Single Nucleotide Polymorphisms

SNPs are the simplest type of genetic variation among a population of organisms. A single nucleotide polymorphism can have a variety of phenotypic effects, depending on the context in which it occurs. Within a protein-coding gene, a SNP could create non-synonymous codons that would result in different amino acids encoded. SNPs within promoter regions might alter the affinity of transcription factors, resulting in changes to gene expression levels. SNPs within splice junctions might result in altered splicing, producing a protein variant with additional/missing exons.

Identifying potential SNPs in assembled transcriptome contigs:

Remember that contigs are contiguous DNA sequences made up of overlapping (aligned) sequencing reads. One way to identify SNPs is to examine the assembly alignment and find individual nucleotide differences in the reads that make up the contig. How might you determine whether these single nucleotide differences are likely to be SNPs or whether they represent sequencing errors?

Potential SNPs could be examined in more detail to determine whether they occur in the protein-coding portion of a gene or in the UTRs (untranslated regions of the mRNA).

What questions would you be interested in addressing by identifying SNPs in the Aiptasia transcriptome?

One way to get started:

For Aiptasia, you have access to an assembled transcriptome generated from a single genetic clone of Aiptasia pallida.You can access this data either through the public website AiptasiaBase, or through the individual sequencing and annotation files.

You might want to start by examining a few different contig assemblies in AiptasiaBase, so that you can get a sense of how to find potential SNPs in the assemblies.

Step 1) Navigate to AiptasiaBase

Step 2) Logon to AiptasiaBase by selecting "login" from the left sidebar. You will be prompted for a username and password. Use username "Aiptasia" and password "pallida"