Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes-and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement. (Résumé d'auteur

LRR-RLK family from two Citrus species: Genome-wide identification and evolutionary aspects

Background: Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors. Results: We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR- 34 RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively. Conclusions: This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species

A genealogy of the citrus family

Clarification of the genetic relationships among species opens new possibilities for enhancing citrus diversity and disease resistanc

Methods for Producing Transgenic Plants Resistant to CTV

[EN] Conventional breeding of citrus types demands a long-term effort due to their complex reproductive biology and long juvenile period. As a compelling alternative, genetic engineering of mature tissues allows the insertion of specific traits into specific elite cultivars, including well-known and widely grown varieties and rootstocks, thus reducing the time and costs involved in improving and evaluating them. Conventional breeding for resistance to CTV in citrus varieties has been largely unsuccessful as well as cloning of the genes conferring resistance to specific citrus types. RNA interference (RNAi), based on producing dsRNAs (usually using intron-hairpin constructs) highly homologous to specific CTV sequences to trigger RNA silencing, has been employed to produce virus-resistant transgenic citrus plants. The most successful construct has been an intron-hairpin vector carrying full-length, untranslatable versions of the genes p25, p20, and p23 from the virus. Using it, we have generated full resistance against CTV in Mexican lime. Moreover, this strategy is applicable to all those citrus varieties amenable to mature transformation, including sweet oranges, sour oranges, mandarins, Citrus macrophylla, and limes.Soler, N.; Plomer, M.; Fagoaga, C.; Moreno, P.; Navarro, L.; Flores Pedauye, R.; Peña, L. (2019). Methods for Producing Transgenic Plants Resistant to CTV. Methods in Molecular Biology. 2015:229-243. https://doi.org/10.1007/978-1-4939-9558-5_17S229243201