**6. Databases for lncRNAs**

**5. Expression profiling of lncRNAs**

118 Next Generation Plant Breeding

biological roles through expression profiling.

**5.2. Expression under biotic and abiotic stresses**

**5.1. During developmental stages of different tissues**

The expression of lncRNAs is regulated through different environmental and biological factors and delving into their diverse biological roles. They exhibit spatial and temporal expression during different developmental stages of various plant tissues. In contrast to the animals, a little is known about the functioning of lncRNAs in plants. The available reports reveal their role in nodule formation [26], lateral root development [67], vegetative and gametophytic development [68], cell-wall synthesis [69], flowering time [27, 54], and several others. The expression profiles developed using high-throughput RNA-seq data from various plants organs marks lncRNAs as an indispensable unit of the transcriptome. For instance, the expression profiles of lncRNAs from root, leaf, stem, spike, and grain in three developmental stages of *T. aestivum* have suggested the role in developmental processes. Furthermore, the lncRNAs show differential expression pattern comparable to the mRNA and highlight their function in related stages [31]. Besides this, the differential expression of lncRNAs in 11 different tissues of chickpea and 13 of maize also strengthens the findings [30]. These results also highlight the higher number of lncRNAs in actively dividing cells and reproductive tissues in comparison to the other [30, 33, 42, 43]. Depending on the expression values, they can be divided into different categories ranging from very low to very high expressing lncRNAs [30, 31]. Furthermore, fragments per kilobase of transcripts per million mapped reads (FPKM), reads per kilobase of transcripts per million mapped reads (RPKM) or transcripts per million (TPM) has to be determined for normalization and estimation of expression level [70]. The alteration in the expression level of various tissues within sundry plants can be correlated with the different genetic makeup and depth of transcriptome sequencing data. Tissue specificity index (TSI) is also calculated for studying the differential expression pattern of lncRNAs. The value of TSI ranges from zero to one, zero for housekeeping genes and one or near to one for sternly tissue-specific genes [31]. The criteria of TSI has revealed that lncRNAs are involved in flower and fruit development in *Fragaria vesca* [34], flower development in *Cicer arietinum* [30], development of fiber in *Gossypium arboreum* [71], and in development of root and floral tissues in *Morus notabilis* [72]. In addition to TSI, cell-type specificity can be interpreted for the expression of lncRNAs in specific cells [29]. For instance, in *Arabidopsis* cell-type specific lncRNAs have been identified in specialized cells but the expression was lower in comparison to mRNA [73]. The knowledge of lncRNAs is limited in plants, but the elevation in the survey of high-throughput RNA-seq data has allowed the prediction of their

The expression of lncRNAs gets affected by biotic and/or abiotic factors in plants, but the mechanism remains poorly understood. Stress-responsive lncRNAs have emerged as an important component of plant defense machinery. The differential expression patterns in response to various stresses, including biotic and abiotic stresses, suggest the diverse function of lncRNAs at different intervals of stress exposure. For instance, the expression of 1832 lincRNAs gets remarkably affected after 2 h and/or 10 h of drought, salt, cold, and/or ABA (abscisic acid) treatments New high-throughput technologies have aided in the exponential rise of RNA-seq data from various plant species. A significant amount of lncRNAs has been identified and characterized for their diverse biological roles. Therefore, it is necessary to organize this data in web-based platforms or databases for further improvement, updates, and analysis [29]. Along with the aid of several computational tools, the data can be analyzed for phylogenetic relationships, expression patterns, molecular interactions, single nucleotide polymorphism, epigenetic variations, etc., and assist in understanding the lncRNAs in plants. The information in these databases can be managed specifically for single or numerous plant species. For instance, PLncRNAdb is specific for four plants species including *A. thaliana*, *A. lyrata*, *P. trichocarpa*, and *Z. mays* and consist of 5000 lncRNAs [74]. The information on 37 plants and 6 algae with data of >120,000 lncRNAs can be accessed on GreeNC database [75]. NONCODE v4 and PLncDB have information on 3853 and >13,000 lncRNA transcripts, respectively in Arabidopsis. Some databases cover the infor mation on both coding and non-coding transcripts like PlantNATsDB accumulating data of 70 plant species on NATs [76]. Besides this, some databases are plant-specific like TAIR10, PNRD, PlantNATsDB, etc., while certain databases (e.g., RNACentral, lncRNAdb v2.0, and NONCODE v4) consist of information from other organisms also in addition to plants [29]. These well-managed databases will allow the researchers to further study the lncRNA in more depth.
