**5. Expression profiling of lncRNAs**

## **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 biological roles through expression profiling.

in *Arabidopsis*. However, the expression of one of the candidate stress responsive lincRNA increased after treatment by elf18 (EF-Tu), which activates pathogen-associated molecular pat tern responses [22]. Likewise, in *T. aestivum*, 283 lncRNAs were identified as fungal-responsive lncRNAs, out of which 254 and 52 lincRNAs were specifically expressed after infestation with *Blumeria graminis* f. sp. tritici and *Puccinia striiformis* f. sp. tritici, respectively [41]. Later, a total of 44,698 lncRNAs were identified in *T. aestivum* consisting of both stress responsive and tissue-specific lncRNAs [31]. In response to tomato yellow-leaf curl virus, 1565 lncRNAs were expressed in *Solanum lycopersicum* [40]. In case of *Populus trichocarpa*, 2542 lncRNAs were expressed under drought stress condition [37]. The exploration of lncRNAs in various plant species in response to different stress conditions exhibit the dynamic role in plant defense.

Role of Next-Generation RNA-Seq Data in Discovery and Characterization of Long Non-Coding…

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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.

roles have been discussed here to highlight the importance of lncRNAs in plants.

The present knowledge on the function of lncRNAs is still limited in plants and a large portion of their function and mechanism is yet to be identified. In spite of this, the biological role of lncRNA has been studied in several plant species as discussed in **Table 2**. Some biological

The participation of lncRNAs in producing the male sterile lines in *O. sativa* is an important example of plant fertility. These male sterile lines are necessary for the hybridization and

**6. Databases for lncRNAs**

**7. Biological roles of lncRNAs**

**7.1. lncRNA in plant fertility**

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

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 in *Arabidopsis*. However, the expression of one of the candidate stress responsive lincRNA increased after treatment by elf18 (EF-Tu), which activates pathogen-associated molecular pat tern responses [22]. Likewise, in *T. aestivum*, 283 lncRNAs were identified as fungal-responsive lncRNAs, out of which 254 and 52 lincRNAs were specifically expressed after infestation with *Blumeria graminis* f. sp. tritici and *Puccinia striiformis* f. sp. tritici, respectively [41]. Later, a total of 44,698 lncRNAs were identified in *T. aestivum* consisting of both stress responsive and tissue-specific lncRNAs [31]. In response to tomato yellow-leaf curl virus, 1565 lncRNAs were expressed in *Solanum lycopersicum* [40]. In case of *Populus trichocarpa*, 2542 lncRNAs were expressed under drought stress condition [37]. The exploration of lncRNAs in various plant species in response to different stress conditions exhibit the dynamic role in plant defense.
