024).

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics31, 3210–3212 (2015). PubMed

Blum, M. et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research49, D344–D354 (2021). PubMed PMC

Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol38, 5825–5829 (2021). PubMed PMC

Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res47, D309–D314 (2019). PubMed PMC

Emmrich, P. M. F. et al. A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume. 2020.04.24.058164 Preprint at 10.1101/2020.04.24.058164 (2020).