Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

Area of Science:

• Genomics and Evolutionary Biology
• Bioinformatics and Computational Biology

Background:

• Genomic and transcriptomic data are unevenly distributed across species, with reptiles being significantly underrepresented.
• Lack of standardized assembly and annotation protocols hinders comparative analyses in reptilian research.

Purpose of the Study:

• To create a comprehensive and standardized resource for reptilian genomic and transcriptomic data.
• To improve annotation completeness and facilitate comparative studies across major reptilian lineages.

Main Methods:

• Sequencing of complementary DNA libraries from leopard geckos and corn snakes.
• Integration of published reptilian sequence data from Squamata, tuatara, crocodiles, and turtles.
• Annotation of all assemblies using the LANE runner 2.0 software pipeline.

Main Results:

• The LANE runner 2.0 pipeline increased annotation completeness for reptilian transcriptomes and genomes.
• Phylogenetic analyses based on concatenated protein alignments resolved evolutionary relationships, positioning turtles and tuatara.
• The Reptilian Transcriptomes Database 2.0 was established, providing a unified resource for reptilian genetic data.

Conclusions:

• The Reptilian Transcriptomes Database 2.0 is a valuable, continuously updated resource for diverse research areas in reptilian biology.
• Standardized annotation protocols are crucial for advancing comparative genomics and evolutionary studies in underrepresented taxa.
• This database will facilitate future research in differential expression, molecular ecology, and phylogenomics.