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NCBI Salvia splendens Annotation Release 100

The RefSeq genome records for Salvia splendens 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 Salvia splendens Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Jun 25 2021
Date of submission of annotation to the public databases: Jun 30 2021
Software version: 9.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
SspV2GCF_004379255.1Beijing Forestry University05-20-2021Reference23 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

FeatureSspV2
Genes and pseudogenes help71,090
  protein-coding55,480
  non-coding8,729
  Transcribed pseudogenes0
  Non-transcribed pseudogenes6,881
  genes with variants14,966
  Immunoglobulin/T-cell receptor gene segments0
  other0
mRNAs79,239
  fully-supported69,387
  with > 5% ab initio help8,403
  partial311
  with filled gap(s) help0
  known RefSeq (NM_) help0
  model RefSeq (XM_)79,239
non-coding RNAs help16,214
  fully-supported13,053
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help15,089
pseudo transcripts help0
  fully-supported0
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help0
CDSs79,326
  fully-supported69,387
  with > 5% ab initio help8,574
  partial311
  with major correction(s) help250
  known RefSeq (NP_) help0
  model RefSeq (XP_) help79,326

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.1.4 (Simão et al 2015, PMID: 26059717) was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the eudicots_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation (C:complete [S:single-copy, D:duplicated], F:fragmented, M:missing, n:number of genes used).

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 55393 coding genes, 50023 genes had a protein with an alignment covering 50% or more of the query and 23637 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 (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 nameAssembly accession% Masked with WindowMasker
SspV2GCF_004379255.139.98%

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, minimap2, or ProSplign and passed to Gnomon, NCBI's gene prediction software.

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