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

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 viros...

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Autores principales: Xiong, Wei, van Workum, Dirk-Jan M, Berke, Lidija, Bakker, Linda V, Schijlen, Elio, Becker, Frank F M, van de Geest, Henri, Peters, Sander, Michelmore, Richard, van Treuren, Rob, Jeuken, Marieke, Smit, Sandra, Schranz, M Eric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627274/
https://www.ncbi.nlm.nih.gov/pubmed/37740775
http://dx.doi.org/10.1093/g3journal/jkad204
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author Xiong, Wei
van Workum, Dirk-Jan M
Berke, Lidija
Bakker, Linda V
Schijlen, Elio
Becker, Frank F M
van de Geest, Henri
Peters, Sander
Michelmore, Richard
van Treuren, Rob
Jeuken, Marieke
Smit, Sandra
Schranz, M Eric
author_facet Xiong, Wei
van Workum, Dirk-Jan M
Berke, Lidija
Bakker, Linda V
Schijlen, Elio
Becker, Frank F M
van de Geest, Henri
Peters, Sander
Michelmore, Richard
van Treuren, Rob
Jeuken, Marieke
Smit, Sandra
Schranz, M Eric
author_sort Xiong, Wei
collection PubMed
description 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 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-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 indicated 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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spelling pubmed-106272742023-11-07 Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding Xiong, Wei van Workum, Dirk-Jan M Berke, Lidija Bakker, Linda V Schijlen, Elio Becker, Frank F M van de Geest, Henri Peters, Sander Michelmore, Richard van Treuren, Rob Jeuken, Marieke Smit, Sandra Schranz, M Eric G3 (Bethesda) Plant Genetics and Genomics 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 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-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 indicated 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. Oxford University Press 2023-09-23 /pmc/articles/PMC10627274/ /pubmed/37740775 http://dx.doi.org/10.1093/g3journal/jkad204 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Plant Genetics and Genomics
Xiong, Wei
van Workum, Dirk-Jan M
Berke, Lidija
Bakker, Linda V
Schijlen, Elio
Becker, Frank F M
van de Geest, Henri
Peters, Sander
Michelmore, Richard
van Treuren, Rob
Jeuken, Marieke
Smit, Sandra
Schranz, M Eric
Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
title Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
title_full Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
title_fullStr Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
title_full_unstemmed Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
title_short Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
title_sort genome assembly and analysis of lactuca virosa: implications for lettuce breeding
topic Plant Genetics and Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627274/
https://www.ncbi.nlm.nih.gov/pubmed/37740775
http://dx.doi.org/10.1093/g3journal/jkad204
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