obsolete

Displaying 1 - 5 of 5

AaegL1.1

The AaegL1.1 gene set was released in July 2006. It is derived from the Aedes aegypti AaegL1 assembly. The gene set corresponds to the final release of the Aedes annotation prior to paper writing. This is the set which has been submitted to GenBank and hosted at VectorBase and Ensembl.

Gene build name: 
AaegL1.1
Release date: 
Saturday, January 7, 2006

AaegL1

The Aedes aegypti Liverpool LVP strain genome sequence is a joint effort between the Broad Institute and The Institute for Genomic Research (TIGR).

Gene Count: 
16 691
Protein-coding gene count: 
15 419
Other gene count: 
1 272
Transcript count: 
18 061
Protein-coding transcript count: 
16 789
Other transcript count: 
1 272
Manually reviewed genes: 
0
Genes updated by VB users: 
0
Peptide Count: 
16 789
Exon Count: 
0
Gene build status: 
Deprecated
Total gene updates: 
0

AgamP3.3

The AgamP3.3. gene set was released in February 2006.

Gene build name: 
AgamP3.3
Release date: 
Monday, January 2, 2006

AgamP3

As described in Holt et al. (2002), plasmid and BAC DNA libraries were constructed with stringently size-selected PEST strain DNA. Two BAC libraries were constructed, one (ND-TAM) using DNA from whole adult male and female mosquitoes and the other (ND-1) using DNA from ovaries of PEST females collected about 24 hours after the blood meal. Plasmid libraries containing inserts of 2.5, 10 and 50 kb were constructed with DNA derived from either 330 male or 430 female mosquitoes.

Gene Count: 
13 765
Protein-coding gene count: 
13 277
Other gene count: 
488
Transcript count: 
14 127
Protein-coding transcript count: 
13 639
Other transcript count: 
488
Manually reviewed genes: 
261
Genes updated by VB users: 
667
Peptide Count: 
13 639
Exon Count: 
0
Gene build status: 
Deprecated
Total gene updates: 
928

AgamP3.4

AgamP3.4 was released at VectorBase in July 2007.

The same annotation is visible at Ensembl from release 45.

Changes from previous gene set AgamP3.3

Significant differences from the previous annotation include:

  • Many more manually-appraised gene models, including most models on chromosome arm 2L.
  • Better identification of repeats (especially transposons) leading to a reduction in models that may be transposon-derived.
  • Improved handling of community-provided annotation.
  • Use of selected VectorBase transcript models from Aedes aegypti as an additional evidence source
  • Improvements to protein-based models due to better parameterization of GeneWise

Details of genebuild

The AgamP3.4 gene annotation was prepared by combining sets of transcript models made by different approaches.

  1. Manually-curated models (including alternative transcripts).
  2. Models built with GeneWise using Anopheles proteins (from public databases or contributed directly by Anopheles researchers) were given EST-based extensions, and merged to give a non-redundant set (allowing alternative transcripts).
  3. Models built with GeneWise using arthropod proteins (primarily from Drosophila (FlyBase 4.3 set) and Aedes (AaegL1.1) that have EST support), plus selected Arthropoda entries from Uniprot) were given EST-based extensions where possible, and merged to give a non-redundant set (not allowing alternative transcripts).
  4. EST-based models built solely from A. gambiae ESTs using the ClusterMerge algorithm.
  5. Protein-based models built with GeneWise using other Metazoa entries from Uniprot were given EST-based extensions (rarely possible), and merged to give a non-redundant set (not allowing alternative transcripts).
  6. SNAP ab initio predictions that have an identifiable Pfam domain but do not overlap with repeats.

The final gene set was produced by the progressive addition of models from the different approaches. First, Set 1 & 2 transcripts were combined, giving priority to manually-curated models in cases of conflict. Set 3 genes were then added, but only where there was no overlap with a Set 1/2 model. Genes from sets 4, 5 and 6 were similarly added in turn, only where there was no overlap with a higher priority model.

In addition, tRNA genes were predicted using the program tRNAScan-SE, and a small number of miRNA genes were predicted by homology with miRBase entries.

References:

GeneWise and its use within the Ensembl system for gene model annotation.

  • E.Birney et al., Genome Res. 2004 14:988-95
  • V.Curwen et al., Genome Res. 2004 14:942-50

EST alignment to genomes using Exonerate.

  • G. Slater et al., BMC Bioinformatics. 2005 6:31

      Cluster-Merge algorithm.

      • E.Eyras et al., Genome. Res. 2004 14:976-87

      Ab initio gene finding by SNAP.

      • I. Korf, BMC Bioinformatics. 2004 5:59

      tRNAscan-SE.

Gene build name: 
AgamP3.4
Release date: 
Sunday, January 7, 2007

AgamP3

As described in Holt et al. (2002), plasmid and BAC DNA libraries were constructed with stringently size-selected PEST strain DNA. Two BAC libraries were constructed, one (ND-TAM) using DNA from whole adult male and female mosquitoes and the other (ND-1) using DNA from ovaries of PEST females collected about 24 hours after the blood meal. Plasmid libraries containing inserts of 2.5, 10 and 50 kb were constructed with DNA derived from either 330 male or 430 female mosquitoes.

Gene Count: 
12 945
Protein-coding gene count: 
12 457
Other gene count: 
488
Transcript count: 
13 621
Protein-coding transcript count: 
13 133
Other transcript count: 
488
Manually reviewed genes: 
3 534
Genes updated by VB users: 
1 441
Peptide Count: 
13 133
Exon Count: 
0
Gene build status: 
Deprecated
Total gene updates: 
4 975

AgamP3.5

AgamP3.5 was released at VectorBase in September 2009. The same annotation is visible at EnsemblGenome from release 3 (autumn 2009).

Changes from previous gene set AgamP3.4

Significant differences from the previous annotation include:

  • Many more manually-appraised gene models, including most models on chromosome arm 3L and X

Details of genebuild

The AgamP3.5 gene annotation is an update of the AgamP3.4 gene set, replacing some of the gene models, rather than a new gene build, where all the gene models are regenerated.

Many additional manual/community annotated genes were available, making it essential to update the gene set. The newly available genes were incorporated in the existing gene set (AgamP3.4) as follow:

  • where a manual or a community model was available, the gene was replaced by the new model,
  • when no new model were available, the gene remained unchanged.
  • Genes might have been added or removed.
  • Conflict between manual or community models were resolved by a manual inspection.
Gene build name: 
AgamP3.5
Release date: 
Tuesday, September 1, 2009

AgamP3

As described in Holt et al. (2002), plasmid and BAC DNA libraries were constructed with stringently size-selected PEST strain DNA. Two BAC libraries were constructed, one (ND-TAM) using DNA from whole adult male and female mosquitoes and the other (ND-1) using DNA from ovaries of PEST females collected about 24 hours after the blood meal. Plasmid libraries containing inserts of 2.5, 10 and 50 kb were constructed with DNA derived from either 330 male or 430 female mosquitoes.

Gene Count: 
13 254
Protein-coding gene count: 
12 604
Other gene count: 
650
Transcript count: 
14 753
Protein-coding transcript count: 
14 103
Other transcript count: 
650
Manually reviewed genes: 
7 445
Genes updated by VB users: 
362
Peptide Count: 
14 103
Exon Count: 
0
Gene build status: 
Deprecated
Total gene updates: 
7 807

MOZ2

Although photographs of the BAC in situ hybridizations have been archived, the initial physical mapping of scaffolds was based on the assignment of BAC clones to lettered subdivisions in the polytene chromosome complement. This resulted in some ambiguity in physical map assignments and in orientation, particularly of the shorter scaffolds. In the initial MOZ1 assembly, 30 of the largest scaffolds (187,844,042 bp) were mapped and oriented and an additional 112 scaffolds were mapped but not oriented (45,266,526 bp), for a total of 84% of the assembly sequence having a formal map assignment. In some instances, more than one small scaffold mapped to the same lettered subdivision, in which case order and possibly orientation were assigned arbitrarily. The remaining 8845 unmapped scaffolds were arbitrarily assigned to an 'unmapped chromosome.' The MOZ1 assembly was the subject of the initial genome annotation described in Holt et al. (2002), and the assembly and associated annotation were displayed on the EBI/Sanger Ensembl Genome Browser on 29 May 2002.

The first update to the MOZ1 assembly, MOZ2 involved the results of a concerted effort to correct some of the ambiguities in scaffold map locations and orientations by manual analysis of the archived BAC chromosome hybridization photographs and by the hybridization of a small number of new BAC clones selected to resolve questions of scaffold orientation. The new AGP file, and early draft of which was first displayed on the A. gambiae genome poster published in the 4 October 2002 issue of Science, formed the basis of a new annotation and gene build displayed on 1 October 2003 (MOZ2) (Mongin et al. 2004). This assembly was also 278 Mb. The automated Ensembl gene-building system was used, repeated sequence elements and regions of low complexity were masked, coding regions were identified using BLAST and ESTs were mapped to the genome.

Assembly name: 
MOZ2
Release date: 
Wednesday, October 1, 2003

PEST

The Anopheles gambiae PEST strain was chosen for genome sequencing because it had both a fixed, standard chromosomal arrangement and a sex-linked pink eye mutation that could readily be used as an indicator of cross-colony contamination. The pink eye mutation originated in a colony called A. gambiae LPE established in 1951 at the London School of Hygiene and Tropical Medicine from mosquitoes collected in Lagos, Nigeria.

Scaffold count: 
8 987
Assembly status: 
Deprecated
Sequencing method: 
Sanger shotgun
Assembly software: 
Celera Assembler
Average depth of coverage: 
10.2X
Finishing status: 
chromosomes
Genome Size (bp): 
278,000,000
Subscribe to obsolete