Sugarcane transcriptome analysis in response to infection caused by Acidovorax avenae subsp. avenae

Abstract

Sugarcane is an important tropical crop mainly cultivated to produce ethanol and sugar. Crop productivity is negatively affected by Acidovorax avenae subsp avenae (Aaa), which causes the red stripe disease. Little is known about the molecular mechanisms triggered in response to the infection. We have investigated the molecular mechanism activated in sugarcane using a RNA-seq approach. We have produced a de novo transcriptome assembly (TR7) from sugarcane RNA-seq libraries submitted to drought and infection with Aaa. Together, these libraries present 247 million of raw reads and resulted in 168,767 reference transcripts. Mapping in TR7 of reads obtained from infected libraries, revealed 798 differentially expressed transcripts, of which 723 were annotated, corresponding to 467 genes. GO and KEGG enrichment analysis showed that several metabolic pathways, such as code for proteins response to stress, metabolism of carbohydrates, processes of transcription and translation of proteins, amino acid metabolism and biosynthesis of secondary metabolites were significantly regulated in sugarcane. Differential analysis revealed that genes in the biosynthetic pathways of ET and JA PRRs, oxidative burst genes, NBS-LRR genes, cell wall fortification genes, SAR induced genes and pathogenesis-related genes (PR) were upregulated. In addition, 20 genes were validated by RT-qPCR. Together, these data contribute to a better understanding of the molecular mechanisms triggered by the Aaa in sugarcane and opens the opportunity for the development of molecular markers associated with disease tolerance in breeding programs.

Time-series expression profiling of sugarcane leaves infected withPuccinia kuehniireveals an ineffective defense system leading to susceptibility

“…Infection by 543 Acidovorax avenae subsp. avenae resulted in enrichment of oxidation-reduction 544 pathways with up and downregulated sugarcane genes [42]. 545 We note that oxidative pathways are possibly connected with some of the previously 546 presented results.…”

“…Furthermore, this kind 462 of response can be delayed in compatible interactions [107]. Hence, high expression of 463 PAL-encoding genes is a common attribute of resistant cultivars [31,34], including 464 those of sugarcane [39,40,42]. In the P. kuehnii pathosystem the five DEGs annotated 465 as PAL were repressed at 12 hai, but three of them were upregulated in the next hours, 466 returning to the basal level at 5 dai (Fig 2-C).…”

“…To achieve an overview of the showed temporary activation at 36 hai of genes encoding these last two enzymes [103]. 445 Several authors noted that genes encoding enzymes of the phenylpropanoid pathway are 446 differentially expressed in the first hours or many days after infection [33,38,39,42]. 447 Other authors observed that upregulation of these genes can be associated with 448 resistance [40,90].…”

Biosynthesis of silver nanoparticle from pomelo (Citrus Maxima) and their antibacterial activity against acidovorax oryzae RS-2

“…Acidovorax oryzae (Ao) is a Gram-negative pathogenic bacteria that infects huge variety of crops including corn, oat, melon, millet, orchid, sugar cane and rice [1]. It causes seed born disease in rice which is known as bacterial brown stripe (BBS), which is responsible for causing heavy economic losses in many countries including China [2][3][4][5]. Due to the economic importance of BBS, it is necessary to have novel biocidal, disinfecting or antibacterial agents to complement conventional antibiotics [6].…”

Bulked segregant RNA-Seq reveals differential genes and non-synonymous genetic variants linked to sucrose accumulation in sugarcane

“…Deep sequencing of transcriptome (RNA-seq) has the potential to uncover the causal variations of a desirable trait both at the genic as well as at allelic level. At the genic level, there have been a few reports in sugarcane on differentially expressed genes (DEGs) associated with to sucrose accumulation (De Setta et al 2014;Cardoso-Silva et al, 2014;Thirugnanasambandam et al 2017Thirugnanasambandam et al , 2019, lignin accumulation (Vicentini et al 2015;Kasirajan et al 2018), photosynthesis (Mattiello et al 2015), response to infections from Gluconacetobacter (Vargas et al 2014), and smut pathogen (Wu et al 2013;Que et al 2014;Su et al, 2015;Brigida et al 2016). Recently, Singh et al (2018) investigated the allele specific expressions linked to molecular mechanism behind high biomass accumulation using BSR-Seq of parents, the F1 and 20 F2 clones of sugarcane.…”