Assessment of gene copy number variation of Scots pine thaumatin-like protein gene using real-time PCR based methods

Šķipars, Vilnis; Rauda, Elza; Šņepste, Ilze; Krivmane, Baiba; Ruņģis, Dainis

doi:10.1007/s11295-017-1209-x

Cited by 5 publications

(2 citation statements)

References 68 publications

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“…TLPs are responsible for a wide array of pathogen resistance in plants and have been reported to express PM resistance in Vitis vinifera (grape) and hops (Kappagantu et al 2017a; Kappagantu et al 2017b; Yan et al 2017). TLPs copy number expansions in spruce are responsible for defense against Botrytis and other fungal pathogens (Šķipars 2017). TLP antifungal properties are believed to be due to their β-1,3-glucanase activity (Trudel et al 1998; Grenier et al 1999; Adams 2004).…”

Section: Resultsmentioning

confidence: 99%

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

McKernan

Helbert

Kane

et al. 2020

Preprint

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Cannabis is a diverse and polymorphic species. To better understand cannabinoid synthesis inheritance and its impact on pathogen resistance, we shotgun sequenced and assembled a Cannabis trio (sibling pair and their offspring) utilizing long read single molecule sequencing. This resulted in the most contiguous Cannabis sativa assemblies to date. These reference assemblies were further annotated with full-length male and female mRNA sequencing (Iso-Seq) to help inform isoform complexity, gene model predictions and identification of the Y chromosome. To further annotate the genetic diversity in the species, 40 male, female, and monoecious cannabis and hemp varietals were evaluated for copy number variation (CNV) and RNA expression. This identified multiple CNVs governing cannabinoid expression and 82 genes associated with resistance to Golovinomyces chicoracearum, the causal agent of powdery mildew in cannabis. Results indicated that breeding for plants with low tetrahydrocannabinolic acid (THCA) concentrations may result in deletion of pathogen resistance genes. Low THCA cultivars also have a polymorphism every 51 bases while dispensary grade high THCA cannabis exhibited a variant every 73 bases. A refined genetic map of the variation in cannabis can guide more stable and directed breeding efforts for desired chemotypes and pathogen-resistant cultivars. Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

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Section: Resultsmentioning

confidence: 99%

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

McKernan

Helbert

Kane

et al. 2020

Preprint

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show abstract

“…Although CNV may explain phenotypic variation in important adaptive traits, there are very few studies that have investigated intraspecific or population level CNV in conifers. These studies have mostly focused on individual loci, such as the thaumatin-like protein gene in Pinus sylvestris (PsTLP) 25,26 and the (+)-3-carene synthase gene in Picea sitchensis (PsTPS-3car) 27,28 or mapped genomic CNV at the species level 29–31 . In P. glauca two genomic scans detected more than 1,300 and 3,900 CNVs, representing around 10% and 32% of the genes tested, respectively and, significant over-representation of defence response genes 32,33 .…”

Section: Introductionmentioning

confidence: 99%

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1with large variations in white spruce but not Norway spruce

Hung,

Wu,

Zeltiņš

et al. 2023

Preprint

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Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and Betaglu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of Betaglu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of Betaglu-1 and Ugt5b genes. We observed very large copy numbers of Betaglu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of Betaglu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.

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Characterization of a Pinus sylvestris thaumatin-like protein gene and determination of antimicrobial activity of the in vitro expressed protein

Šņepste

Šķipars

Krivmane

et al. 2018

Tree Genetics & Genomes

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Assessment of gene copy number variation of Scots pine thaumatin-like protein gene using real-time PCR based methods

Cited by 5 publications

References 68 publications

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1with large variations in white spruce but not Norway spruce

Characterization of a Pinus sylvestris thaumatin-like protein gene and determination of antimicrobial activity of the in vitro expressed protein

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