Pan-transcriptomics and its applications

The comparative genomic studies carried out on microbial genomes in the early 2000s revealed that using a reference genome from a single organism is not as reliable as it was thought to be and that there exists considerable variation in the intraspecie genomes. This marked the introduction of a new study area in genomics, which was termed pan-genomics, which divided the genome of the specie into three parts, core genome, dispensable genome, and unique genes. This study area primarily focused on microbial genomes but researchers tried to carry out studies on complex eukaryotic genomes, especially of plants and humans. Diversity between the species and in a single specie due to structural variation lead to a conclusion that the current reference genome and transcriptome is incomplete to represent the total gene repertoire and gene readouts of the species; so, building a pan-transcriptome is necessary for studying and analyzing complex genomes and variation between species. Moreover, pan-regulon analysis is also an effective approach in generating pan-transcriptomic data as it will help in understanding the similarities and differences between genomes and to see whether the observed expression of genes is because of the presence or absence of a gene or because of the polymorphism in regulons. Very few studies have been conducted on pan-transcriptome and pan-regulon analysis till now. Here, we discuss the importance of the pan-transcriptome, software tools such as WoPPER, JCoast, Trimmomatic along with some others that are used to build and interpret pan-transcriptomic data and pan-transcriptomic analysis of prokaryotes and eukaryotes. Potential future advances and strategies and open difficulties from the vantage purpose of the previously mentioned biological discipline have also been reviewed in this chapter.