Data from: Reference genome of the Californian trapdoor spider Aptostichus stephencolberti Bond 2008 (Araneae: Mygalomorphae: Euctenizidae)
Data files
Jul 02, 2026 version files 5.83 GB
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As_combined_library.fasta
8.86 MB
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As_divergence_summary_table.tsv
759.66 KB
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As.familyLevelCount.txt
390.40 KB
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As.filteredRepeats.bed
435.51 MB
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As.filteredRepeats.gff
1.32 GB
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As.highLevelCount.txt
1.24 KB
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qqAptStep1.0.pri_annotated_ref_complete.cds.fna
34.17 MB
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qqAptStep1.0.pri_annotated_ref_complete.genomic.fna
3.69 GB
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qqAptStep1.0.pri_annotated_ref_complete.genomic.gff
116.49 MB
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qqAptStep1.0.pri_annotated_ref_complete.genomic.gtf
168.88 MB
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qqAptStep1.0.pri_annotated_ref_complete.proteins.faa
10.50 MB
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qqAptStep1.0.pri_annotated_ref_complete.transcripts.fna
46.13 MB
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qqAptStep1.0.pri_annotated_ref_sra_metadata.dat
672 B
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README.md
9.51 KB
Abstract
We present a reference genome annotation for the trapdoor spider Aptostichus stephencolberti. This species, described in 2008, is endemic to the highly fragmented coastal dune habitats of Northern California from Monterey to the San Francisco Bay Area. Trapdoor spiders are ideal taxa for landscape-scale genomic studies owing to their extreme site fidelity and limited dispersal capabilities; these same characteristics make them prone to extinction. Dune habitats along California's coast are a diverse yet fragile ecosystem, sensitive to shoreline development, rising sea levels, and invasive species. Genomic studies of species like A. stephencolberti can reveal novel areas of endemism and high conservation value that may not be evident in species with wider ranges and greater dispersal capabilities. As part of the California Conservation Genomics Project, we constructed the A. stephencolberti reference genome from high-quality long-read sequences, scaffolded with proximity ligation Omni-C data. This dataset is the resultant genome-automated annotation generated using the NCBI refseq pipeline and RNA-seq data from whole adults. It comprises 14,067 genes with a BUSCO annotation completeness of 95.56%. This resource, the first for the family Euctenizidae, will facilitate future study and resulting conservation actions of A. stephencolberti and other Aptostichus sp. populations associated with the rapidly changing California coastal dune ecosystem.
Dataset DOI: 10.5061/dryad.9s4mw6mxk
Description of the data and file structure
This is an annotation of a reference genome assembly for the trapdoor spider Aptostichus stephencolberti, that was collected as part of the California Conservation Genomics Project.
Files and variables
File: qqAptStep1.0.pri_annotated_ref_sra_metadata.dat
Description: SRA metadata (NCBI SRA accessions, read counts, lengths, etc) for A. stephencolberti RNAseq data aligned to the reference genome and used to support the. annotation.
File: qqAptStep1.0.pri_annotated_ref_complete.genomic.fna
Description: The reference genome fasta file that was actually annotated, included here for reference in case new versions of the genome reference supersede this one in the future.
File: qqAptStep1.0.pri_annotated_ref_complete.transcripts.fna
Description: Output nucleotide transcripts from the NCBI Eukaryotic Genome Annotation Pipeline v0.4.1-alpha annotation pipeline.
File: qqAptStep1.0.pri_annotated_ref_complete.genomic.gtf
Description: output gtf annotation file from the NCBI Eukaryotic Genome Annotation Pipeline.
gtf format: similar to the gff3 format below the columns for gtf format are:
- seqname - name of the chromosome or scaffold;
- source - name of the program that generated this feature, or the data source (database or project name)
- feature - feature type name, e.g. Gene, Variation, Similarity
- start - Start position* of the feature, with sequence numbering starting at 1.
- end - End position* of the feature, with sequence numbering starting at 1.
- score - A floating point value.
- strand - defined as + (forward) or - (reverse).
- frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
- attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.
File: qqAptStep1.0.pri_annotated_ref_complete.genomic.gff
Description: output off annotation file from the NCBI Eukaryotic Genome Annotation Pipeline.
GFF column information: - This is a NCBI gff3 format, the full specification can be found here: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/file-formats/annotation-files/about-ncbi-gff3/ briefly:
Column 1: “seqid” Accession.version. In this case the NCBI scaffold identifier. Column 2: “source” For annotations produced by one of NCBI’s pipelines, the method used to generate the annotation is provided in column 2. For example: Gnomon. Column 3: “type” The SOFA feature type most equivalent to the feature found in the source annotation. The original GenBank feature type is also provided by the “gbkey” attribute in column 9. For example: gene, mRNA, exon, CDS, intron. Columns 4 & 5: “start” and “end” Start and end coordinates of the feature in 1-based coordinates. Column 6: “score” Currently only provided for alignments, if they contain a score named “score”. The definition of this score may vary depending on the type of alignment. Column 7: “strand” The strand of the feature (+ or -). Column 8: “phase” The phase of the CDS feature, which is related to /codon_start in the flatfile specification. Column 9: “attributes” A semicolon delimited list of official and additional attributes describing the feature.
Note that the header of the file has the sequence scaffold names.
File: qqAptStep1.0.pri_annotated_ref_complete.proteins.faa
Description: output protein amino acid sequences from the NCBI Eukaryotic Genome Annotation Pipeline in fasta format.
File: qqAptStep1.0.pri_annotated_ref_complete.cds.fna
Description: output coding nucleotide sequences from the NCBI Eukaryotic Genome Annotation Pipeline in fasta format.
Genome Annotation Metrics
| Feature type | Genes | mRNAs | lncRNAs | CDS | |
|---|---|---|---|---|---|
| Feature count | 14,067 | 15,972 | 768 | 15,972 | |
| BUSCO completeness | C | S | D | F | M |
| (Arachnida_odb10) n=2768 | 95.56% | 91.78% | 3.78% | 0.54% | 3.90% |
A note on file starting "As_" All these files were generated with EarlGrey - a Transposable element annotation pipeline that was ran on the A. stephencolberti reference genome (primary allele). The citation for earlGrey is (Baril T, Galbraith J, Hayward A (2024). Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline (I Arkhipova, Ed.). Molecular Biology and Evolution 41: msae068. and it can be found on GitHub here: https://github.com/TobyBaril/EarlGrey
File: As_combined_library.fasta
Description: These are the repeat sequences the earlGrey TE pipeline found in the A. stephencolberti reference genome primary allele sequence. They are in a standard fasta format.
File: As_divergence_summary_table.tsv
Description: Earl grey summary table showing the divergences between different copies of Transposable element repeats found in A. stephencolberti. This is a tab-delimited file with 12 columns: 1. subclass, 2. superfamily, 3. family, 4. total_bp, 5. mean_width, 6. min_width, 7. max_width, 8. sd_width, 9. mean_div, 10. min_div, 11. max_div, 12. sd_div where div is sequence divergence calculated by the earlGrey repeat annotation pipeline.
File: As.familyLevelCount.txt
Description: Genome coverage and repeat count for the different TE families found in the A. stephencolberti reference genome. A tab-delimited text file with 3 columns: 1. TE Family, 2. Coverage (bp), 3. Copy Number
File: As.filteredRepeats.bed
Description: A standard bed file format for the location of the repeats found by ear grey in A. stephencolberti. Only the first 6 columns are used: 1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671). 2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0. 3. chromEnd - The ending position of the feature in the chromosome or scaffold. 4. name - here an example is DNA/TcMar-Tc1 5. the repeat family number - i.e. the line JBNQXO010000001.1 6111011 6114817 DNA/TcMar-Tc1 4010 + in the bed file refers to the sequence >rnd-4_family-4010#DNA/TcMar-Tc1 in the As_combined_library.fasta file , 6. strand - Defines the strand. Either "." (=no strand) or "+" or "-".
File: As.filteredRepeats.gff
Description: A standard gff3 format text file with the locations of Transposable elements found by earlgrey in A. stephencolberti. Columns are in the same format as described above for qqAptStep1.0.pri_annotated_ref_complete.genomic.gff. Similar to the bed file above, the first line of the gif: JBNQXO010000001.1 Earl_Grey DNA/TcMar-Tc1 1 4170 35332 + . ID=RND-5_FAMILY-4331_1;Name=RND-5_FAMILY-4331;tstart=4902;tend=9139 also refers to the sequence >rnd-5_family-4331#DNA/TcMar-Tc1 in As_combined_library.fasta
File: As.highLevelCount.txt
Description: High-level count of the copy number and number of bases for broad types of TEs found by earlGrey in the A. stephencolberti reference. There are 6 columns of this tab-delimited file: 1. TE Classification 2. Coverage (bp) 3. Copy Number 4. % Genome Coverage 5. Genome Size 6. TE Family Count
Code/software
We annotated the reference assembly for each species using the NCBI Eukaryotic Genome Annotation Pipeline v0.4.1-alpha (hereafter, “EGAPx”), which is published in the NCBI RefSeq database (O’Leary et al., 2016) and accessible through the NCBI GitHub page (“ncbi/egapx”). Annotation features were identified by aligning transcripts and proteins from related taxa in the RefSeq database using BLAST (Camacho et al., 2009). Novel, species-specific RNA-Seq reads generated from two whole adults were also aligned to the assembly using the alignment software STAR (Dobin et al., 2013). Additional features are predicted using HMM-based gene models using the NCBI Gnomon software. We evaluated the quality and completeness of our annotation by comparing the longest protein for each annotated coding gene to Arachnida (odb10) using BUSCO v5.7.1 (Manni et al., 2021).
Access information
Other publicly accessible locations of the data:
- For the reference genome and raw reads: NCBI BioProject PRJNA1013550
Data was derived from the following sources:
- The reference genome sequence that this genome annotation is derived from was also deposited into the NCBI BioProject PRJNA1013550; additionally, transcriptome data was generated from NCBI BioSamples SAMN41406138-9 and has SRA accessions SRS21376458-9.
We annotated the reference assembly for each species using the NCBI Eukaryotic Genome Annotation Pipeline v0.4.1-alpha (hereafter, “EGAPx”), which is published in the NCBI RefSeq database (O’Leary et al., 2016) and accessible through the NCBI GitHub page (“ncbi/egapx”). Annotation features were identified by aligning transcripts and proteins from related taxa in the RefSeq database using BLAST (Camacho et al., 2009). Novel, species-specific RNA-Seq reads generated from two whole adults were also aligned to the assembly using the alignment software STAR (Dobin et al., 2013). Additional features are predicted using HMM-based gene models using the NCBI Gnomon software. We evaluated the quality and completeness of our annotation by comparing the longest protein for each annotated coding gene to Arachnida (odb10) using BUSCO v5.7.1 (Manni et al., 2021).