Previous ways I tried to download it:

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/032/359/415/GCA_032359415.1_NEU_Acer_K2/GCA_032359415.1_NEU_Acer_K2_genomic.gtf.gz
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/032/359/415/GCA_032359415.1_NEU_Acer_K2/GCA_032359415.1_NEU_Acer_K2_genomic.fna.gz
gunzip GCA_032359415.1_NEU_Acer_K2_genomic.gtf.gz
gunzip GCA_032359415.1_NEU_Acer_K2_genomic.fna.gz

curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCA_032359415.1/download?include_annotation_type=GENOME_FASTA,GENOME_GFF,RNA_FASTA,CDS_FASTA,PROT_FASTA,SEQUENCE_REPORT&filename=GCA_032359415.1.zip"
#then unzip it

GCA_032359415.1_NEU_Acer_K2_genomic.fna #this is the genomic FASTA file
GCA_032359415.1_NEU_Acer_K2_genomic.gtf #this is the GTF file

When I used curl to download the whole folder, these are the files I got:

But, in the .gtf and .gff files above, when I try to grep ‘intron’ or ‘three_prime_UTR’, I can’t find any non-coding regions in these files. These are necessary for alignment.

So, I am going to try to download them again, because when I read through the Selwyn and Vollmer 2023 paper, they specifically state that the genome assembly can be accessed through NCBI BioProject: PRJNA948411 and RNA sequencing data used for annotation can be accessed from NCBI BioProject: PRJNA949884. So maybe I accidentally downloaded the wrong files and that’s why they’re missing introns and UTRs.

https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_032359415.1/

I downloaded it this way and it’s the exact same as running the “curl” script above. the files are the same.