**8. Different repositories and databases of ncRNA research**

In the recent past, non-coding RNAs have grabbed the attention of many researchers for their role in gene regulation. Different databases for housekeeping non-coding RNA and regulatory ncRNA have been developed which provided the scientists with a lot of information for their functional study. The sequence of tRNA was the one first compiled and published in 1989 with 455 tRNA sequences and 981 tRNA genes [156]. The primitive database for non-coding RNA was ncRNAdb which had 30,000 sequences with no specificities [157] and later the amount of information drastically increased and individual databases for each non-coding RNA are developed, such as silva for rRNA, miRNase for miRNA, snOPY for small nucleolar RNA*.*

Countless novel techniques had been emerged in the past decade, which led to the discovery of several new ncRNAs and ncRNA genes that are functionally characterized by modern biotechnological tools. Eukaryotic sRNAs, such as miRNA and siRNA, are short sequenced RNA molecules with a length of a maximum of 25 nucleotides. Detection algorithms of sRNA from RNA seq data involve mapping of single or paired-end reads to a reference genome later converted into genome-wide distribution. This is feasible when the size of sRNA is small and where the distribution remains uniform throughout the transcript. However, in bacteria with a lengthier sRNA ranging from 50 to 350 nucleotides, algorithms have to be designed in such a way to overcome the challenges imposed due to the extremely variable number of small transcripts. One such tool is APERO (analysis of paired-end RNA-seq output), which is used to detect bacterial sRNAs from the sequence data of RNA neglecting the need of converting the reads to genome-wide coverage which leads to the loss


#### **Table 6.**

*miRNA in plant immunity.*


#### **Table 7.** *Other ncRNAs in plant immunity.*

*Non-Coding RNA and Its Prospective Utilization in Plant Breeding DOI: http://dx.doi.org/10.5772/intechopen.106429*

of information. Instead, it is based on detecting the 5'end of the small transcripts and recognizing the extension of the transcript where the conserved information of sequenced fragments increases the accuracy [158]. **Table 8** brings together different databases available for the advanced panel of research on ncRNAs.

Recent years have witnessed the advancement in sequencing methodologies, such as long-end sequencing and optical mapping, for more accurate and faster sequencing at affordable rates. Cufflinks, and CIRCexplorer [159, 160] are some of the bioinformatics tools used for the discovery of ncRNA. Molecular approaches, such as cloning and hybridization techniques, were able to detect and characterize ncRNAs, but they came with a lot of false positives. Currently, the most reliable approach for predicting and functionally characterizing ncRNAs are NGS (Next Generation Sequencing) and CRISPR-Cas9 genome editing techniques [161]. The list of databases developed for non-coding RNA and specific ncRNA is given below. (https://rnacentral.org/expert-databases) [162].

### **9. Conclusion**

Non-coding RNAs (ncRNAs) possess little or no protein-coding capacity yet are indeed functional. They make up a huge and significant percentage of eukaryotic transcriptomes. It modulates expression levels at various stages of protein synthesis, playing an important regulative involvement in practically all biological processes. MicroRNAs (miRNAs), small interference RNAs (siRNAs), circular RNAs (circRNAs), and long non-coding RNAs (lncRNAs) are the major non-coding RNAs. These can either operate as long ncRNAs or be converted into small RNAs. They are classed worldwide based on their size, function, and genetic origin. Non-coding modulates its targets via interacting with DNA, RNA, and proteins. These have a role in multiple epigenetic mechanisms controlling phenotypes, as well as the specification of various physiological pathways. MicroRNAs control the level of gene expression by increasing the disintegration of target mRNAs or inhibiting translation. They are involved in many aspects of plant growth and have the power to reconfigure responses to various biotic and abiotic stresses. The modulation of immunological responses in plants has been linked to non-coding RNAs, DNA and RNA methylation, along with


#### **Table 8.** *Different databases and their specifications.*

other epigenetic changes. Regulatory ncRNAs in plants are being highlighted as potential targets for molecular breeding of agricultural trait improved crop plants, such as improved abiotic and biotic stress tolerance, herbicide resistance, yield, enhancement, and plants with amazing nutritional value with prospective high agricultural importance. Non-coding RNAs (ncRNAs) are also observed to work as a defense system against invading viruses as effectors molecules in RNA-mediated gene silencing and are being exploited in agricultural genetic modification. They also act as key moderators in the level of plant immunity and adaptation to different environments. Plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. Given the discoveries of these ncRNA in the above-discussed processes, be it physical or physiological, they show a new ray of light toward the use of them in crop breeding. In this regard, the areas, especially the quality breeding, stress breeding for abiotic and biotic stresses, have a huge potential. Along with that, looking at their role in changing the flowering and morphogenesis of plants, further research may be carried forward in the direction of their utilization in altering plant growth duration or producing genotypes for off-season breeding. The role of ncRNAs in epigenetics also can be further studied for their exact role in the inheritance pattern of different important traits. Over the last two decades, the research on non-coding RNAs has shown newer insights about their structure, properties, and possible utilities in different fields of life science. Further work is required to be expanded in newer areas to more agriculturally important crops to harness the wonders of ncRNAs.
