Dataset Information

Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens.

ABSTRACT: Citrus bacterial canker (CBC) caused by Xanthomonas axonopodis pv. citri (Xac) was first documented in India and Java in the mid 19th century. Since that time, the known distribution of the disease has steadily increased. Concurrent with the dispersion of the pathogen, the diversity of described strains continues to increase, with novel strains appearing in Saudi Arabia, Iran, and Florida in the last decade. Herbarium specimens of infected plants provide an historical record documenting both the geographic distribution and genetic diversity of the pathogen in the past. However, no method was available to assess the genetic diversity within these herbarium samples. We have developed a method, insertion event scanning (IES), and applied the method to characterize the diversity present within CBC populations documented as herbarium specimens over the past century. IES is based on the specific amplification of junction fragments that define insertion events. The potential for IES in current forensic applications is demonstrated by finding an exact match of pathogen genotypes preserved in herbarium specimens from Japan and Florida, demonstrating the source of the original outbreak of citrus canker in Florida in 1911. IES is a very sensitive technique for differentiating bacterial strains and can be applied to any of the several hundred bacteria for which full genomic sequence data are available.

SUBMITTER: Li W

PROVIDER: S-EPMC2141793 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature

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Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens.

Li Wenbin W Song Qijian Q Brlansky Ronald H RH Hartung John S JS

Proceedings of the National Academy of Sciences of the United States of America 20071112 47

Citrus bacterial canker (CBC) caused by Xanthomonas axonopodis pv. citri (Xac) was first documented in India and Java in the mid 19th century. Since that time, the known distribution of the disease has steadily increased. Concurrent with the dispersion of the pathogen, the diversity of described strains continues to increase, with novel strains appearing in Saudi Arabia, Iran, and Florida in the last decade. Herbarium specimens of infected plants provide an historical record documenting both the ...[more]

PMID: 17998540

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Project description:Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifolia and Ledum palustre subsp. groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years. We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Project description:We have used the citrus GeneChip array (GPL5731) to survey the transcription profiles of sweet orange in response to the bacterial pathogens Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas axonopodis pv. aurantifolii (Xaa). Xac is the causal agent of the citrus canker disease on a wide range of citrus species, including sweet oranges (Citrus sinensis). On the other hand, Xaa is pathogenic to Mexican lime (Citrus aurantifolia) only, and in sweet orange it triggers a defense response. In order to identify the genes induced during the defense response (Xaa-responsive genes) or citrus canker development (Xac-responsive genes), we conducted microarrays hybridization experiments at 6 and 48 hours after bacterial infiltration (habi). The analysis revealed that genes commonly modulated by Xac and Xaa are associated with basal defenses normally triggered by pathogen-associated molecular patterns, including those involved in reactive oxygen species production and lignification. Significantly, Xac-infected leaves showed considerable changes in the transcriptional profiles of defense-, cell wall-, vesicle trafficking- and cell growth-related genes between 6 and 48 habi. This is consistent with the notion that Xac suppresses host defenses near the beginning of the infection and simultaneously changes the physiological status of the host to promote cell enlargement and division. Finally, Xaa triggered a MAP kinase signaling pathway involving WRKY and ethylene-responsive transcriptional factors known to activate downstream defense genes. Keywords: Comprehensive transcriptional analysis of the Citrus-Xanthomonas interaction Adult leaves of sweet orange were infiltrated with the bacterial suspensions or water (mock control). Two stages were selected after bacterial infiltration for RNA extraction and hybridization on Affymetrix microarrays. In total, these experiments consist of two biological replicates of six samples: water-infiltrated leaves, Xaa-infiltrated leaves and Xac-infiltrated leaves, at both 6 and 48 (habi).

Project description:Background and aimsPaper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred.MethodsDNA from 47 herbarium specimens of B. papyrifera collected from 1882 to 2006 from different islands of the Pacific was obtained under ancient DNA protocols. Genetic characterization was based on the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker, the chloroplast ndhF-rpl32 intergenic spacer and a set of ten microsatellites developed for B. papyrifera.Key resultsMicrosatellites allowed detection of 15 genotypes in Near and Remote Oceanian samples, in spite of the vegetative propagation of B. papyrifera in the Pacific. These genotypes are structured in two groups separating West and East Polynesia, and place Pitcairn in a pivotal position. We also detected the presence of male plants that carry the Polynesian chloroplast DNA (cpDNA) haplotype, in contrast to findings in contemporary B. papyrifera populations where only female plants bear the Polynesian cpDNA haplotype.ConclusionsFor the first time, genetic diversity was detected among paper mulberry accessions from Remote Oceania. A clear separation between West and East Polynesia was found that may be indicative of pulses during its dispersal history. The pattern linking the genotypes within Remote Oceania reflects the importance of central Polynesia as a dispersal hub, in agreement with archaeological evidence.

Dataset Information

Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens.

Publications

Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens.

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