Whole genome sequencing, de novo assembly, and comparative analysis of varanus salvator and megaustenia siamensis

Abstract

Background: Understanding the animal genome structure and function is pivotal for expanding our current knowledge of evolution, biodiversity, cosmeceutical and medical applications. Each species has a unique characteristic feature. Varanus salvator is a reptile (vertebrate) prevalent in Thailand. It has evolved over millions of years to adapt and survive in urban environments, polluted canals, and garbage dumps. It still survives without noticeable effects. Megaustenia siamensis, an invertebrate, is famous for its ability to produce biological adhesive substances enabling it to stick to trees’ leaves even in heavy rain. However, there is very little genomics or transcriptomics data for V. salvator and M. siamensis. Herein, High-throughput whole-genome assembly would serve as a genomic reference of V. salvator and M. siamensis. The transcriptomics would lead to the discovery of proteins involving in bioactive compound syntheses, which may have high potential in cosmeceutical and medical applications. Method: We generated reference genomes using a hybrid approach of short-read and long-read sequencing platforms. Performing comparative genomics within and between species to understand the evolution and adaptation. We also studied positively selected genes which were associated with V.salvator-specific traits and M.siamensis-specific traits. Furthermore, we sought for potential bioactive compounds, antimicrobial peptides, and differential expression between foot and mantle from transcriptomic data. Result: The final size of the reference genome assembly of V. salvator was 1.7 Gb with an N50 scaffold size of 71Mb featuring 87.5% completeness of the genome assembly. Our comparative genomic analysis revealed that V. salvator is closely related to V. komodoensis. We also found a positive selection in V. salvator genome within the genes controlling blood clotting and innate immunity genes. The final size of the reference genome assembly of M. siamensis was 2.59 Gb with an N50 scaffold size of 84.3Mb featuring 85.9% completeness of the genome assembly. The phylogenetic tree showed that M. siamensis was most closely to A. vulgaris, which is a group of land snails. Positive selection was found in pathways related to ubiquitin-proteasome. Moreover, RNA from foot and mantle tissues suggested the major components of the glue, which comprised lectin-like proteins (C-lectin, H-lectin, and C1q) and matrilin-like proteins (VWA and EGF). The result also reveals 44 potential antimicrobial peptides (AMPs). Conclusion: The draft genome data are expected to provide useful information for future studies and contribute significantly to understanding the biological insight. Furthermore, the transcriptome data reveal the highest protein composition and bioactive compounds, which might be useful for medical applications.