Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA’s function in nicotine biosynthesis

Abstract

tobacco (Nicotiana tabacum) is considered as the model plant for alkaloid research, of which nicotine accounts for 90%. Many nicotine biosynthetic genes have been identified and were known to be regulated by jasmonate-responsive transcription factors. As an important regulator in plant physiological processes, whether small RNAs are involved in nicotine biosynthesis is largely unknown. Here, we combine transcriptome, small RnAs and degradome analysis of two native tobacco germplasms YJ1 and ZY100 to investigate small RNA's function. YJ1 leaves accumulate twofold higher nicotine than ZY100. Transcriptome analysis revealed 3,865 genes which were differently expressed in leaf and root of two germplasms, including some known nicotine and jasmonate pathway genes. By small RNA sequencing, 193 miRNAs were identified to be differentially expressed between YJ1 and ZY100. Using in silico and degradome sequencing approaches, six nicotine biosynthetic genes and seven jasmonate pathway genes were predicted to be targeted by 77 miRNA loci. Three pairs among them were validated by transient expression in vivo. Combined analysis of degradome and transcriptome datasets revealed 51 novel miRNA-mRNA interactions that may regulate nicotine biosynthesis. The comprehensive analysis of our study may provide new insights into the regulatory network of nicotine biosynthesis. Around 20% of plants are known to produce alkaloids, a diverse class of more than 12,000 different N-containing natural product compounds which are important for plant defense and medical use 1,2. Cultivated tobacco (Nicotiana tabacum), as a natural allotetraploid, is possibly evolved from hybridization of two diploids N. tomentosiformis and N. sylvestris 3,4. Nicotine accounts for around 90% of total alkaloids in tobacco, which made tobacco as a model plant to study the biosynthesis, transportation, accumulation, and degradation of alkaloids. Extensive studies have established that nicotine is produced in roots before being transported to and accumulating in leaves 5-7. Nicotine functions as a defense toxin to many insect herbivores 8. Mechanical wounding and woundingelicited jasmonate signaling are known to increase the accumulation of nicotine 9-11. For instance, substantially increased nicotine synthesis and accumulation is known to result from the agricultural practice known as topping, wherein the early developing inflorescence organs are removed by producers to prevent seed production 12,13. Nicotine is synthesized from putrescine, which is derived from arginine or ornithine 14. Most of the enzymes involved in this pathway have been identified and characterized in the course of many decades of research, including ornithine decarboxylase (ODC), putrescine N-methyltransferase (PMT), aspartate oxidase (AO), quinolinate synthase (QS), quinolinate phosphoribosyl transferase (QPT), N-methylputrescine oxidase (MPO), and berberine bridge enzyme-like (BBL), among others 4,6,14. There has also been extensive research about the genetic control

Genome-Wide Identification and Comparative Profiling of MicroRNAs Reveal Flavonoid Biosynthesis in Two Contrasting Flower Color Cultivars of Tree Peony

“…On this basis, a total of 5 known miRNAs and 320 novel miRNAs were identified in "High Noon" and "Roufurong" floral tissues. Differing from a large number of known miRNAs in other species such as P. lactiflora (Zhao et al, 2017a), L. chinensis (Liu et al, 2017), and N. tabacum (Jin et al, 2020), the number of novel miRNAs identified in our study was much higher than that of known miRNAs. It may be attributed to the specificity of tree peony genome.…”

The Implementation of Unified Application Data Collection and Analysis in Tobacco Enterprise Platform Design

“…After long-term business development and demonstration, relational database has been widely used. Since then, the storage and utilization of data have entered a new era [13]. Dean published "Capital Budget," which changed the focus of financial management from the emphasis on external financing to the rational allocation of funds within the company, which made a qualitative leap in the company's financial management [14].…”

Genetic regulation and manipulation of nicotine biosynthesis in tobacco: strategies to eliminate addictive alkaloids

“…In tobacco, comprehensive screenings of non-coding RNA species have revealed the relevance of some of these RNAs in regulating genes in the nicotine pathway ( Chen et al , 2019 ; Jin et al , 2020 ; Zheng et al , 2022 ). One pair of regulatory RNAs, the miRNA nta-miRX27 and its corresponding eTM nta-TMX27, target a key nicotine biosynthesis gene, QPT2 , to regulate nicotine levels in tobacco ( Li et al , 2015 ).…”