A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences

Bayer, Randall J.; Mabberley, D. J.; Morton, Cynthia M.; Miller, Cathy H.; Sharma, Ish; Pfeil, Bernard E.; Rich, Sarah; Hitchcock, Roberta; Sykes, S. R.

doi:10.3732/ajb.0800341

Cited by 188 publications

(222 citation statements)

References 59 publications

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“…These and other distinct clades that we have identified are therefore more appropriately considered species within the genus Citrus, on a par with those that formerly were referred to as the three 'true' or 'biological' species (C. reticulata, C. maxima and C. medica). Additionally, the related genus, Poncirus, a subject of continuous controversy since it was originally proposed to be within the genus Citrus 12,46 , is clearly a distinct clade that is separate from Citrus based on sequence divergence and wholegenome phylogeny.…”

Section: Resultsmentioning

confidence: 99%

“…Citrus phylogeny is controversial 1,5,6,11,12 , in part owing to the difficulty of identifying pure or wild progenitor species, because of substantial interspecific hybridization that has resulted in several clonally propagated and cultivated accessions. Some authors assign separate binomial species designations to clonally propagated genotypes 1,6 .…”

Section: Article Researchmentioning

confidence: 99%

“…In southeast Asia, this marked climate alteration caused major changes in biota, including the migration of mammals 18 and rapid radiation of various plant lineages 19,20 . Australian citrus species form a distinct clade that was proposed to be nested with citrons 12 , although distinct generic names (Eremocitrus and Microcitrus) were assigned in botanical classifications by Swingle 1, 5 . Both molecular dating analysis 21 and our whole-genome phylogenetic analysis do not support an Australian origin for citrus 22 .…”

Section: Article Researchmentioning

confidence: 99%

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Genomics of the origin and evolution of Citrus

Terol

Ibáñez

et al. 2018

Nature

602

604

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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...

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Section: Resultsmentioning

confidence: 99%

Section: Article Researchmentioning

confidence: 99%

Section: Article Researchmentioning

confidence: 99%

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Genomics of the origin and evolution of Citrus

Terol

Ibáñez

et al. 2018

Nature

602

604

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“…Furthermore, previous phylogenetic data based on molecular markers demonstrate that Poncirus, Fortunella, and Citrus are divergent (Nicolosi et al 2000;Barkley et al 2006;Pang et al 2007), although cpDNA sequences place C. medica as more distant from other Citrus spp. than these related genera (Bayer et al 2009). The alleles sequenced in this study were amplified using primers that targeted two trinucleotide repeat loci, one compound and one imperfect (cAGG9 and CCT01), and one imperfect dinucleotide repeat locus (GT03).…”

Section: Resultsmentioning

confidence: 99%

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

et al. 2009

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Sixty-five microsatellite alleles amplified from ancestral citrus accessions classified in three separate genera were evaluated for sequence polymorphism to establish the basis of inter-and intra-allelic genetic variation, evaluate the extent of size homoplasy, and determine an appropriate model (stepwise or infinite allele) for analysis of citrus microsatellite alleles. Sequences for each locus were aligned and subsequently used to determine relationships between alleles of different taxa via parsimony. Interallelic size variation at each SSR locus examined was due to changes in repeat copy number with one exception. Sequencing these alleles uncovered new distinct point mutations in the microsatellite region and the region flanking the microsatellite. Several of the point mutations were found to be genus, species, or allele specific, and some mutations were informative about the inferred evolutionary relationships among alleles. Overall, homoplasy was observed in alleles from all three loci, where the core microsatellite repeat was changed causing alleles of the same size class to be identical in state but not identical by descent. Because nearly all changes in allele size (with one exception) were due to expansion or contraction of the repeat motif, this suggests that a stepwise mutation model, which assumes homoplasy may occur, would be the most appropriate for analyzing Citrus SSR data. The collected data indicate that microsatellites can be a useful tool for evaluating Citrus species and two related genera since repeat motifs were reasonably well retained. However, this work also demonstrated that the number of microsatellite alleles is clearly an underestimate of the number of sequence variants present.

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“…Mexican orange (Choisya ternata Kunth, Rutaceae, subfamily Rutoideae, Bayer et al, 2009) is a small evergreen ornamental shrub with leaves which when bruised give off a strong and pungent smell. The abundantly produced and highly fragrant flowers make Mexican Orange an important and popular horticultural plant.…”

Section: Introductionmentioning

confidence: 99%

Identification of a new antinociceptive alkaloid isopropyl N-methylanthranilate from the essential oil of Choisya ternata Kunth

Radulović

Miltojević

McDermott

et al. 2011

Journal of Ethnopharmacology

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Ethnopharmacological relevance: Mexican people employed infusion of leaves of Choisya ternata Kunth for their antispasmodic and "simulative properties". Aim of the study:In the present study the detailed GC and GC-MS analyses of the essential oil of Choisya ternata Kunth (Rutaceae) were performed. The presence of a minor constituent isopropyl N-methylanthranilate (1) was revealed among other identified volatiles. A synthesis of 1 was undertaken in order to corroborate this find and obtain gram quantities that would allow the testing of its biological activity (peripheral and central antinociceptive activity). Material and methods:The oils were investigated by GC and GC-MS. Synthesized compounds were spectrally characterized (UV-Vis, IR, 1D and 2D NMR, MS). The obtained synthetic samples of compounds were assayed for peripheral and central antinociceptive activity in two models (effects on acetic acid induced writhing in mice and the hot plate test for nociception). showed the lowest activity (with the methyl ester at 3 mg/kg still better than acetylsalicylic acid, at 200 mg/kg, in the first, or comparable with morphine, at 5 mg/kg, in the second test). Conclusion:This study once again revealed that detailed investigations of plant species with ethnopharmacologically documented activity may yield new natural compounds -a new alkaloid (ternanthranin), a volatile simple anthranilate that can be considered responsible for the antinociceptive activity of the crude plant extracts.

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A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences

Cited by 188 publications

References 59 publications

Genomics of the origin and evolution of Citrus

Genomics of the origin and evolution of Citrus

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

Identification of a new antinociceptive alkaloid isopropyl N-methylanthranilate from the essential oil of Choisya ternata Kunth

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