For each genome release, there are generally a number of changes that

affect the total number or type of gene models (annotations) for that

annotated genome.

FlyBase curates standard comments indicating the nature of the

change to the gene model in each of the affected gene reports. These

comments are attributed to a "FlyBase analysis" type reference for that

genome release.

The type of changes and the comments that may be found on the gene

reports are listed here. The list contains all the different types of

changes that may be commented for any genome release, a particular

genome release may not contain all the different types of changes.

This particular reference is the "FlyBase analysis" reference for

release 4.3 of the annotated D.melanogaster genome.

A. Changes affecting gene model number.

There are 4 main types of changes.

1. New Gene Models.

When a gene model is made where previously there was none annotated on

the genome, a comment of the following type is listed in the "OTHER

COMMENTS" subsection of the "OTHER INFORMATION" section of the relevant

gene report, attributed to this reference.

"New annotation (CGxxxxx) in release 4.3 of the genome annotation."

where CGxxxxx is the annotation symbol.

2. Restored Gene Models.

A gene model that had previously been deleted in an earlier release of

the genome (due to lack of sufficient supporting evidence) may be

restored in a later release of the genome if new evidence for the gene

model becomes available. In this case, a comment of the following type

is listed in the "OTHER COMMENTS" subsection of the "OTHER INFORMATION"

section of the relevant gene report, attributed to this reference.

"Annotation CGxxxxx restored in release 4.3 of the genome annotation."

where CGxxxxx is the annotation symbol.

3. Deleted Gene Models.

A gene model may be deleted due to lack of sufficient supporting

evidence. In this case, although there will no longer be a gene model

on gbrowse, the gene report is not deleted, so that data about the gene

from the literature is still available on FlyBase, and a comment of the

following type is listed in the "OTHER COMMENTS" subsection of the

"OTHER INFORMATION" section of the relevant gene report, attributed to

this reference.

"Annotation CGxxxxx eliminated in release 4.3 of the genome annotation."

where CGxxxxx is the annotation symbol.

4. Merged Gene Models.

Gene models that were previously separate may be merged, due to new

supporting evidence. In this case, a comment of the following type is

listed in the "RELATIONSHIP TO OTHER GENES" subsection of the "OTHER

INFORMATION" section of the gene report representing the new merged

gene model, attributed to this reference.

"Annotations CGxxxxx and CGyyyyy merged as CGzzzzz in release 4.3 of the genome annotation."

where CGzzzzz is the annotation symbol of the new merged gene model.

5. Split Gene Models

A gene model may be split into two or more separate gene models, due to new

supporting evidence. In this case, a comment of the following type is

listed in the "RELATIONSHIP TO OTHER GENES" subsection of the "OTHER

INFORMATION" section of the gene report representing each new separate

gene model, attributed to this reference.

"Annotation CGxxxxx split into CGyyyyy and CGzzzzz in release 4.3 of the genome annotation."

where CGyyyyy and CGzzzzz are the annotation symbols of the new separate gene models.

B. Changes affecting gene model type.

If a gene model is changed from protein coding (annotation symbol

begins with "CG") to non-protein coding (annotation symbol begins with

"CR") or vice versa, a comment of the following type is listed in the

"OTHER COMMENTS" subsection of the "OTHER INFORMATION" section of the

relevant gene report, attributed to this reference.

"Annotation CGxxxxx renamed CRxxxxx in release 4.3 of the genome annotation."

or

"Annotation CRxxxxx renamed CGxxxxx in release 4.3 of the genome annotation."

C. Additional comments.

The following types of additional comments may also be attributed to this reference.

1. Dicistronic gene models.

If a new dicistronic gene model is created, a comment of the following

type is listed in the "RELATIONSHIP TO OTHER GENES" subsection of the

"OTHER INFORMATION" section of the gene reports representing each open

reading frame, attributed to this reference.

"One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by X, Y."

Where X and Y are the gene symbols representing each open reading frame.

2. Gene models sharing untranslated sequences.

If two separate gene models are newly identified to share untranslated

sequences but have non-overlapping open reading frames, a comment of

the following type is listed in the "RELATIONSHIP TO OTHER GENES"

subsection of the "OTHER INFORMATION" section of the gene reports

representing each open reading frame, attributed to this reference.

"One or more of the processed transcripts for this gene share(s) untranslated sequences with a transcript of an adjacent gene, but encode(s) a single open reading frame (ORF). The non-overlapping ORFs that share untranslated sequences are represented by X, Y."

Where X and Y are the gene symbols representing each non-overlapping open reading frame.

3. Known mutations in the sequenced strain.

If a mutation in the sequence strain is newly identified in a genome

release, an allele representing this mutation is created and a comment

of the following type is listed in the "COMMENTS" section of the allele

report, attributed to this reference.

"Mutation found during genome annotation of the strain used in the genome sequencing project."