NCBI Solanum lycopersicum Annotation Release 103

The RefSeq genome records for Solanum lycopersicum 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
• 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 NCBI Solanum lycopersicum Annotation Release 103

Annotation release ID: 103
Date of Entrez queries for transcripts and proteins: Aug 2 2018
Date of submission of annotation to the public databases: Aug 8 2018
Software version: 8.1

Assemblies

The following assemblies were included in this annotation run:

Assembly name	Assembly accession	Submitter	Assembly date	Reference/Alternate	Assembly content
SL3.0	GCF_000188115.4	Solanaceae Genomics Project	04-18-2018	Reference	14 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

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

Feature counts

Feature	SL3.0
Genes and pseudogenes	31,273
protein-coding	25,613
non-coding	4,396
transcribed pseudogenes	36
non-transcribed pseudogenes	1,223
genes with variants	7,123
immunoglobulin/T-cell receptor gene segments	0
other	5
mRNAs	37,532
fully-supported	34,625
with > 5% ab initio	2,598
partial	239
with filled gap(s)	62
known RefSeq (NM_)	2,532
model RefSeq (XM_)	35,000
non-coding RNAs	9,202
fully-supported	7,789
with > 5% ab initio	0
partial	4
with filled gap(s)	3
known RefSeq (NR_)	116
model RefSeq (XR_)	8,214
pseudo transcripts	40
fully-supported	36
with > 5% ab initio	0
partial	0
with filled gap(s)	2
known RefSeq (NR_)	5
model RefSeq (XR_)	34
CDSs	37,658
fully-supported	34,625
with > 5% ab initio	2,639
partial	230
with major correction(s)	263
known RefSeq (NP_)	2,532
model RefSeq (XP_)	35,126

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 25487 coding genes, 23087 genes had a protein with an alignment covering 50% or more of the query and 10982 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
SL3.0	GCF_000188115.4	16.42%	34.45%

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.

	SL3.0 Primary Assembly
Number of sequences retrieved from Entrez	2,667
Number (%) of sequences not aligning	2 (0.07%)
Number (%) of sequences with multiple best alignments (split genes)	5 (0.19%)
Number (%) of sequences with CDS coverage < 95%	13 (0.51%)

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 Pass	Total
SL3.0 (Current) Coverage: 88.51%	SL3.0 (Current) Coverage: 88.86%
SL2.50 (Previous) Coverage: 99.04%	SL2.50 (Previous) Coverage: 99.07%
Percent Identity: 99.99%	Percent Identity: 99.97%

Comparison of the current and previous annotations

The annotation produced for this release (103) was compared to the annotation in the previous release (102) 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.

	SL3.0 (Current) to SL2.50 (Previous)
Identical	18%
Minor changes	69%
Major changes	6%
New	7%
Deprecated	5%
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
• 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