v7.0  (2018-03-09)

RATT was used to transfer gene models from V5 to V7, with the Pacbio setting on unmasked genome. 
The transferred annotation was mainly used for identifying consensus and assigning identifiers to Augustus models.

Augustus was run on both hard-masked and unmasked reference using all the available full length 
non-chimaeric isoseq reads (male, female and somules) plus RNAseq from all available life-stages. 

Hard masked genome was mainly used with a small number of genes being manually added in from unmasked 
and RATT transfer to fill holes in the annotation. In addition, we have carefully curated > 2000 
gene models using WebApollo.


This annotation update is a significant improvement made possible by the upgrade of 
genome sequence V5.2 to V7.0.  As a result of moving from a very fragmented assembly to a very 
contiguous assembly and comparing the results of direct annotation-transfer (using RATT with pacbio 
setting) and gene finding (using Augustus based on RNAseq evidence), many previously incomplete or 
absent gene models are now correctly resolved and many spurious gene models have been deleted.  
In general, Augustus has been observed to have produced excellent gene models with good annotation 
of UTRs which was previously lacking in V5.2.  We have been careful to preserve the original gene 
IDs as "Previous Systematic IDs (PSID)" where genes have been merged/split or newly created. Where 
a 1:1 correspondence exists between RATT transferred and Augustus genes, the original Smp ID has 
been preserved.  In the new annotation, novel genes or merged/split genes have been named with 
an "Smp_3" prefix (eg Smp_300010).


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v7.1  (2018-03-22)

- Structural changes: in this update, we recovered 12 models which have Pfam domains in v5.2 but lost in previous v7.0 annotation. 
In addition, we checked and curated ~ 210 overlapping genes models (mostly are UTR regions).

- We added functional annotations for v7.1. These include product description (based on TAS/NAS in v5.2 and SwissProt hit), 
PMID information, as well as InterPro / Pfam / GO accessions (based on InterProScan).