Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets

Doizy, Anna; Prin, Amaury; Cornu, Guillaume; Chiroleu, Frédéric; Rieux, Adrien

doi:10.1093/bioadv/vbad026

Cited by 17 publications

(4 citation statements)

References 16 publications

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“…2016 ). Based on the ML phylogenetic tree reconstructed from the CP gene dataset, the temporal signal of this sequence dataset was visualized and tested in PhyloStemS ( Doizy et al 2023 ) to regress phylogenetic root-to-tip distances against the sampling date using the root that minimized the residual mean squares. In addition, the significance of the temporal signal was evaluated by a date-randomization test.…”

Section: Methodsmentioning

confidence: 99%

Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Billard,

Barro,

Sérémé

et al. 2023

Virus Evolution

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The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential implications for crop protection. Here we describe a five-years (2015-2019) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon and Karfiguela). It confirmed one irrigated site as a disease hotspot, and also found one rainfed lowland site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a five-meter distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site-scale (ca. 520 ha), and also within various specific fields (25 meters side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20% or less in 2015-2016, to more than 65% in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation in controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.

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Section: Methodsmentioning

confidence: 99%

Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Billard,

Barro,

Sérémé

et al. 2023

Virus Evolution

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show abstract

“…The roottotip() function in BactDating was applied to identify the presence of a significant root-to-tip regression which was assessed for significance following 1000 random permutations of sampling dates [ 30 ]. Phylostems was also applied to visualize the extent of temporal correlation at each node in the phylogeny [ 31 ]. Both tools supported a measurably evolving alignment, justifying application of phylogenetic tip-calibration using all the southern African Bd CAPE isolates in our collection.…”

Section: Methodsmentioning

confidence: 99%

Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild

Sewell,

van Dorp,

Ghosh

et al. 2024

Proc. R. Soc. B.

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Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the micro-endemic Tanzanian Kihansi spray toad ( Nectophrynoides asperginis ) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation; however, a subsequent outbreak of chytridiomycosis caused by Batrachochytrium dendrobatidis ( Bd ) led to the spray toad's extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of Bd from archived toad mortalities that the outbreak was caused by invasion of the Bd CAPE lineage and not the panzootic lineage Bd GPL. Molecular dating reveals an emergence of Bd CAPE across southern Africa overlapping with the timing of the spray toad's extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by Bd CAPE yet no signs of ill-health or decline suggests these other species can tolerate Bd when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams’ construction, invasion by Bd CAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.

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“…The resulting multi-fasta alignment was then used as input for IQ-TREE (version 2.0.3) (Minh et al 2020) using automated model-selection to obtain an ML tree. The final SNP tree was visualized using the ggtree (Yu et al 2017) package in R. The rooted tree was then used as input for the online tool Phylostems (Doizy et al 2023), which computes temporal signals for molecular tip-dating.…”

Section: Construction Of a 49-gene Tree For Publicly Available Rssc G...mentioning

confidence: 99%

Genotypic and Phenotypic Analyses ShowRalstonia solanacearumCool Virulence is a Quantitative Trait Not Restricted to “Race 3 biovar 2”

Dewberry,

Sharma,

Prom

et al. 2024

Preprint

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MostRalstonia solanacearumspecies complex strains cause bacterial wilts in tropical or subtropical zones, but the group known as Race 3 biovar 2 (R3bv2) is cool virulent and causes potato brown rot at lower temperatures. R3bv2 has invaded potato-growing regions around the world but is not established in the United States. Phylogenetically, R3bv2 corresponds to a subset of theR. solanacearumphylotype IIB clade, but little is known about the distribution of the cool virulence phenotype within phylotype IIB. Therefore, genomes of 76 potentially cool virulent phylotype IIB strains and 30 public genomes were phylogenetically analyzed. A single clonal lineage within the sequevar 1 subclade of phylotype IIB that originated in South America has caused nearly all brown rot outbreaks worldwide. To correlate genotypes with relevant phenotypes, we quantified virulence of tenRalstoniastrains on tomato and potato at both 22°C and 28°C. Cool virulence on tomato did not predict cool virulence on potato. We found that cool virulence is a quantitative trait. Strains in the sequevar 1 pandemic clonal lineage caused the most disease, while other R3bv2 strains were only moderately cool virulent. However, some non-R3bv2 strains were highly cool virulent and aggressively colonized potato tubers. Thus, cool virulence is not consistently correlated with strains historically classified as R3bv2 group. To aid detection of sequevar 1 strains, this group was genomically delimited in the LINbase web server and a sequevar 1 diagnostic primer pair was developed and validated. We discuss implications of these results for the R3bv2 definition.

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Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences datasets

Cited by 17 publications

References 16 publications

Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot

Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild

Genotypic and Phenotypic Analyses ShowRalstonia solanacearumCool Virulence is a Quantitative Trait Not Restricted to “Race 3 biovar 2”

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