[maker-devel] Gene loss in subsequent round of maker for fungal genome annotation

[Urmi]

Hello maker community,

I am trying to run maker 3.01.02-beta on a fungal genome. I am using
available EST and protein sequences from a different strain of the same
species using parameters "est" and "protein" in the maker_opts.ctl file.
Here is the protocol I am using:

   1. Run maker with repeat masking and providing transcript and protein
   sequences from related species (Run A)
   2. Create SNAP model with CEGMA
   3. Train Augustus with BUSCO
   4. Run (run B ) with the new SNAP (done at step 2) and augustus species
   with options turned off (est2genome=0) and (protein2genome=0) data, provide
   gff file (altest_gff=runA_cdna2genome.gff,
   protein_gff=runA_protein2genome.gff3)
   5. Create SNAP model from run B.
   6. Train Augustus with transcripts from run B and BUSCO
   7. Run (run C ) with the new SNAP (done at step 5) and augustus species
   with options turned off (est2genome=0) and (protein2genome=0) data, provide
   gff file (altest_gff=runA_cdna2genome.gff,
   protein_gff=runA_protein2genome.gff3), keep_preds=1

As a result of this, I get following gene numbers:

   - run A: 12796 total genes out of which 12771 have AED < 0.5
   - run B:10713 total genes out of which 10701 have AED < 0.5
   - run C: 12651 total genes out of which 12582 have AED < 0.5

Looking at the gff files in detail, it is observerd that there are some
gene models in run A which are lost in run B and gain in run C. I don't
understand why there is gene loss for run B. Here is an example:

*RunA*

contig1 maker   gene    20468   21193   .       +       .
>>  ID=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34
>
> contig1 maker   mRNA    20468   21193   100     +       .
>>  ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34;Name=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|0|1|0|241
>
> contig1 maker   exon    20468   21193   .       +       .
>>  ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:1;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
>
> contig1 maker   CDS     20468   21193   .       +       0
>>  ID=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1:cds;Parent=maker-contig1-exonerate_protein2genome-gene-0.34-mRNA-1
>
> contig1 blastn  expressed_sequence_match        20468   21193   726     +
>>      .       ID=contig1:hit:983:3.2.0.0;Name=jgi|test_1|140804|est
>> target_length=726
>
> contig1 blastn  match_part      20468   21193   726     +       .
>>  ID=contig1:hsp:998:3.2.0.0;Parent=contig1:hit:983:3.2.0.0;Target=jgi|test_1|140804|est
>> 1 726 +;Gap=M726
>
> contig1 est2genome      expressed_sequence_match        20468   21193
>>  3630    +       .
>>  ID=contig1:hit:1022:3.2.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100
>
> contig1 est2genome      match_part      20468   21193   3630    +       .
>>
>>  ID=contig1:hsp:1110:3.2.0.0;Parent=contig1:hit:1022:3.2.0.0;Target=jgi|test_1|140804|est
>> 1 726 +;Gap=M726
>
>
*RunB:*

> contig1 est_gff:est2genome      expressed_sequence_match        20468
>>  21193   3630    +       .
>>  ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
>
> contig1 est_gff:est2genome      match_part      20468   21193   3630    +
>>      .
>>  ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est
>> 1 726 +;Gap=M726
>
>
*RunC: *

> contig1 maker   gene    20468   21193   .       +       .
>>  ID=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5
>
> contig1 maker   mRNA    20468   21193   .       +       .
>>  ID=snap_masked-contig1-processed-gene-0.5-mRNA-1;Parent=snap_masked-contig1-processed-gene-0.5;Name=snap_masked-contig1-processed-gene-0.5-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|-1|0|1|-1|1|1|0|241;_merge_warning=1
>
> contig1 maker   exon    20468   21193   .       +       .
>>  ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:1;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
>
> contig1 maker   CDS     20468   21193   .       +       0
>>  ID=snap_masked-contig1-processed-gene-0.5-mRNA-1:cds;Parent=snap_masked-contig1-processed-gene-0.5-mRNA-1
>
> contig1 snap_masked     match   20468   21193   42.956  +       .
>>  ID=contig1:hit:5240:4.5.0.0;Name=snap_masked-contig1-abinit-gene-0.5-mRNA-1;target_length=4075195
>
> contig1 snap_masked     match_part      20468   21193   42.956  +       .
>>
>>  ID=contig1:hsp:12911:4.5.0.0;Parent=contig1:hit:5240:4.5.0.0;Target=snap_masked-contig1-abinit-gene-0.5-mRNA-1
>> 1 726 +;Gap=M726
>
> contig1 est_gff:est2genome      expressed_sequence_match        20468
>>  21193   3630    +       .
>>  ID=contig1:hit:1051:3.12.0.0;Name=jgi|test_1|140804|est;target_length=726;aligned_coverage=100;aligned_identity=100;aligned_coverage=100;aligned_identity=100;score=3630;target_length=726
>
> contig1 est_gff:est2genome      match_part      20468   21193   3630    +
>>      .
>>  ID=contig1:hsp:1166:3.12.0.0;Parent=contig1:hit:1051:3.12.0.0;Target=jgi|test_1|140804|est
>> 1 726 +;Gap=M726
>
>
Please could anyone shed come light on this?


Many thanks in advance.

Urmi
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