NCBI Canis lupus familiaris Annotation Release 106

The RefSeq genome records for Canis lupus familiaris 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
• 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 Canis lupus familiaris Annotation Release 106

Annotation release ID: 106
Date of Entrez queries for transcripts and proteins: Dec 8 2020
Date of submission of annotation to the public databases: Jan 8 2021
Software version: 8.5

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
ROS_Cfam_1.0	GCF_014441545.1	The Roslin Institute	09-03-2020	Reference	40 assembled chromosomes; unplaced scaffolds
UMICH_Zoey_3.1	GCF_005444595.1	University of Michigan	05-30-2019	Alternate	39 assembled chromosomes; unplaced scaffolds
UNSW_CanFamBas_1.0	GCF_013276365.1	University of New South Wales	06-11-2020	Alternate	39 assembled chromosomes; unplaced scaffolds
UU_Cfam_GSD_1.0	GCF_011100685.1	Uppsala University	03-10-2020	Alternate	39 assembled chromosomes; unplaced scaffolds
Dog10K_Boxer_Tasha	GCF_000002285.5	Dog Genome Sequencing Consortium	10-06-2020	Alternate	40 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	ROS_Cfam_1.0	UMICH_Zoey_3.1	UNSW_CanFamBas_1.0	UU_Cfam_GSD_1.0	Dog10K_Boxer_Tasha
Genes and pseudogenes	42,271	41,434	41,231	43,286	40,373
protein-coding	20,949	20,593	20,567	21,175	20,087
non-coding	15,885	15,613	15,499	16,461	15,286
transcribed pseudogenes	32	30	29	40	22
non-transcribed pseudogenes	5,179	5,054	4,995	5,401	4,887
genes with variants	16,156	14,474	15,004	15,365	15,006
immunoglobulin/T-cell receptor gene segments	226	144	141	209	91
other	0	0	0	0	0
mRNAs	66,768	59,965	62,957	63,650	62,334
fully-supported	64,949	58,301	61,344	61,854	60,735
with > 5% ab initio	952	893	876	997	856
partial	164	176	132	180	132
with filled gap(s)	1	1	0	3	0
known RefSeq (NM_)	2,200	2,187	2,177	2,188	2,094
model RefSeq (XM_)	64,568	57,778	60,780	61,462	60,240
non-coding RNAs	33,074	32,325	31,987	33,681	31,834
fully-supported	30,856	30,222	29,820	31,177	29,722
with > 5% ab initio	0	0	0	0	0
partial	0	0	0	0	0
with filled gap(s)	0	0	0	0	0
known RefSeq (NR_)	500	485	482	499	470
model RefSeq (XR_)	32,109	31,438	31,060	32,533	30,919
pseudo transcripts	43	42	40	52	38
fully-supported	36	37	33	41	35
with > 5% ab initio	0	0	0	0	0
partial	1	1	1	1	1
with filled gap(s)	0	0	0	0	0
known RefSeq (NR_)	5	5	5	5	2
model RefSeq (XR_)	38	37	35	47	36
CDSs	66,992	60,107	63,098	63,860	62,437
fully-supported	64,949	58,301	61,344	61,854	60,735
with > 5% ab initio	1,103	1,025	1,011	1,144	986
partial	161	174	126	176	123
with major correction(s)	1,177	2,332	1,384	1,321	891
known RefSeq (NP_)	2,200	2,187	2,177	2,188	2,107
model RefSeq (XP_)	64,568	57,778	60,780	61,462	60,240

Detailed reports

The counts below do not include pseudogenes.

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 21175 coding genes, 20586 genes had a protein with an alignment covering 50% or more of the query and 17488 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 name	Assembly accession	% Masked with RepeatMasker	% Masked with WindowMasker
ROS_Cfam_1.0	GCF_014441545.1	42.05%	32.10%
UMICH_Zoey_3.1	GCF_005444595.1	42.00%	31.94%
UNSW_CanFamBas_1.0	GCF_013276365.1	42.36%	32.24%
UU_Cfam_GSD_1.0	GCF_011100685.1	43.87%	33.65%
Dog10K_Boxer_Tasha	GCF_000002285.5	42.41%	32.25%

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 or ProSplign and passed to Gnomon, NCBI's gene prediction software.

Depending on the other evidence available, long 454 reads (with average length above 250 nt) may be aligned as traditional evidence and reported in the Transcript alignments section or aligned with RNA-Seq reads and reported in the RNA-Seq alignments section.

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.

	ROS_Cfam_1.0 Primary Assembly	UMICH_Zoey_3.1 Primary Assembly	UNSW_CanFamBas_1.0 Primary Assembly	UU_Cfam_GSD_1.0 Primary Assembly	Dog10K_Boxer_Tasha Primary Assembly
Number of sequences retrieved from Entrez	2,743	2,743	2,743	2,743	2,743
Number (%) of sequences not aligning	18 (0.66%)	13 (0.47%)	12 (0.44%)	10 (0.36%)	78 (2.84%)
Number (%) of sequences with multiple best alignments (split genes)	1 (0.04%)	2 (0.07%)	0 (0.00%)	0 (0.00%)	0 (0.00%)
Number (%) of sequences with CDS coverage < 95%	18 (0.81%)	16 (0.73%)	5 (0.23%)	6 (0.27%)	14 (0.66%)

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)

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
Dog10K_Boxer_Tasha (Current) Coverage: 98.26%	Dog10K_Boxer_Tasha (Current) Coverage: 98.42%
CanFam3.1 (Previous) Coverage: 94.97%	CanFam3.1 (Previous) Coverage: 96.47%
Percent Identity: 99.81%	Percent Identity: 99.73%

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
UMICH_Zoey_3.1 (Alternate) Coverage: 98.57%	UMICH_Zoey_3.1 (Alternate) Coverage: 99.05%
ROS_Cfam_1.0 (Reference) Coverage: 96.51%	ROS_Cfam_1.0 (Reference) Coverage: 98.18%
Percent Identity: 99.56%	Percent Identity: 99.49%

First Pass	Total
UNSW_CanFamBas_1.0 (Alternate) Coverage: 98.51%	UNSW_CanFamBas_1.0 (Alternate) Coverage: 98.72%
ROS_Cfam_1.0 (Reference) Coverage: 96.52%	ROS_Cfam_1.0 (Reference) Coverage: 98.26%
Percent Identity: 99.49%	Percent Identity: 99.42%

First Pass	Total
UU_Cfam_GSD_1.0 (Alternate) Coverage: 93.58%	UU_Cfam_GSD_1.0 (Alternate) Coverage: 96.26%
ROS_Cfam_1.0 (Reference) Coverage: 97.04%	ROS_Cfam_1.0 (Reference) Coverage: 98.45%
Percent Identity: 99.56%	Percent Identity: 99.47%

First Pass	Total
Dog10K_Boxer_Tasha (Alternate) Coverage: 98.21%	Dog10K_Boxer_Tasha (Alternate) Coverage: 98.35%
ROS_Cfam_1.0 (Reference) Coverage: 94.91%	ROS_Cfam_1.0 (Reference) Coverage: 96.84%
Percent Identity: 99.57%	Percent Identity: 99.48%

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.

	Dog10K_Boxer_Tasha (Current) to CanFam3.1 (Previous)
Identical	11%
Minor changes	54%
Major changes	15%
New	19%
Deprecated	11%
Other	1%
Download the report	tabular, Genome Workbench

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

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

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

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

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
• 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