NCBI Hydra vulgaris Annotation Release GCF_037890685.1-RS_2024_06

The genome sequence records for Hydra vulgaris RefSeq assembly GCF_037890685.1 (HydraT2T_105) 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
• 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 "GCF_037890685.1-RS_2024_06".

Date of Entrez queries for transcripts and proteins: Jun 11 2024
Date of submission of annotation to the public databases: Jun 19 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
HydraT2T_105	GCF_037890685.1	University of Vienna	03-28-2024	Reference	17 assembled chromosomes
HydraT2T_AEP	GCF_038396675.1	University of Vienna	04-02-2024	Alternate	15 assembled chromosomes

Gene and feature statistics

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

Feature counts

Feature	HydraT2T_105	HydraT2T_AEP
Genes and pseudogenes	31,215	28,925
protein-coding	21,916	22,797
non-coding	8,965	5,638
Transcribed pseudogenes	0	1
Non-transcribed pseudogenes	333	488
genes with variants	8,170	6,311
Immunoglobulin/T-cell receptor gene segments	0	0
other	1	1
mRNAs	34,750	33,388
fully-supported	28,341	25,468
with > 5% ab initio	5,487	7,358
partial	69	68
with filled gap(s)	1	0
known RefSeq (NM_)	189	134
model RefSeq (XM_)	34,561	33,254
non-coding RNAs	14,638	8,444
fully-supported	14,010	7,634
with > 5% ab initio	0	0
partial	0	1
with filled gap(s)	0	0
known RefSeq (NR_)	10	3
model RefSeq (XR_)	14,245	8,081
pseudo transcripts	0	1
fully-supported	0	1
with > 5% ab initio	0	0
partial	0	0
with filled gap(s)	0	0
known RefSeq (NR_)	0	0
model RefSeq (XR_)	0	1
CDSs	34,763	33,388
fully-supported	28,341	25,468
with > 5% ab initio	5,625	7,427
partial	29	40
with major correction(s)	86	99
known RefSeq (NP_)	189	134
model RefSeq (XP_)	34,574	33,254

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 metazoa_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 22664 coding genes, 12058 genes had a protein with an alignment covering 50% or more of the query and 2717 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
HydraT2T_105	GCF_037890685.1	52.35%
HydraT2T_AEP	GCF_038396675.1	45.70%

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:

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
HydraT2T_105 (Current) Coverage: 96.51%	HydraT2T_105 (Current) Coverage: 98.77%
Hydra_105_v3 (Previous) Coverage: 98.26%	Hydra_105_v3 (Previous) Coverage: 98.52%
Percent Identity: 97.66%	Percent Identity: 97.64%

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.

First Pass	Total
HydraT2T_AEP (Alternate) Coverage: 15.14%	HydraT2T_AEP (Alternate) Coverage: 17.78%
HydraT2T_105 (Reference) Coverage: 16.55%	HydraT2T_105 (Reference) Coverage: 18.93%
Percent Identity: 81.93%	Percent Identity: 82.90%

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 a link to the details of the comparison in tabular format.

	HydraT2T_105 (Current) to Hydra_105_v3 (Previous)
Identical	10%
Minor changes	50%
Major changes	16%
New	23%
Deprecated	15%
Other	1%
Download the report	tabular

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
• 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