RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars

Saranya, C.; Natarajan, Purushothaman; Mhatre, Priyank Hanuman; Mahajan, Mahesh; Nivitha, S.; Palanisamy, Venkatasalam E.; Reddy, Umesh K.; Sundararaj, P.

doi:10.3390/plants11081008

Cited by 5 publications

(6 citation statements)

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“…A milestone in potato omics-based research was the availability of several reference-quality, chromosome-scale and haplotype-resolved genome assemblies, which helped in understanding the complexity and evolution of the potato genome (Potato Genome Sequencing Consortium 2011 ; Tang et al 2022 ; Sun et al 2022 ; Hoopes et al 2022 ; Bao et al 2022 ; Freire et al 2021 ; Leisner et al 2018 ; Zhou et al 2020 ). These potato whole-genome sequencing projects have also contributed to the significant rise in potato transcriptome studies and reported spatiotemporal changes occurring in various potato tissues using RNA-seq (e.g., Massa et al 2011 ; Chandrasekar et al 2022 ; Tiwari et al 2020 ; Pieczynski et al 2018 ; Chen et al 2019 ; Cao et al 2020 ; Tai et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…They observed that the drought- and rehydration-responsive genes are mainly involved in flavonoid, lipid and sugar metabolism, among others. Chandrasekar et al ( 2022 ) investigated the transcriptional dynamics between resistant and susceptible cultivars against potato cyst nematode (PCN) to identify resistant mechanisms induced by PCN. They identified several disease-resistance genes and transcription factors (TFs) up-regulated in a resistant cultivar (Kufri Swarna).…”

Section: Introductionmentioning

confidence: 99%

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StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

Bonthala,

Stich

2024

Plant Cell Rep

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Key message We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Abstract Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de. This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

Bonthala,

Stich

2024

Plant Cell Rep

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“…A milestone in potato omics-based research was the availability of several reference-quality, chromosome-scale and haplotype-resolved genome assemblies, which helped in understanding the complexity and evolution of the potato genome (Potato Genome Sequencing ). These potato whole-genome sequencing projects have also contributed to the signi cant rise in potato transcriptome studies and reported spatiotemporal changes occurring in various potato tissues using RNA-seq (e.g., Massa et al, 2011;Chandrasekar et al, 2022;Tiwari et al, 2020;Pieczynski et al, 2018;Chen et al, 2019;Cao et al, 2020;Tai et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…They observed that the drought-and rehydration-responsive genes are mainly involved in avonoid, lipid and sugar metabolism, among others. Chandrasekar et al (2022) investigated the transcriptional dynamics between resistant and susceptible cultivars against potato cyst nematode (PCN) to identify resistant mechanisms induced by PCN. They identi ed several disease-resistance genes and transcription factors (TFs) up-regulated in a resistant cultivar (Kufri Swarna).…”

Section: Introductionmentioning

confidence: 99%

A global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

Bonthala,

Stich

2023

Preprint

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Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publically available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We examplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource, which can be accessed at http://134.99.224.164/conekt. This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.

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“…RNAseq assays in potato, targeting diseases such as Phytophthora infestans [19] or nematodes [20], salt stress [21], anthocyanin accumulation in tubers [22] and nitrogen response [23], were performed.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Two Tetraploid Potato Varieties under Water-Stress Conditions

Alvarez-Morezuelas

Barandalla

Ritter

et al. 2022

IJMS

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Potato (Solanum tuberosum L.) is one of the most important crops worldwide, but due to its sensitivity to drought, its production can be affected by water availability. In this study, the varieties Agria and Zorba were used to determine the expression differences between control and water-stressed plants. For this purpose, they were sequenced by RNAseq, obtaining around 50 million transcripts for each variety and treatment. When comparing the significant transcripts obtained from control and drought-stressed plants of the Agria variety, we detected 931 genes that were upregulated and 2077 genes that were downregulated under stress conditions. When both treatments were compared in Zorba plants, 735 genes were found to be upregulated and 923 genes were found to be downregulated. Significantly more DEGs were found in the Agria variety, indicating a good stress response of this variety. “Abscisic acid and environmental stress-inducible protein TAS14-like” was the most overexpressed gene under drought conditions in both varieties, but expression differences were also found in numerous transcription factors and heat shock proteins. The principal GO term found was “cellular components”, more specifically related to the cell membrane and the cell wall, but other metabolic pathways such as carbohydrate metabolism and osmotic adjustment were also identified. These results provide valuable information related to the molecular mechanisms of tolerance to water stress in order to establish the basis for breeding new, more tolerant varieties.

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RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars

Cited by 5 publications

References 88 publications

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

A global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes

Transcriptome Analysis of Two Tetraploid Potato Varieties under Water-Stress Conditions

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