Genomics of the origin and evolution of CitrusGuohong albert Wu 1 , Javier Terol 2 , Victoria ibanez 2 , antonio López-García 2 , estela Pérez-román 2 , carles borredá 2 , concha Domingo 2 , francisco r. Tadeo 2 , Jose carbonell-caballero 3 , roberto alonso 3 , franck curk 4 , Dongliang Du 5 , Patrick Ollitrault 6 , Mikeal L. roose 7 , Joaquin Dopazo 3,8 , frederick G. Gmitter Jr 5 , Daniel S. rokhsar 1,9,10 & Manuel Talon 2The genus Citrus and related genera (Fortunella, Poncirus, Eremocitrus and Microcitrus) belong to the angiosperm subfamily Aurantioideae of the Rutaceae family, which is widely distributed across the monsoon region from west Pakistan to north-central China and south through the East Indian Archipelago to New Guinea and the Bismarck Archipelago, northeastern Australia, New Caledonia, Melanesia and the western Polynesian islands 1 . Native habitats of citrus and related genera roughly extend throughout this broad area (Extended Data Fig. 1a and Supplementary Table 1), although the geogra phical origin, timing and dispersal of citrus species across southeast Asia remain unclear. A major obstacle to resolving these uncertainties is our poor understanding of the genealogy of complex admixture in cultivated citrus, as has recently been shown 2 . Some citrus are clonally propagated apomictically 3 through nucellar embryony, that is, the development of non-sexual embryos originating in the maternal nucellar tissue of the ovule, and this natural process may have been co-opted during domestication; grafting is a relatively recent phenomenon 4 . Both modes of clonal propagation have led to the domestication of fixed (desirable) genotypes, including interspecific hybrids, such as oranges, limes, lemons, grapefruits and other types.Under this scenario, it is not surprising that the current chaotic citrus taxonomy-based on long-standing, conflicting proposals 5,6 -requires a solid reformulation consistent with a full understanding of the hybrid and/or admixture nature of cultivated citrus species. Here we analyse genome sequences of diverse citrus to characterize the diversity and evolution of citrus at the species level and identify citrus admixtures and interspecific hybrids. We further examine the network of relatedness among mandarins and sweet orange, as well as the pattern of the introgression of pummelos among mandarins for clues to the early stages of citrus domestication. Diversity and evolution of the genus CitrusTo investigate the genetic diversity and evolutionary history of citrus, we analysed the genomes of 58 citrus accessions and two outgroup genera (Poncirus and Severinia) that were sequenced to high coverage, including recently published sequences 2,3,7 as well as 30 new genome sequences described here. For our purpose, we do not include accessions related by somatic mutations. These sequences represent a diverse sampling of citrus species, their admixtures and hybrids (Supplementary Tables 2, 3 and Supplementary Notes 1, 2). Our collection includes accessions from eight previously unsequ...

GH3 genes are main components of the hormonal mechanism regulating growth and development and, hence, are deeply involved in a broad range of physiological processes. They are implicated in hormonal homeostasis through the conjugation to amino acids of the free form of essential plant growth regulators such as indoleacetic and jasmonic acids. In this work, we showed that OsGH3.1 overexpression in rice caused dwarfism and significantly reduced both free auxin content and cell elongation. Functional classification of the transcriptomic profiling revealed that most genes involved in auxin biosynthesis and auxin signaling inhibition were induced and repressed, respectively. Many genes related to cell organization and biogenesis were also significantly downregulated. The survey also showed that, although the response to abiotic stresses was not clearly stimulated, OsGH3.1 overexpression did activate a significant number of defense-related genes. In successive bioassays, it was demonstrated that the resistance of rice plants to pathogen infection, evaluated with two different Magnaporthe grisea strains, was higher in the transformants overexpressing OsGH3.1. Taken together, these results indicate that OsGH3.1 overexpression reduces auxin content, inhibits cell growth and cell wall loosening, and enhances resistance to a fungal pathogen. Our results provide evidence that auxin homeostasis can regulate the activation of the defense response in rice.

No abstract

Abscission is a cell separation process by which plants can shed organs such as fruits, leaves, or flowers. The process takes place in specific locations termed abscission zones. In fruit crops like citrus, fruit abscission represents a high percentage of annual yield losses. Thus, understanding the molecular regulation of abscission is of capital relevance to control production. To identify genes preferentially expressed within the citrus fruit abscission zone (AZ-C), we performed a comparative transcriptomics assay at the cell type resolution level between the AZ-C and adjacent fruit rind cells (non-abscising tissue) during ethylene-promoted abscission. Our strategy combined laser microdissection with microarray analysis. Cell wall modification-related gene families displayed prominent representation in the AZ-C. Phylogenetic analyses of such gene families revealed a link between phylogenetic proximity and expression pattern during abscission suggesting highly conserved roles for specific members of these families in abscission. Our transcriptomic data was validated with (and strongly supported by) a parallel approach consisting on anatomical, histochemical and biochemical analyses on the AZ-C during fruit abscission. Our work identifies genes potentially involved in organ abscission and provides relevant data for future biotechnology approaches aimed at controlling such crucial process for citrus yield.

SUMMARYWe have investigated OsHKT2;1 natural variation in a collection of 49 cultivars with different levels of salt tolerance and geographical origins. The effect of identified polymorphism on OsHKT2;1 activity was analysed through heterologous expression of variants in Xenopus oocytes. OsHKT2;1 appeared to be a highly conserved protein with only five possible amino acid substitutions that have no substantial effect on functional properties. Our study, however, also identified a new HKT isoform, No-OsHKT2;2/1 in Nona Bokra, a highly salt-tolerant cultivar. No-OsHKT2;2/1 probably originated from a deletion in chromosome 6, producing a chimeric gene. Its 5¢ region corresponds to that of OsHKT2;2, whose full-length sequence is not present in Nipponbare but has been identified in Pokkali, a salt-tolerant rice cultivar. Its 3¢ region corresponds to that of OsHKT2;1. No-OsHKT2;2/1 is essentially expressed in roots and displays a significant level of expression at high Na + concentrations, in contrast to OsHKT2;1. Expressed in Xenopus oocytes or in Saccharomyces cerevisiae, No-OsHKT2;2/1 exhibited a strong permeability to Na + and K + , even at high external Na + concentrations, like OsHKT2;2, and in contrast to OsHKT2;1. Our results suggest that No-OsHKT2;2/1 can contribute to Nona Bokra salt tolerance by enabling root K + uptake under saline conditions.