De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing

Kang, Sang-Ho; Lee, Jong-Yeol; Lee, Tae‐Ho; Park, Soo-Yun; Kim, Chang-Kug

doi:10.1371/journal.pone.0208344

Cited by 10 publications

(10 citation statements)

References 70 publications

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“…Lack of a well annotated rye reference genome and the differential response of hybrids towards ergot prompted us to perform functional annotations on the combined transcriptome assemblies of DH372 and Helltop. In the combined transcriptome assemblies, majority of contigs got top hit to Triticeae, which is in line with previous high quality de novo assemblies of wheat, barley and other cereals [42][43][44][45] . We also observed that a number of contigs in the de novo assembly of Helltop that got hit to Sorghum bicolor and Eragrostis curvula.…”

Section: Discussionsupporting

confidence: 86%

De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)

Mahmood

Orabi²,

Kristensen³

et al. 2020

Sci Rep

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Rye is used as food, feed, and for bioenergy production and remain an essential grain crop for cool temperate zones in marginal soils. Ergot is known to cause severe problems in cross-pollinated rye by contamination of harvested grains. The molecular response of the underlying mechanisms of this disease is still poorly understood due to the complex infection pattern. RNA sequencing can provide astonishing details about the transcriptional landscape, hence we employed a transcriptomic approach to identify genes in the underlying mechanism of ergot infection in rye. In this study, we generated de novo assemblies from twelve biological samples of two rye hybrids with identified contrasting phenotypic responses to ergot infection. The final transcriptome of ergot susceptible (DH372) and moderately ergot resistant (Helltop) hybrids contain 208,690 and 192,116 contigs, respectively. By applying the BUSCO pipeline, we confirmed that these transcriptome assemblies contain more than 90% of gene representation of the available orthologue groups at Virdiplantae odb10 . We employed a de novo assembled and the draft reference genome of rye to count the differentially expressed genes (DEGs) between the two hybrids with and without inoculation. The gene expression comparisons revealed that 228 genes were linked to ergot infection in both hybrids. The genome ontology enrichment analysis of DEGs associated them with metabolic processes, hydrolase activity, pectinesterase activity, cell wall modification, pollen development and pollen wall assembly. In addition, gene set enrichment analysis of DEGs linked them to cell wall modification and pectinesterase activity. These results suggest that a combination of different pathways, particularly cell wall modification and pectinesterase activity contribute to the underlying mechanism that might lead to resistance against ergot in rye. Our results may pave the way to select genetic material to improve resistance against ergot through better understanding of the mechanism of ergot infection at molecular level. Furthermore, the sequence data and de novo assemblies are valuable as scientific resources for future studies in rye.

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Section: Discussionsupporting

confidence: 86%

De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)

Mahmood

Orabi²,

Kristensen³

et al. 2020

Sci Rep

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show abstract

“…In particular, C/VIF releases glucose and fructose in irreversible reactions, which is essential to plant growth, storage compound accumulation, and stress response [42]. Conversely, in late-seed development, late embryogenesis-abundant (LEA) proteins and heat shock proteins (HSPs) appeared to be more abundant than early seeds like the adlay species [43].…”

Section: Differential Gene Expression Analysis During Seed Developmentmentioning

confidence: 99%

De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

Kang

Lee

et al. 2020

PLoS ONE

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Senna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.

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“…In particular, C/VIF releases glucose and fructose in irreversible reactions, which is essential to plant growth, storage compound accumulation, and stress response [40]. Conversely, in late-seed development, late embryogenesis-abundant (LEA) proteins and heat shock proteins (HSPs) appeared to be more abundant than early seeds like the adlay species [41].…”

Section: Resultsmentioning

confidence: 99%

De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

Kang

Lee

et al. 2019

Preprint

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AbstractSenna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of S. tora using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in S. tora.

show abstract

De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing

Cited by 10 publications

References 70 publications

De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)

De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea)

De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

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