From genomes to forest management – tackling invasive<i>Phytophthora</i>species in the era of genomics

Keriö, Susanna; Daniels, Hazel A.; Gómez-Gallego, Mireia; Tabima, Javier F.; Lenz, Ryan R.; Søndreli, Kelsey L.; Grünwald, Niklaus J.; Williams, N.; McDougal, Rebecca; LeBoldus, Jared M.

doi:10.1080/07060661.2019.1626910

Cited by 20 publications

(16 citation statements)

References 260 publications

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“…This, in turn, increases the chance of interspecific mating between the native and the introduced Phytophthora species, which might present a serious threat to biosecurity (Beckerman et al 2014 ; Callaghan and Guest 2015 ). Early detection and characterization of invasive Phytophthora species and especially of hybrids is therefore essential in the prevention or containment of disease outbreaks (Keriö et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Poucke¹,

Haegeman²,

Goedefroit³

et al. 2021

IMA Fungus

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The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.

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Section: Introductionmentioning

confidence: 99%

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Poucke¹,

Haegeman²,

Goedefroit³

et al. 2021

IMA Fungus

View full text Add to dashboard Cite

show abstract

“…For instance, a high-quality genome is useful for genome-wide scans of selection, trait association mapping, and timing invasion events ( Nielsen et al 2005 ; DeGiorgio et al 2016 ; North et al 2021 ). With improved understanding and forecasting at each stage of the invasion process, managers can make decisions on invasions much more accurately than in the past ( Bergeron et al 2019 ; Keriö et al 2020 ). Hence, sequencing whole genomes for these nonmodel organisms provide crucial tools to efficiently manage and predict future invasions.…”

Section: Introductionmentioning

confidence: 99%

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Ramachandran

Huebner

Daly

et al. 2021

Genome Biology and Evolution

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The invasive Japanese stiltgrass ( Microstegium vimineum ) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12-Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long-terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1–2 Myr, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.

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“…North et al 2021, DeGiorgio et al, 2016; Nielsen et al, 2005). With improved understanding and forecasting at each stage of the invasion process, managers can make decisions on invasions much more accurately than in the past (Bergeron et al 2019, Keriö et al 2020). Hence, sequencing whole genomes for these non-model organisms provide crucial tools to efficiently manage and predict future invasions.…”

Section: Introductionmentioning

confidence: 99%

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

Ramachandran

Huebner

Daly

et al. 2021

Preprint

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The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.

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From genomes to forest management – tackling invasivePhytophthoraspecies in the era of genomics

Cited by 20 publications

References 260 publications

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

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