NCBI Gallus gallus Annotation Release 106

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:

• Annotation Release information: The name of the release, important dates, the software version
• Assemblies: A brief description of the annotated assembly(ies)
• Gene and feature statistics: The counts and characteristics of the annotated features
• BUSCO results: Annotation completeness assessed with BUSCO
• Alignment of the annotated proteins to a set of high-quality proteins: The number of annotated proteins with hits to a set of high-quality proteins
• Masking of genomic sequence: How much of the genome was masked
• Transcript and protein alignments: The number and type of evidence retrieved from public databases and used for gene prediction
• Similarity of current and previous assembly: The similarity of the current and previous assembly
• Similarity of alternate and reference assemblies: The similarity of the alternate assemblies to the reference
• Comparison of the current and previous annotations: What proportion of the genes changed in this annotation

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 106

Annotation release ID: 106
Date of Entrez queries for transcripts and proteins: Dec 23 2021
Date of submission of annotation to the public databases: Mar 3 2022
Software version: 9.0

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
bGalGal1.mat.broiler.GRCg7b	GCF_016699485.2	Vertebrate Genomes Project	01-19-2021	Reference	42 assembled chromosomes; unplaced scaffolds
bGalGal1.pat.whiteleghornlayer.GRCg7w	GCF_016700215.2	Vertebrate Genomes Project	10-01-2021	Alternate	41 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	bGalGal1.mat.broiler.GRCg7b	bGalGal1.pat.whiteleghornlayer.GRCg7w
Genes and pseudogenes	25,635	25,564
protein-coding	18,023	17,981
non-coding	7,330	7,310
Transcribed pseudogenes	26	27
Non-transcribed pseudogenes	172	123
genes with variants	12,408	12,278
Immunoglobulin/T-cell receptor gene segments	70	108
other	14	15
mRNAs	68,670	68,341
fully-supported	64,886	64,467
with > 5% ab initio	518	501
partial	253	302
with filled gap(s)	13	19
known RefSeq (NM_)	8,379	8,351
model RefSeq (XM_)	60,291	59,990
non-coding RNAs	16,124	16,135
fully-supported	14,982	15,003
with > 5% ab initio	0	0
partial	2	1
with filled gap(s)	0	0
known RefSeq (NR_)	939	948
model RefSeq (XR_)	14,471	14,514
pseudo transcripts	26	27
fully-supported	21	24
with > 5% ab initio	0	0
partial	0	0
with filled gap(s)	0	0
known RefSeq (NR_)	6	6
model RefSeq (XR_)	20	21
CDSs	68,753	68,449
fully-supported	64,886	64,467
with > 5% ab initio	719	727
partial	247	278
with major correction(s)	358	376
known RefSeq (NP_)	8,379	8,350
model RefSeq (XP_)	60,304	59,990

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.1.4 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.

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 18010 coding genes, 16591 genes had a protein with an alignment covering 50% or more of the query and 11471 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 (if calculated), for each assembly. RepeatMasker results are only calculated for organisms with complete Dfam HMM model collections.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.

Assembly name	Assembly accession	% Masked with WindowMasker
bGalGal1.mat.broiler.GRCg7b	GCF_016699485.2	20.54%
bGalGal1.pat.whiteleghornlayer.GRCg7w	GCF_016700215.2	20.22%

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 Entrez	9,470	9,470
Number (%) of sequences not aligning	95 (1.00%)	131 (1.38%)
Number (%) of sequences with multiple best alignments (split genes)	1 (0.01%)	6 (0.06%)
Number (%) of sequences with CDS coverage < 95%	28 (0.33%)	45 (0.54%)

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)

CAGE alignments

The following CAGE 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 Pass	Total
bGalGal1.pat.whiteleghornlayer.GRCg7w (Current) Coverage: 90.81%	bGalGal1.pat.whiteleghornlayer.GRCg7w (Current) Coverage: 91.20%
bGalGal1.pat.whiteleghornlayer.GRCg7w (Previous) Coverage: 100.00%	bGalGal1.pat.whiteleghornlayer.GRCg7w (Previous) Coverage: 100.00%
Percent Identity: 100.00%	Percent Identity: 99.97%

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 Pass	Total
bGalGal1.pat.whiteleghornlayer.GRCg7w (Alternate) Coverage: 97.83%	bGalGal1.pat.whiteleghornlayer.GRCg7w (Alternate) Coverage: 98.75%
bGalGal1.mat.broiler.GRCg7b (Reference) Coverage: 97.46%	bGalGal1.mat.broiler.GRCg7b (Reference) Coverage: 98.41%
Percent Identity: 99.26%	Percent Identity: 99.21%

Comparison of the current and previous annotations

The annotation produced for this release (106) was compared to the annotation in the previous release (105) 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 bGalGal1.mat.broiler.GRCg7b (Previous)	bGalGal1.pat.whiteleghornlayer.GRCg7w (Current) to bGalGal1.pat.whiteleghornlayer.GRCg7w (Previous)
Identical	20%	17%
Minor changes	69%	61%
Major changes	7%	10%
New	4%	11%
Deprecated	4%	4%
Other	<1%	1%
Download the report	tabular, Genome Workbench	tabular, Genome Workbench

References

• RefSeq: Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Nucleic Acids Research 2014, 42(Database issue):D756-63
• BUSCO: Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. Molecular biology and evolution 2021.38(10):4647-4654
• RepeatMasker: Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. http://www.repeatmasker.org
• WindowMasker: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Bioinformatics 2006, 2:134-41
• Splign: Kapustin Y, Souvorov A, Tatusova T, Lipman D. Biology Direct 2008, 3:20
• Minimap2: Li H. Bioinformatics 2018 Sep 15;34(18):3094-3100