Transposable elements (TEs) exert an increasingly diverse spectrum of influences on eukaryotic genome structure, function, and evolution. A deluge of genomic, transcriptomic, and proteomic data provides the foundation for turning any non-model eukaryotic species into an emerging model to study all aspects of organismal biology, ultimately shaping future directions for biomedical, environmental, and biodiversity research. However, in contrast to the progress in gene annotation achieved and standardized over the past decade, identification and annotation of the mobile genome component still need to catch up to the standards accepted for host gene annotation. New genome sequences and comprehensive transcriptome data can provide valuable resources for studying shellfish biology and improvement in essential aquaculture species.
While culturing new species in shellfish aquaculture, further understanding the role of epigenetic change within organism-environment interactions is necessary. When dissecting the epigenetic landscapes in novel genomes, a comprehensive description of its mobilome component must be provided in addition to the standard genic and transcriptomic datasets. Each step of TE identification, classification, and annotation should be focused on improving TE boundary designation, reducing identification error rates, and providing accurate information on the type and integrity of TE insertions. However, detecting and identifying TEs in newly sequenced species is still challenging and time-consuming, and different workflows have been proposed. I summarize some workflows and analysis pipelines for generating TE models in de novo assemblies for non-model organisms and, overall, improving their epigenetic landscape analysis.