A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

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.

The MLO1 powdery mildew susceptibility gene in Lathyrus species: The power of high‐density linkage maps in comparative mapping and synteny analysis

“…The suggested high conservation between both Lathyrus species genomes should be confirmed by more detailed syntenic studies involving flow cytometry or fluorescence in situ hybridization assays, since no direct comparative mapping is yet possible between the L. sativus and L. cicera genetic linkage maps. At the microsynteny level, comparative mapping studies should be facilitated when the scaffolding of the assembly of the L. sativus genome (Emmrich et al., 2020) to the pseudochromosome level becomes completed. High‐density genetic maps, such as the L. sativus genetic map developed here, will accelerate the anchoring of super‐scaffolds onto seven pseudomolecules, representing the L. sativus chromosomes.…”

A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly

“…The metrics of our Alpinia nigra draft assembly indicate that this genome is of high completeness. It has a high contiguity (N50 = 48 kbp) for a genome assembled using short-reads, that is comparable or better than other assemblies produced using DISCOVAR de novo , such as those of malaria mosquito (N50 = 22.3 kb) [ 58 ], Guinea yam (N50 = 2.7–3.3 kb) [ 59 ], grass pea (N50 = 5.7 kbp) [ 60 ] and wheat (N50 = 16.7 kbp) [ 61 ]. Given a 91% BUSCO completeness score and high completeness indicated by the k-mer comparison plot ( Figure 4 ), it is likely to have a good representation of genic regions.…”

Genetics and breeding for climate change in Orphan crops

“…There are no records of any additional trait mapping studies either using bi-parental or diverse populations. Both simple sequence repeat (SSR) and SNP markers have been developed in grass pea (Yang et al 2014 ; Hao et al 2017 ), and a draft genome sequence is now available (Emmrich et al 2020 ) to enable routine molecular analysis for trait mapping and characterization. More robust populations will also need to be developed to enable precise analysis of complex traits.…”

“…Over the last five years alone, 30 orphan crops representing 13 families have had their genomes sequenced (Table 1 ). The selection criteria for genome sequencing included importance to local food security and nutritional value (Chang et al 2019; Hendre et al 2019 ; Jamnadass et al 2020 ), and tolerance to environmental stresses (Song et al 2019 ; Emmrich et al 2020 ). The sizes of genomes sequenced ranged from 0.217 Gb ( Moringa oleifera ) to about 1.5 Gb ( Eleusine coracana ) (Table 1 ), which is relatively small compared to the full range of plant genome size (Liu et al 2019 ).…”