KamounLab Publications
Published December 7, 2021 | Version 1.0
Poster Open

Phylogenomics reveals a complex evolutionary history of Fabaceae NLR immune receptors

Authors/Creators

  • 1. ITQB NOVA and TSL
  • 2. ITQB NOVA
  • 3. TSL

Description

The legume family (Fabaceae) is the third-largest angiosperm family and is considered one of the most important crop families. Biotic stress constrains legume yield, and resistance gene breeding is currently considered the most sustainable management method to deal with pathogen pressure in the field. Many legumes share the same pathogens, but whether they share the same resistance genetic basis is currently unknown. To address this question, our initial goal was to identify resistance (R) genes in the Fabaceae family. As a first step towards uncovering the Fabaceae resistance genes repertoire, we undertook a phylogenomic analysis of nucleotide-binding leucine-rich repeat proteins (NLRs) in 23 legume species. These analyses uncovered large variations in overall NLR abundance as well as in the distribution of the different NLR classes. The distribution of the NLR classes did not always match the species phylogeny. For instance, pea (Pisum sativum) and grass pea (Lathyrus sativus) have significantly different NLR repertoires, despite being closely related. The Fabaceae NLR repertoire will be an important tool for comparative resistance mapping studies and for R gene enriched Genome-Wide Association Studies. The outcome of these analyses will be used to accomplish the long-term goal of my project: to develop tools to assist legume breeding programs for durable resistance.

Notes

This poster was developed for the British Society for Plant Pathology conference: BSPP2021 - Our Plants, Our Future held on the 6-8th December 2021 at Edgbaston Conference Centre, University of Birmingham, UK. Most genomes were obtained from the publically available Legume Information System (LIS) Data Store.

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References

  • Cardoso, D. B. O. S., Pennington, R. T., De Queiroz, L. P., Boatwright, J. S., Van Wyk, B. E., Wojciechowski, M. F., & Lavin, M. (2013). Reconstructing the deep-branching relationships of the papilionoid legumes. South African Journal of Botany, 89, 58-75.
  • Mundt, C. C. (2014). Durable resistance: a key to sustainable management of pathogens and pests. Infection, Genetics and Evolution, 27, 446-455.
  • de Queiroz, L. P., Pastore, J. F. B., Cardoso, D., Snak, C., Lima, A. L. D. C., Gagnon, E., ... & Egan, A. N. (2015). A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships. Molecular Phylogenetics and Evolution, 90, 1-19.
  • Kourelis, J., Sakai, T., Adachi, H., & Kamoun, S. (2021). RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLoS Biology, 19(10), e3001124.
  • Arrighi, J. F., Cartieaux, F., Brown, S. C., Rodier-Goud, M., Boursot, M., Fardoux, J., ... & Giraud, E. (2012). Aeschynomene evenia, a model plant for studying the molecular genetics of the Nod-independent rhizobium-legume symbiosis. Molecular plant-microbe interactions, 25(7), 851-861.
  • Bertioli, D. J., Cannon, S. B., Froenicke, L., Huang, G., Farmer, A. D., Cannon, E. K., ... & Ozias-Akins, P. (2016). The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature genetics, 48(4), 438-446.
  • Bertioli, D. J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., ... & Schmutz, J. (2019). The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature genetics, 51(5), 877-884.
  • Emmrich, P. M., Sarkar, A., Njaci, I., Kaithakottil, G. G., Ellis, N., Moore, C., ... & Wang, T. L. (2020). A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume. bioRxiv.
  • Hane, J. K., Ming, Y., Kamphuis, L. G., Nelson, M. N., Garg, G., Atkins, C. A., ... & Singh, K. B. (2017). A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution. Plant biotechnology journal, 15(3), 318-330.
  • Hufnagel, B., Marques, A., Soriano, A., Marquès, L., Divol, F., Doumas, P., ... & Péret, B. (2020). High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nature communications, 11(1), 1-12.
  • Kang, Y. J., Kim, S. K., Kim, M. Y., Lestari, P., Kim, K. H., Ha, B. K., ... & Lee, S. H. (2014). Genome sequence of mungbean and insights into evolution within Vigna species. Nature communications, 5(1), 1-9.
  • Kang, Y. J., Satyawan, D., Shim, S., Lee, T., Lee, J., Hwang, W. J., ... & Lee, S. H. (2015). Draft genome sequence of adzuki bean, Vigna angularis. Scientific reports, 5(1), 1-8.
  • Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., ... & Matsumoto, T. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6(1), 1-10.
  • Kreplak, J., Madoui, M. A., Cápal, P., Novák, P., Labadie, K., Aubert, G., ... & Burstin, J. (2019). A reference genome for pea provides insight into legume genome evolution. Nature Genetics, 51(9), 1411-1422.
  • Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., ... & Huala, E. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic acids research, 40(D1), D1202-D1210.
  • Lonardi, S., Muñoz‐Amatriaín, M., Liang, Q., Shu, S., Wanamaker, S. I., Lo, S., ... & Close, T. J. (2019). The genome of cowpea (Vigna unguiculata [L.] Walp.). The Plant Journal, 98(5), 767-782.
  • Maria Isabel Chacón, Jorge Duitama, Paul Gepts and Clara Bermudez (Phaseolus lunatus genome)
  • Moghaddam, S. M., Oladzad, A., Koh, C., Ramsay, L., Hart, J. P., Mamidi, S., ... & McClean, P. E. (2021). The tepary bean genome provides insight into evolution and domestication under heat stress. Nature communications, 12(1), 1-14.
  • Pecrix, Y., Staton, S. E., Sallet, E., Lelandais-Brière, C., Moreau, S., Carrère, S., ... & Gamas, P. (2018). Whole-genome landscape of Medicago truncatula symbiotic genes. Nature Plants, 4(12), 1017-1025.
  • Tomato Genome Consortium, X. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400), 635.
  • Varshney, R. K., Chen, W., Li, Y., Bharti, A. K., Saxena, R. K., Schlueter, J. A., ... & Jackson, S. A. (2012). Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature biotechnology, 30(1), 83.
  • Varshney, R. K., Song, C., Saxena, R. K., Azam, S., Yu, S., Sharpe, A. G., ... & Cook, D. R. (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature biotechnology, 31(3), 240-246.
  • De Vega, J. J., Ayling, S., Hegarty, M., Kudrna, D., Goicoechea, J. L., Ergon, Å., ... & Skøt, L. (2015). Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific reports, 5(1), 1-10.
  • Xie, M., Chung, C. Y. L., Li, M. W., Wong, F. L., Wang, X., Liu, A., ... & Lam, H. M. (2019). A reference-grade wild soybean genome. Nature communications, 10(1), 1-12.
  • Zhang, R., Wang, Y. H., Jin, J. J., Stull, G. W., Bruneau, A., Cardoso, D., ... & Yi, T. S. (2020). Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Systematic Biology, 69(4), 613-622.