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 ( DOI

Kislev, M. E. Origins of the cultivation of DOI

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. DOI

Lambein, F., Travella, S., Kuo, Y.-H., Van Montagu, M. & Heijde, M. Grass pea ( PubMed

Campbell, C. G.

Rajarammohan, S. PubMed DOI PMC

Edwards, A. PubMed DOI 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. PubMed DOI PMC

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

Macas, J., Neumann, P. & Pozárková, D. Zaba: a novel miniature transposable element present in genomes of legume plants. PubMed DOI

Yang, T. PubMed DOI PMC

Sanches, M. DOI

Jones, A. PubMed DOI PMC

Schalamun, M. PubMed DOI PMC

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved PubMed DOI 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. DOI

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.

Danecek, P. PubMed DOI PMC

Durand, N. C. PubMed DOI PMC

Dudchenko, O. PubMed DOI PMC

Durand, N. C. PubMed DOI PMC

Vondrak, T. PubMed DOI PMC

Aliyeva-Schnorr, L., Ma, L. & Houben, A. A Fast Air-dry Dropping Chromosome Preparation Method Suitable for FISH in Plants. PubMed PMC

Macas, J. PubMed DOI 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. PubMed DOI PMC

Macas, J. PubMed DOI PMC

Neumann, P. PubMed DOI PMC

Neumann, P. PubMed PMC

Macas, J.

Ávila Robledillo, L. PubMed DOI PMC

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. PubMed DOI PMC

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. PubMed DOI PMC

Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: fast processing of NGS alignment formats. PubMed DOI PMC

Stovner, E. B. & Sætrom, P. epic2 efficiently finds diffuse domains in ChIP-seq data. PubMed DOI

Novak, P. kavonrtep/TideCluster: 0.0.8. DOI

Gao, Y., Liu, B., Wang, Y. & Xing, Y. TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. PubMed DOI PMC

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

Novak, P. kavonrtep/dante_ltr: 0.2.3.2. DOI

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. PubMed DOI

Novák, P., Neumann, P. & Macas, J. Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. PubMed DOI

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. PubMed DOI 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. PubMed DOI 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. PubMed DOI 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. PubMed DOI

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. PubMed DOI

Kreplak, J. PubMed DOI

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

Bayer, M. PubMed DOI PMC

Kuznetsov, D. PubMed DOI PMC

Vigouroux, M.

Vigouroux, M.

Vigouroux, M.

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. PubMed DOI

Blum, M. PubMed DOI 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. PubMed DOI PMC

Huerta-Cepas, J. PubMed DOI PMC

Emmrich, P. M. F.