Isoform Sequencing Based Transcriptome Resource for Flathead Grey Mullet (mugil Cephalus)

Mugil cephalus, commonly known as flathead grey mullet, is an important candidate brackish water food fish species of herbivorous nature positioned at lower trophic levels of the food chain. The biology, genetics, ecology, and fishing aspects of grey mullet were thoroughly reviewed by Whitfield et al. (2012). In the Indian context, though captive broodstock of grey mullet was developed about two decades back (Abraham et al., 2000), large-scale successful induced breeding trials were realized only recently (Sukumaran et al., 2021). Further, the reproductive period of captive grey mullet is reported to be asynchronous between the Eastern and Western Coast stocks of India. The peak reproductive periods are November and June–August for Eastern and Western grey mullet captive stocks, respectively (Sukumaran et al., 2021). A year-round commercial seed production with captive broodstock could not be realized till date due to constraints in captive maturation and seasonal spawning behavior of the species. The availability of genomic and transcriptomic resources would lead to a better understanding of the regulatory pathways involved in captive maturation and breeding of grey mullet. Such information would also facilitate the conduct of functional studies and derive meaningful inferences out of them for the improvement of grey mullet. Conventionally, transcriptome resources are established by sequencing RNA on an Illumina sequencer wherein the short RNA sequence reads are assembled to generate full-length transcripts. With the development of Pacific Biosciences (PacBio) Single Molecule Real-Time (SMRT) sequencing, the full-length isoform-level transcript sequences could be generated directly without the necessity of assembly. Recently, the PacBio Isoform Sequencing (IsoSeq) based full-length transcript resources were made available for candidate brackish water aquaculture species (Zhang et al., 2019; Katneni et al., 2020; Pootakham et al., 2020) with potential applications to an understanding of economic traits and role in genome annotation. Furthermore, the IsoSeq transcripts can be easily annotated (Zeng et al., 2018) and would help in the discovery of splice sites and structural annotation of the genome. For grey mullet, transcript information based on short-read sequence datasets is available (Byadgi et al., 2016; Dor et al., 2020), but no full-length transcript resource is available. So far, a