NCBI Physcomitrella patens Annotation Release 100

The RefSeq genome records for Physcomitrella patens 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

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 Physcomitrella patens Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Mar 26 2018
Date of submission of annotation to the public databases: Apr 4 2018
Software version: 8.0

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
Phypa V3	GCF_000002425.4	Moss Genome Consortium	01-24-2018	Reference	29 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	Phypa V3
Genes and pseudogenes	23,747
protein-coding	20,454
non-coding	2,820
transcribed pseudogenes	36
non-transcribed pseudogenes	437
genes with variants	10,553
immunoglobulin/T-cell receptor gene segments	0
other	0
mRNAs	47,895
fully-supported	46,955
with > 5% ab initio	622
partial	57
with filled gap(s)	4
known RefSeq (NM_)	0
model RefSeq (XM_)	47,895
non-coding RNAs	7,579
fully-supported	6,762
with > 5% ab initio	0
partial	1
with filled gap(s)	0
known RefSeq (NR_)	0
model RefSeq (XR_)	7,066
pseudo transcripts	41
fully-supported	38
with > 5% ab initio	0
partial	0
with filled gap(s)	0
known RefSeq (NR_)	0
model RefSeq (XR_)	41
CDSs	48,022
fully-supported	46,955
with > 5% ab initio	711
partial	57
with major correction(s)	91
known RefSeq (NP_)	85
model RefSeq (XP_)	47,937

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 Arabidopsis thaliana known RefSeq proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 20327 coding genes, 15490 genes had a protein with an alignment covering 50% or more of the query and 3599 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: Arabidopsis thaliana known RefSeq 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
Phypa V3	GCF_000002425.4	47.75%	51.64%

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

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

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