The genome of <i>Lactuca saligna</i>, a wild relative of lettuce, provides insight into non‐host resistance to the downy mildew <i>Bremia lactucae</i>

Xiong, Wei; Berke, Lidija; Michelmore, Richard W.; Workum, Dirk-Jan M van; Becker, Frank; Schijlen, Elio; Bakker, Linda V.; Peters, Sander; Treuren, R. van; Jeuken, Marieke; Bouwmeester, Klaas; Schranz, M. Eric

doi:10.1111/tpj.16212

Cited by 7 publications

(6 citation statements)

References 131 publications

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“…3 ). Two of the 3 inversions that were previously described between L. saligna and L. sativa were validated and further characterized: one is specific to L. saligna on Chr5 and one is specific to L. sativa on Chr8 ( Xiong et al 2023 ). Furthermore, synteny also revealed a large inversion specific to L. virosa on tentative Chr7 (Scaffold8) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…3 ), which might convey resilience to important traits like resistance against various pathogens or pests. In our previous study, an extensive search of resistance genes was performed for lettuce and its wild relative L. saligna ( Xiong et al 2023 ). Using the new L. virosa assembly, we identified and classified immunity-related genes encoding NLR and RLK proteins for L. virosa and compared them to L. sativa and L .…”

Section: Resultsmentioning

confidence: 99%

“…After 8 weeks, plants were transplanted to larger pots containing potting soil and grown under greenhouse conditions. Tissue sampling was performed when plants were close to bolting, and DNA was extracted using the same protocol described in Xiong et al . (2023) .…”

Section: Methodsmentioning

confidence: 99%

“…NLRs were searched for in the predicted proteomes of L. virosa and L. sativa, and retrieved from the L. saligna genome ( Xiong et al 2023 ). HMMER v3.3.2 ( Finn et al 2011 ) was used to search Hidden Markov Models (HMMs) profiles obtained from Pfam or the UC Davis database for structural domains of NLR proteins (E-value cutoff = 1e-10): PF00931.23 and NBS_712.hmm ( https://niblrrs.ucdavis.edu/At_RGenes/HMM_Model/HMM_Model_NBS_Ath.html ) for the NB domain; PF01582.20 and PF13676.6 for TIR (TOLL/interleukin-1 receptor); PF05659.11 and PF18052.1 for CC (coiled-coil); and 8 HMMs for the LRR (leucine-rich repeat) domain (PF00560.33, PF07723.13, PF07725.13, PF12799.7, PF13306.6, PF13516.6, PF13855.6, PF14580.6).…”

Section: Methodsmentioning

confidence: 99%

“…Here, we present a near chromosome-level de novo assembly of L. virosa (CGN04683) using a combination of long-read and short-read sequencing plus Bionano and Dovetail scaffolding. We contextualize the L. virosa genome within the lettuce gene pool together with the L. sativa and L. saligna ( Xiong et al 2023 ) genomes. First, we show shared and specific homology groups across the 3 species.…”

Section: Introductionmentioning

confidence: 99%

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Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong,

van Workum,

Berke

et al. 2023

G3: Genes, Genomes, Genetics

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Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x=2n=18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the three Lactuca species as core, accessory and unique. In addition, we identified three interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using three-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicate the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong,

van Workum,

Berke

et al. 2023

G3: Genes, Genomes, Genetics

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Genome assembly and analysis ofLactuca virosa: implications for lettuce breeding

Xiong

Workum

Berke

et al. 2023

Preprint

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Lettuce (Lactuca sativaL.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. Genetic variation of important traits in close relatives is necessary to meet lettuce breeding goals.Lactuca virosa(2x=2n=18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) thanLactuca sativa(2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present ade novoreference assembly ofL. virosawith high continuity and complete gene space. This assembly facilitated comparisons to the genome ofL. sativaand to that of the wild speciesL. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the threeLactucaspecies as core, accessory and unique. In addition, we identified three interspecific chromosomal inversions compared toL. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using three-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion ofL. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases amongLactucaspp.and indicate the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation inL. virosa, which is beneficial for the breeding of improved lettuce varieties.

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Lactucasuper-pangenome reduces bias towards reference genes in lettuce research

van Workum,

Mehrem,

Snoek

et al. 2024

Preprint

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Breeding of lettuce (Lactuca sativaL.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on fourLactucaspecies (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines. With the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance againstBremia lactucaein variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relativesLactuca serriola, Lactuca salignaandLactuca virosa. The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops.

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The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non‐host resistance to the downy mildew Bremia lactucae

Cited by 7 publications

References 131 publications

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Genome assembly and analysis ofLactuca virosa: implications for lettuce breeding

Lactucasuper-pangenome reduces bias towards reference genes in lettuce research

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