Each directory contains 3 files:

<name>_assembly_v_03212011.fasta.gz
<name>_assembly_v_10072011.fasta.gz
<name>.trans.estscan.pep.10072011.fasta.gz

Files are labeled according to the date release.
The assembly files contain the assembled transcripts.
The trans.estscan.pep files contain predicted peptide sequences.