Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

Rieux, Adrien; Campos, Paola; Duvermy, Arnaud; Scussel, Sarah; Martin, Darren P.; Gaudeul, Myriam; Lefeuvre, Pierre; Becker, Norbert; Lett, Jean‐Michel

doi:10.1038/s41598-021-00518-w

Cited by 12 publications

(11 citation statements)

References 77 publications

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“…Phylogeny reconstruction showed the historical strain to have originated from a secondary diversification area of the pathogen in North America from where one or a few dispersal events caused P. infestans emergence in Europe (Martin et al 2013, Ristaino 2020, Saville et al 2016, Yoshida et al 2014, Yoshida et al 2015, Yoshida et al 2013). Similar studies reconstructing the evolutionary history of crop pathogens from full genomes have been successfully realized on viruses as well (Al Rwahnih et al 2015, Malmstrom et al 2007, Rieux et al 2021, Smith et al 2014). We recently described the history of the local emergence of the bacterial crop pathogen Xanthomonas citri pv.…”

Section: Introductionmentioning

confidence: 77%

Herbarium Specimen Sequencing Allows Precise Datation ofXanthomonas citripv.citriDiversification History

Campos

Pruvost

Boyer

et al. 2022

Preprint

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Over the past decade, the field of ancient genomics has triggered considerable progress in the study of various pathogens, including those affecting crops. In this context, herbarium collections have been an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography may shed light into the emergence and evolutionary history of plant pathogens. In this study, we reconstructed 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected citrus herbarium specimens using a shotgun-based deep sequencing strategy. Following authentication of the historical genomes based on ancient DNA damage patterns, we compared them to a large set of modern genomes to reconstruct their phylogenetic relationships, pathogeny-associated genes content and estimate several evolutionary parameters, using Bayesian tip-dating calibration and phylogeography inferences. Our results reveal that Xci originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world. This updated scenario links Xci specialization to Neolithic climatic change and the development of agriculture, and its diversification to the human-driven expansion of citriculture through the early East-West trade and later colonization. The analysis of data obtained from such historical specimens is challenging and must undergo adapted treatment before being compared to modern samples. Nevertheless, we confirm here that herbarium collections are a precious tool to improve the knowledge of the evolutionary history of plant pathogens.

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Section: Introductionmentioning

confidence: 77%

Herbarium Specimen Sequencing Allows Precise Datation ofXanthomonas citripv.citriDiversification History

Campos

Pruvost

Boyer

et al. 2022

Preprint

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“…The historical genome of a 90-yr-old ACMV was reconstructed from small RNA sequences in an herbarium specimen (Rieux et al, 2021). Evolutionary divergence times estimated with the historical genome were significantly higher than those estimated without and are more in accord with historical disease records.…”

Section: Cassava Mosaic Viruses and Vectorsmentioning

confidence: 93%

A Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021

Jeger¹,

Fielder²,

Beale³

et al. 2022

Preprint

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A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks had been obtained via surveys or similar methodologies. The second approach involved retrieving new pest presence records added to the CABI Distribution Database in 2021. The literature review for the first approach had two stages. Stage 1 aimed to identify publications on plant diseases caused by pathogen taxonomic groups and led to retrieval of 99 core articles describing studies in 62 categories (pathogen species or species complexes) across more than 40 host species in 6 continents. In Stage 2, the core articles were augmented with further articles providing more context and information for the pathogen species identified in Stage 1. When both sets of articles were combined, the pathogen species with more than 5 articles were: Bursephalenchus xylophilus, Candidatus Liberibacter asiaticus, cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, Fusarium oxysporum f.sp cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs, Puccinia striiformis f.sp tritici, Xylella fastidiosa, and Zymoseptoria tritici. The automated search of the CABI Distribution Database led to 617 new distribution records from 283 plant pathogens in 2021 and was followed by manual review of all pathogens with more than 4 new records, to identify confirmed first reports in a new location. A total of 15 pathogens was identified: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, Ca. Liberibacter asiaticus, citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, Fusarium oxysporum f.sp. cubense Tropical Race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Although 3 very important pathogens – Ca. Liberibacter asiaticus, citrus tristeza virus and Fusarium oxysporum f.sp cubense – were represented in the results of both approaches, in general the two approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap in the results.

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“…Regarding RNA, usually considered as a highly labile molecule rapidly degraded upon cell death, it has been shown that plant virus small RNAs are surprisingly more stable than long RNAs and DNA molecules (Hartung et al, 2015;Rieux et al, 2021;Smith et al, 2014). This property was used by Rieux et al (2021) to assemble a genome of Cassava mosaic virus (ACMV) using small RNAs extracted from a 90 years-old Cassava herbarium plant herbarium samples. Analysis of small RNAs from ancient cellular microorganisms has not yet been reported.…”

Section: Future Prospectsmentioning

confidence: 99%

Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities

Grasso,

Bianciotto,

Marmeisse

2024

Microbial Biotechnology

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By deciphering information encoded in degraded ancient DNA extracted from up to million‐years‐old samples, molecular paleomicrobiology enables to objectively retrace the temporal evolution of microbial species and communities. Assembly of full‐length genomes of ancient pathogen lineages allows not only to follow historical epidemics in space and time but also to identify the acquisition of genetic features that represent landmarks in the evolution of the host–microbe interaction. Analysis of microbial community DNA extracted from essentially human paleo‐artefacts (paleofeces, dental calculi) evaluates the relative contribution of diet, lifestyle and geography on the taxonomic and functional diversity of these guilds in which have been identified species that may have gone extinct in today's human microbiome. As for non‐host‐associated environmental samples, such as stratified sediment cores, analysis of their DNA illustrates how and at which pace microbial communities are affected by local or widespread environmental disturbance. Description of pre‐disturbance microbial diversity patterns can aid in evaluating the relevance and effectiveness of remediation policies. We finally discuss how recent achievements in paleomicrobiology could contribute to microbial biotechnology in the fields of medical microbiology and food science to trace the domestication of microorganisms used in food processing or to illustrate the historic evolution of food processing microbial consortia.

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Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

Cited by 12 publications

References 77 publications

Herbarium Specimen Sequencing Allows Precise Datation ofXanthomonas citripv.citriDiversification History

Herbarium Specimen Sequencing Allows Precise Datation ofXanthomonas citripv.citriDiversification History

A Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021

Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities

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