By Nico Lois following NCBI Entrez Utilities.
This short workflow downloads NCBI data through a *nix terminal. Species, genera, families may be searched with the command esearch -query "taxa". This command also allows to search for a species (or any taxa) and a specific part of the genome. esearch -query "taxa AND COI".
Querying help.
I reccommend going through the bash file DownloadNCBI_workflow.sh line by line and check on the commented lines as they may be useful for you.
Please share and report any issues you may find!