Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome

Verwaaijen B, Wibberg D, Nelkner J, Gordin M, Rupp O, Winkler A, Bremges A, Blom J, Grosch R, Pühler A, Schlüter A (2018)
Journal of Biotechology 267: 12-18.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar.
Stichworte
Ultra-fast sequencing; Plant genomics; Dual RNAseq approach; Lettuce; R-genes
Erscheinungsjahr
2018
Zeitschriftentitel
Journal of Biotechology
Band
267
Seite(n)
12-18
ISSN
0168-1656
eISSN
1873-4863
Page URI
https://pub.uni-bielefeld.de/record/2917037

Zitieren

Verwaaijen B, Wibberg D, Nelkner J, et al. Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Journal of Biotechology. 2018;267:12-18.
Verwaaijen, B., Wibberg, D., Nelkner, J., Gordin, M., Rupp, O., Winkler, A., Bremges, A., et al. (2018). Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Journal of Biotechology, 267, 12-18. doi:10.1016/j.jbiotec.2017.12.021
Verwaaijen, B., Wibberg, D., Nelkner, J., Gordin, M., Rupp, O., Winkler, A., Bremges, A., Blom, J., Grosch, R., Pühler, A., et al. (2018). Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Journal of Biotechology 267, 12-18.
Verwaaijen, B., et al., 2018. Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Journal of Biotechology, 267, p 12-18.
B. Verwaaijen, et al., “Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome”, Journal of Biotechology, vol. 267, 2018, pp. 12-18.
Verwaaijen, B., Wibberg, D., Nelkner, J., Gordin, M., Rupp, O., Winkler, A., Bremges, A., Blom, J., Grosch, R., Pühler, A., Schlüter, A.: Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome. Journal of Biotechology. 267, 12-18 (2018).
Verwaaijen, Bart, Wibberg, Daniel, Nelkner, Johanna, Gordin, Miriam, Rupp, Oliver, Winkler, Anika, Bremges, Andreas, Blom, Jochen, Grosch, Rita, Pühler, Alfred, and Schlüter, Andreas. “Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome”. Journal of Biotechology 267 (2018): 12-18.

2 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani.
Verwaaijen B, Wibberg D, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A., Sci Rep 9(1), 2019
PMID: 31076623
Salmonella Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species.
Jechalke S, Schierstaedt J, Becker M, Flemer B, Grosch R, Smalla K, Schikora A., Front Microbiol 10(), 2019
PMID: 31156568

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