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Understanding Rattlesnakes: Models for Low-Energy Adaptation and Transcriptomic Research

Rattlesnakes serve as exemplary models for studying low-energy lifestyles, demonstrating remarkable adaptability through down-regulated metabolism and lengthy starvation periods of up to two years. Investigating pit vipers reveals rapid mitochondrial evolution, enhancing our understanding of energy management in reptiles. Current research involves transcriptomic analysis using RNA-Seq to reprogram muscle transcriptomes during starvation and reactivate digestive systems upon feeding. This collaborative project, alongside genome sequencing initiatives, aims to enrich comparative biology, medical research, and student training.

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Understanding Rattlesnakes: Models for Low-Energy Adaptation and Transcriptomic Research

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Presentation Transcript

  1. Why Rattlesnakes? • Model organisms foradaptation to low-energy lifestyles • Low metabolism-down-regulate whole organ systems • Starvation bouts up to two years • Pit Vipers: rapid rates of evolution of mitochondrial genome

  2. Applications: • Transcriptomics of specific tissues using RNASeq during starvation • Reprogram the transcriptome of muscles during prolonged starvation • Reactivation of digestive system upon feeding • Comparative biology in medical research. • Chicken was one of the first vertebrate, non-mammal genomes sequenced • Assemblies of green anole lizard and python.

  3. Progress • Began with pilot 454 sequencing for repeats • Collaboration with faculty at KAUST • Illumina Sequencing • Call by MCBIOS for community project • Share in the assembly and annotation, for training of students and development of programs, publications, funding

  4. Current Data

  5. Transcriptome Assembly • Transcriptome • 50mer assembly 11,000 contigs • No BLAST data yet • Ptitsyn • 10237 with significant BLAST scores • 888 with no annotation

  6. Trinity Assembly

  7. Assembly data • Genome • Velvet on Blacklight (Jeff Pummill) • 43 Kmer; does not include 454 data

  8. Assembly data (cont’d)

  9. Where are the data • Submitted to GenbankBioproject/SRA • Available on secure FTP site at uark.edu • See drhoads@uark.edu for ID and password

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