Raw contig FASTA file, the GTF annotations and the peptide sequences were downloaded from 

http://www.plantmorphogenesis.bio.titech.ac.jp/~algae_genome_project/klebsormidium/kf_download.htm

A repeat-masked version of the contigs was not available.
As the original GTF does not include gene features, we add them by copying mRNA features with

perl -lane 'if($F[2] eq 'mRNA'){$g=$_;$g=~s/mRNA/gene/; print $g}; print;' \
    Klebsormidium_nitens.NIES2285.171026.v11.TITECH.gtf.orig > \
    Klebsormidium_nitens.NIES2285.171026.v11.TITECH.gtf

The rest of files were produced by RSAT-Tools to install this genome.