Draft genome of the aardaker (Lathyrus tuberosus L.), a tuberous legume

Abstract

Objectives Lathyrus tuberosus is a nitrogen-fixing member of the Fabaceae which forms protein-rich tubers. To aid future domestication programs for this legume plant and facilitate evolutionary studies of tuber formation, we have generated a draft genome assembly based on Pacific Biosciences sequence reads. Data description Genomic DNA from L. tuberosus was sequenced with PacBio’s HiFi sequencing chemistry generating 12.8 million sequence reads with an average read length of 14 kb (approximately 180 Gb of sequence data). The reads were assembled to give a draft genome of 6.8 Gb in 1353 contigs with an N50 contig length of 11.1 Mb. The GC content of the genome assembly was 38.3%. BUSCO analysis of the genome assembly indicated a genome completeness of at least 96%. The genome sequence will be a valuable resource, for example, in assessing genomic consequences of domestication efforts and developing marker sets for breeding programs. The L. tuberosus genome will also aid in the analysis of the evolutionary history of plants within the nitrogen-fixing Fabaceae family and in understanding the molecular basis of tuber evolution.

The Exceptionally Large Genomes of the Fabeae Tribe: Comparative Genomics and Applications in Abiotic and Biotic Stress Studies

“…The Pusa-24 L. sativus genome is also available at https://lathyrusgenome.nabi.res.in/index.html online platform, accessed on 15 November 2023, which provides BLAST tools, an ortholog search tool, and direct download of the assembled genome, and associated files. Additionally, an assembly at the contig level is also available for L. tuberosus [27].…”

“…Another Lathyrus species, L. tuberosus ("tuber vetchling", 2n = 2x = 14), has been cultivated for flavorings, fodder (from leaves), oil (from seeds), and as a potato-like food (from tubers) [46]. To aid future domestication programs for this legume plant and facilitate evolutionary studies of tuber formation, genetic and genomic resources are needed for this tuberous legume [27].…”

“…The length of the EIv1 assembly is 8.12 Gbp, including 1.9 Gbp of Ns in scaffolds [40]. For L. tuberosus, the estimated genome size is 6.8 Gbp [27].…”

“…Hybrid assembly methodologies have been used in the L. sativus assembly genomes available, involving short sequencing data (Illumina) with long sequencing data (Pacific Biosciences, Menlo Park, Califórnia, EUA (PacBio) or Oxford Nanopore Technologies, Oxônia, Reino Unido (PromethION)) [25,26,40], while the PacBio was chosen to generate the L. tuberosus draft genome assembly [27]. For Rbp assembly, after filtering for reads >5 kbp and using a long-read assembler, Redbean produced an assembly of 6.2 Gbp based on 34.6X coverage.…”

“…In addition to crops of worldwide importance, the tribe also contains minor crop species (e.g., Lathyrus sativus L.), forage or green manure species (e.g., Vicia sativa L. and V. villosa L.), and ornamental species (e.g., L. odoratus L. and L. tuberosus). Despite the importance of this group, only recently, the genome sequence of some species began to emerge and became available to the scientific community: Pisum sativum [12][13][14], Lathyrus sativus [25,26], Lathyrus tuberosus [27],…”