Whole Transcriptome Profiling Reveals De Novo Genes and Novel MiRNAome in Pandalopsis japonica using Illumina- and PacBio-RNA Sequencing
Pandalopsis japonica (P. japonica) which inhabits the East Sea of Korea is a significant economic species due to its commercial importance. Due to the absence of genomic resources, we employed various next-generation sequencing (seq) techniques. The genome size of P. japonica was estimated at approximately 14-15 Gb by Illumina DNA seq. De novo transcriptome assembly was also constructed through PacBio RNA isoform seq (PacBio Iso-seq), and Illumina RNA seq, resulting in the identification of 18,769 unigenes, of which 11,329 were successfully annotated. Through Gene Ontology (GO) analysis, three key genes related to sexual maturation were identified: Iso0004523 (pole plasm oskar mRNA localization), Iso0011446 (positive regulation of border follicle cell migration), and Iso0002772 (response to estradiol). To identify miRNA regulators of these sexual maturation-related genes, Illumina small RNA seq was performed, revealing 423 orthologous miRNAs and 42 P. japonica-specific miRNAs. Representative two miRNAs, pja-miR-276-3p and pja-miR-276-5p, were validated as key regulators of sexual maturation. Taken together, this study presents the first-ever de novo transcriptome analysis of P. japonica, offering essential genomic information for sexual maturation-related studies in P. japonica.