NCBI Gallus gallus Annotation Release 105

The RefSeq genome records for Gallus gallus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

The annotation products are available in the sequence databases and on the FTP site.

This report provides:

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.


Annotation Release information

This annotation should be referred to as NCBI Gallus gallus Annotation Release 105

Annotation release ID: 105
Date of Entrez queries for transcripts and proteins: Mar 28 2021
Date of submission of annotation to the public databases: Apr 10 2021
Software version: 8.6

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
bGalGal1.mat.broiler.GRCg7bGCF_016699485.2Vertebrate Genomes Project01-19-2021Reference42 assembled chromosomes; unplaced scaffolds
bGalGal1.pat. whiteleghornlayer.GRCg7wGCF_016700215.1Vertebrate Genomes Project01-19-2021Alternate39 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

Counts and length of annotated features are provided below for each assembly.

Feature counts

FeaturebGalGal1.mat.broiler.GRCg7bbGalGal1.pat. whiteleghornlayer.GRCg7w
Genes and pseudogenes help25,40023,605
  protein-coding17,80716,733
  non-coding7,3416,682
  Transcribed pseudogenes2418
  Non-transcribed pseudogenes16282
  genes with variants11,6977,788
  Immunoglobulin/T-cell receptor gene segments6690
  other00
mRNAs59,24242,314
  fully-supported58,29841,441
  with > 5% ab initio help480434
  partial473464
  with filled gap(s) help1319
  known RefSeq (NM_) help6,6896,403
  model RefSeq (XM_)52,55335,911
non-coding RNAs help16,15514,174
  fully-supported15,07613,179
  with > 5% ab initio help00
  partial32
  with filled gap(s) help00
  known RefSeq (NR_) help874834
  model RefSeq (XR_) help14,56212,696
pseudo transcripts help2418
  fully-supported2114
  with > 5% ab initio help00
  partial00
  with filled gap(s) help00
  known RefSeq (NR_) help66
  model RefSeq (XR_) help1812
CDSs59,32142,404
  fully-supported58,29841,441
  with > 5% ab initio help581552
  partial295288
  with major correction(s) help435382
  known RefSeq (NP_) help6,6896,403
  model RefSeq (XP_) help52,56635,911

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.0.2 (Simão et al 2015, PMID: 26059717) was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the aves_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation (C:complete [S:single-copy, D:duplicated], F:fragmented, M:missing, n:number of genes used).

Alignment of the annotated proteins to a set of high-quality proteins

The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 17794 coding genes, 16504 genes had a protein with an alignment covering 50% or more of the query and 11387 had an alignment covering 95% or more of the query.

Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.

Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.

Query: annotated proteins
Target: UniProtKB/Swiss-Prot curated proteins

Masking of genomic sequence

Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker for each assembly. RepeatMasker results are only used for organisms for which a comprehensive repeat library is available.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
bGalGal1.mat.broiler.GRCg7bGCF_016699485.220.54%
bGalGal1.pat.whiteleghornlayer.GRCg7wGCF_016700215.118.98%

Transcript and protein alignments

The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign, minimap2, or ProSplign and passed to Gnomon, NCBI's gene prediction software.

Transcript alignments

RefSeq transcript alignment quality report

The known RefSeq transcripts (NM_ and NR_ accessions) are a set of hiqh-quality transcripts maintained by the RefSeq group at NCBI. Alignment statistics for this group of transcripts, such as percent and number of sequences not aligning at all, percent best alignments split between multiple scaffolds, and percent alignments not covering the full CDS are indicative of the genome quality and are provided below.

bGalGal1.mat.broiler.GRCg7b
Primary Assembly
bGalGal1.pat.whiteleghornlayer.GRCg7w
Primary Assembly
Number of sequences retrieved from Entrez7,7137,713
Number (%) of sequences not aligning90 (1.17%)431 (5.59%)
Number (%) of sequences with multiple best alignments (split genes)1 (0.01%)5 (0.07%)
Number (%) of sequences with CDS coverage < 95% help35 (0.52%)40 (0.62%)

RNA-Seq alignments

The following RNA-Seq reads from the Sequence Read Archive were also used for gene prediction:

  Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)
  Show alignments statistics, by run (ERR, SRR, DRR)

SRA Long Read Alignment Statistics

The following long read RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive were also used for gene prediction:

Protein alignments

Assembly-assembly alignments of current to previous assembly

When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First PassTotal
bGalGal1.mat.broiler.GRCg7b (Current) Coverage: 96.48%bGalGal1.mat.broiler.GRCg7b (Current) Coverage: 97.72%
GRCg6a (Previous) Coverage: 95.97%GRCg6a (Previous) Coverage: 97.43%
Percent Identity: 99.12%Percent Identity: 99.01%

Assembly-assembly alignments of alternate to reference assembly

When multiple assemblies of good quality are available for the organism, the annotation of all is done in coordination. The alternate assemblies are aligned to the reference assembly and the best reciprocal best hits are used to identify corresponding regions, that can then be annotated together.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First PassTotal
bGalGal1.pat.whiteleghornlayer.GRCg7w (Alternate) Coverage: 97.85%bGalGal1.pat.whiteleghornlayer.GRCg7w (Alternate) Coverage: 98.85%
bGalGal1.mat.broiler.GRCg7b (Reference) Coverage: 88.52%bGalGal1.mat.broiler.GRCg7b (Reference) Coverage: 89.68%
Percent Identity: 99.18%Percent Identity: 99.10%

Comparison of the current and previous annotations

The annotation produced for this release (105) was compared to the annotation in the previous release (104) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). If the assembly was updated between the two releases, alignments between the current and the previous assembly were used to match the current and previous gene and transcript features in mapped regions.

The table below summarizes the changes in the gene set for each assembly as a percent of the number of genes in the current annotation release, and provides links to the details of the comparison in tabular format and in a Genome Workbench project.

bGalGal1.mat.broiler.GRCg7b (Current) to GRCg6a (Previous)
Identical help14%
Minor changes help50%
Major changes help14%
New help21%
Deprecated help18%
Other help1%
Download the reporttabular, Genome Workbench

This is the first time that is annotated by the NCBI Eukaryotic Genome Annotation Pipeline.

References

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