NCBI Pongo abelii Annotation Release GCF_028885655.2-RS_2024_02

The genome sequence records for Pongo abelii RefSeq assembly GCF_028885655.2 (NHGRI_mPonAbe1-v2.0_pri) were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies.

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
• 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 "GCF_028885655.2-RS_2024_02".

Date of Entrez queries for transcripts and proteins: Feb 27 2024
Date of submission of annotation to the public databases: Mar 6 2024
Software version: 10.2

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
NHGRI_mPonAbe1-v2.0_pri	GCF_028885655.2	National Human Genome Research Institute, National Institutes of Health	01-05-2024	Reference	26 assembled chromosomes

Gene and feature statistics

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

Feature counts

Feature	NHGRI_mPonAbe1-v2.0_pri
Genes and pseudogenes	41,736
protein-coding	22,189
non-coding	11,986
Transcribed pseudogenes	39
Non-transcribed pseudogenes	7,279
genes with variants	14,807
Immunoglobulin/T-cell receptor gene segments	198
other	45
mRNAs	81,503
fully-supported	80,441
with > 5% ab initio	552
partial	401
with filled gap(s)	0
known RefSeq (NM_)	3,295
model RefSeq (XM_)	78,208
non-coding RNAs	21,095
fully-supported	17,353
with > 5% ab initio	0
partial	1
with filled gap(s)	0
known RefSeq (NR_)	11
model RefSeq (XR_)	20,567
pseudo transcripts	66
fully-supported	57
with > 5% ab initio	0
partial	1
with filled gap(s)	0
known RefSeq (NR_)	4
model RefSeq (XR_)	62
CDSs	81,714
fully-supported	80,441
with > 5% ab initio	671
partial	106
with major correction(s)	1,024
known RefSeq (NP_)	3,308
model RefSeq (XP_)	78,208

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 primates_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 22176 coding genes, 21467 genes had a protein with an alignment covering 50% or more of the query and 19025 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
NHGRI_mPonAbe1-v2.0_pri	GCF_028885655.2	42.22%

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 Nucleotide, Entrez Protein, and SRA, and aligned to the genome.

Transcript alignments

The alignments of the following transcripts with Splign were used for gene prediction:

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.

	NHGRI_mPonAbe1-v2.0_pri Primary Assembly
Number of sequences retrieved from Entrez	3,481
Number (%) of sequences not aligning	0 (0.00%)
Number (%) of sequences with multiple best alignments (split genes)	0 (0.00%)
Number (%) of sequences with CDS coverage < 95%	4 (0.12%)

RNA-Seq alignments

The alignments of the following RNA-Seq reads with STAR 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 alignments of the following long RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive with minimap2 were used for gene prediction:

Protein alignments

The alignments of the following proteins with ProSplign were used for gene prediction:

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.

First Pass	Total
NHGRI_mPonAbe1-v2.0_pri (Current) Coverage: 94.46%	NHGRI_mPonAbe1-v2.0_pri (Current) Coverage: 95.75%
NHGRI_mPonAbe1-v1.1-hic.freeze_pri (Previous) Coverage: 91.69%	NHGRI_mPonAbe1-v1.1-hic.freeze_pri (Previous) Coverage: 94.96%
Percent Identity: 99.19%	Percent Identity: 99.08%

Comparison of the current and previous annotations

The annotations produced for this release were compared to the annotations in the previous release 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.

	NHGRI_mPonAbe1-v2.0_pri (Current) to NHGRI_mPonAbe1-v1.1-hic.freeze_pri (Previous)
Identical	40%
Minor changes	45%
Major changes	8%
New	7%
Deprecated	14%
Other	<1%
Download the report	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
• STAR: Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. Bioinformatics 2013 Jan 1;29(1):15-21.
• Minimap2: Li H. Bioinformatics 2018 Sep 15;34(18):3094-3100