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:

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 nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ROS_Cfam_1.0GCF_014441545.1The Roslin Institute09-03-2020Reference40 assembled chromosomes; unplaced scaffolds
UMICH_Zoey_3.1GCF_005444595.1University of Michigan05-30-2019Alternate39 assembled chromosomes; unplaced scaffolds
UNSW_CanFamBas_1.0GCF_013276365.1University of New South Wales06-11-2020Alternate39 assembled chromosomes; unplaced scaffolds
UU_Cfam_GSD_1.0GCF_011100685.1Uppsala University03-10-2020Alternate39 assembled chromosomes; unplaced scaffolds
Dog10K_Boxer_TashaGCF_000002285.5Dog Genome Sequencing Consortium10-06-2020Alternate40 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureROS_Cfam_1.0UMICH_Zoey_3.1UNSW_CanFamBas_1.0UU_Cfam_GSD_1.0Dog10K_Boxer_Tasha
Genes and pseudogenes help42,27141,43441,23143,28640,373
  protein-coding20,94920,59320,56721,17520,087
  non-coding15,88515,61315,49916,46115,286
  transcribed pseudogenes3230294022
  non-transcribed pseudogenes5,1795,0544,9955,4014,887
  genes with variants16,15614,47415,00415,36515,006
  immunoglobulin/T-cell receptor gene segments22614414120991
  other00000
mRNAs66,76859,96562,95763,65062,334
  fully-supported64,94958,30161,34461,85460,735
  with > 5% ab initio help952893876997856
  partial164176132180132
  with filled gap(s) help11030
  known RefSeq (NM_) help2,2002,1872,1772,1882,094
  model RefSeq (XM_)64,56857,77860,78061,46260,240
non-coding RNAs help33,07432,32531,98733,68131,834
  fully-supported30,85630,22229,82031,17729,722
  with > 5% ab initio help00000
  partial00000
  with filled gap(s) help00000
  known RefSeq (NR_) help500485482499470
  model RefSeq (XR_) help32,10931,43831,06032,53330,919
pseudo transcripts help4342405238
  fully-supported3637334135
  with > 5% ab initio help00000
  partial11111
  with filled gap(s) help00000
  known RefSeq (NR_) help55552
  model RefSeq (XR_) help3837354736
CDSs66,99260,10763,09863,86062,437
  fully-supported64,94958,30161,34461,85460,735
  with > 5% ab initio help1,1031,0251,0111,144986
  partial161174126176123
  with major correction(s) help1,1772,3321,3841,321891
  known RefSeq (NP_) help2,2002,1872,1772,1882,107
  model RefSeq (XP_) help64,56857,77860,78061,46260,240

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 nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
ROS_Cfam_1.0GCF_014441545.142.05%32.10%
UMICH_Zoey_3.1GCF_005444595.142.00%31.94%
UNSW_CanFamBas_1.0GCF_013276365.142.36%32.24%
UU_Cfam_GSD_1.0GCF_011100685.143.87%33.65%
Dog10K_Boxer_TashaGCF_000002285.542.41%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 Entrez2,7432,7432,7432,7432,743
Number (%) of sequences not aligning18 (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% help18 (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 PassTotal
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 PassTotal
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 PassTotal
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 PassTotal
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 PassTotal
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 help11%
Minor changes help54%
Major changes help15%
New help19%
Deprecated help11%
Other help1%
Download the reporttabular, 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

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