Global transcriptome analyses reveal the molecular signatures in the early response of potato ( Solanum tuberosum L.) to

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ORIGINAL ARTICLE

Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection Weilin Cao1 · Liming Gan1 · Kaijie Shang1 · Chenchen Wang1 · Yunzhi Song1 · Hongmei Liu1 · Shumei Zhou1 · Changxiang Zhu1  Received: 27 May 2020 / Accepted: 15 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020

Abstract Main conclusion  Specific and common genes including transcription factors, resistance genes and pathways were significantly induced in potato by Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection. Abstract  The three major pathogens, namely, Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y, can cause late blight, bacterial wilt, and necrotic ringspot, respectively, and thus severely reduce the yield and quality of potatoes (Solanum tuberosum L.). This study was the first to systematically analyze the relationship between transcriptome alterations in potato infected by these pathogens at the early stages. A total of 75,500 unigenes were identified, and 44,008 were annotated into 5 databases, namely, non-redundant (NR), Swiss-Prot protein, clusters of orthologous groups for eukaryotic complete genomes (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 6945 resistance genes and 11,878 transcription factors (TFs) were identified from all transcriptome data. Differential expression analysis revealed that 13,032 (9490 specifics), 9877 (6423 specifics), and 6661 (4144 specifics) differentially expressed genes (DEGs) were generated from comparisons of the P. infestans/control (Pi vs. Pi-CK), R. solanacearum/control (Rs vs. Rs-CK), and PVY/control (PVY vs. PVY-CK) treatments, respectively. The specific DEGs from the 3 comparisons were assigned to 13 common pathways, such as biosynthesis of amino acids, plant hormone signal transduction, carbon metabolism, and starch and sucrose metabolism. Weighted Gene Co-Expression Network Analysis (WGCNA) identified many hub unigenes, of which several unigenes were reported to regulate plant immune responses, such as FLAGELLIN-SENSITIVE 2 and chitinases. The present study provide crucial systems-level insights into the relationship between transcriptome changes in potato infected with the three pathogens. Moreover, this study presents a theoretical basis for breeding broad-spectrum and specific pathogen-resistant cultivars. Keywords  Phytophthora infestans · Potato · Potato virus Y · Ralstonia solanacearum · Resistance gene · Transcription factor

Communicated by Dorothea Bartels. Weilin Cao and Liming Gan have contributed equally to this work. Electronic supplementary material  The online version of this article (https​://doi.org/10.1007/s0042​5-020-03471​-6) contains supplementary material, which is available to authorized users. * Changxiang Zhu [email protected]

Abbreviations DEGs Differentially expressed genes GO Gene Ontology KEGG Ky

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