So here is a shell script I have used, that you could adapt for your needs. In the current form it downloads genome sequence and protein sequences, makes a blast database out of them, then joins all blastdbs in the directory into one alias db, called "SelectedArthropods". It works - mostly - and when it breaks it breaks hard, there is no error checking really :) You need

• NCBI eutils

• wget in your path

  usage: fetchAllGenomesByTaxon.sh "Alcanivorax borkumensis"

The genome is downloaded to the current directory. copies of the esearch results are saved as

Alcanivorax borkumensis.assembly.esearch.docsum,   
Alcanivorax borkumensis.genome.esearch.docsum

in the current directory for your reference.

#!/bin/sh

set -u #exit on onbound variable
#TAXLIST=("Daphnia pulex" "Drosophila melanogaster" "Anopheles gambiae" "Pediculus humanus"
#"Ixodes scapularis" "Apis mellifera"  "Bombyx mori")
#TAXLIST=("Strigamia maritima")
TAXLIST=$@ # provide multiple taxa on the cmd-line
for TAX in "${TAXLIST[@]}" ; do
echo getting genome for: $TAX
   GENOME=$(esearch -db genome -query "$TAX"[orgn] |
       efetch -format docsum | tee "${TAX}.genome.esearch.docsum")
   ACC=`echo $GENOME | xtract -pattern DocumentSummary  -element Assembly_Accession`
   NAME=`echo $GENOME |  xtract -pattern DocumentSummary -element Assembly_Name`
   echo authoritative genome: $ACC $NAME
   RESULT=$(esearch -db assembly -query "$ACC" |
       efetch -format docsum | tee "${TAX}.assembly.esearch.docsum")
   FTPP=`echo $RESULT | xtract -pattern DocumentSummary  -element FtpPath_GenBank`
   TAXID=`echo $RESULT | xtract -pattern DocumentSummary  -element Taxid`
   echo FtpPath: $FTPP
   BASENAME=`basename $FTPP`
   FTPPATHG=$FTPP/$BASENAME'_genomic.fna.gz'
   FTPPATHP=$FTPP/$BASENAME'_protein.faa.gz' 
   echo Downloading $FTPPATHG ...

   ## get genome data
   wget $FTPPATHG
   BASENAME=`basename $FTPPATHG`
   gunzip -f $BASENAME
   BASENAME=`echo $BASENAME | sed s/.gz//`
   makeblastdb -in $BASENAME -dbtype nucl -parse_seqids -taxid $TAXID -title "$TAX $NAME genomic"
   echo Downloading $FTPPATHP ...
   ## get protein data
   wget $FTPPATHP  # this may throw an error if there is no proteome file
   BASENAME=`basename $FTPPATHP`
   gunzip -f $BASENAME
   BASENAME=`echo $BASENAME | sed s/.gz//`
   makeblastdb -in $BASENAME -dbtype prot -parse_seqids -taxid $TAXID -title "$TAX $NAME proteins"


done

### Make a blast db of all fasta files in directory
ls  *.fna > dblist_nuc.txt
blastdb_aliastool -dblist_file dblist_nuc.txt -out SelectedArthropds -title 'selection of arth genomes' -dbtype nucl
ls *.faa > dblist_prot.txt
blastdb_aliastool -dblist_file dblist_prot.txt -out SelectedArthropds -title 'selection of arth proteins' -dbtype prot