Currently, an Illumina MiSeq run costs $900 in reagents and generates 4.5Gb of sequence. The sequence is 2 x 150 bp paired end sequence. As one of the other commenters mentioned, 100X sequencing is the standard coverage target for de novo sequencing. This means 1-2 genomes can be combined and sequenced together in one run. A university core can likely be found that would perform the run for $150-$500.
This amount of sequence will allow the genome to be assembled into 50-200 contigs covering ~99% of the genome. The gaps between contigs would be small.
A sequencing library needs to be prepared from the fungus DNA sample. Short DNA fragments are generated and ligated to oligos with DNA barcodes and sequences compatible with the Illumina flow cell.
Preparing a sequencing library using Illumina's NexteraXT kit is very easy, and costs about $50 / sample for a 24 sample kit. Making a DIY sequencing library would cost about $250 in oligos, and and some minor other equipment (gel boxes, PCR setup, etc).
So the cost for one fungus genome with DIY sequencing library:
$400 sequencing library
$1050-$1400 sequencing run
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$1450 - $1800 total
Sequencing two fungus genomes with a DIY sequencing library:
$700 seq. libraries
$1050-$1400 seq. run
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$875 - $1000 total per genome
Sequencing two fungus genomes with a Nextera sequencing library:
--22 samples in the Nextera kit left over
$1500 Nextera libraries
$1050-$1400 seq. run
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$1225 - $1450 total per genome
Cheers,
Jim Lund
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