The genome sequence of the silver stretch spider, Tetragnatha montana (Simon, 1874) (Araneae: Tetragnathidae)
Alistair P. McGregor, Lauren Sumner-Rooney, Richard Burkmar, Anna Schoenauer, Feng Zhang, Katharina Hoff
TL;DR
This paper presents the genome sequence of the silver stretch spider, Tetragnatha montana, including a detailed assembly of its chromosomes and mitochondrial DNA.
Contribution
The paper provides the first genome assembly for Tetragnatha montana, including scaffolded chromosomal pseudomolecules and the mitochondrial genome.
Findings
The genome assembly spans 784.7 megabases and is scaffolded into 13 chromosomal pseudomolecules.
The mitochondrial genome is 15.49 kilobases in length and has been fully assembled.
Abstract
We present a genome assembly from an individual female Tetragnatha montana (the silver stretch spider; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 784.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Click any figure to enlarge with its caption.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5| Project accession data | ||
|---|---|---|
| Assembly identifier | qqTetMont2.1 | |
| Species |
| |
| Specimen | qqTetMont2 | |
| NCBI taxonomy ID | 500645 | |
| BioProject | PRJEB63621 | |
| BioSample ID | SAMEA7520006 | |
| Isolate information | qqTetMont2, female: cephalothorax (PacBio
| |
| Assembly metrics
|
| |
| Consensus quality (QV) | 62.0 |
|
|
| 100.0% |
|
| BUSCO
| C:97.6%[S:91.8%,D:5.8%],
|
|
| Percentage of assembly
| 99.3% |
|
| Sex chromosomes | XX |
|
| Organelles | Mitochondrial genome: 15.49 kb |
|
| Raw data accessions | ||
| PacificBiosciences Sequel IIe | ERR11641071 | |
| Hi-C Illumina | ERR11641146 | |
| Genome assembly | ||
| Assembly accession | GCA_963680715.1 | |
|
| GCA_963680735.1 | |
| Span (Mb) | 784.7 | |
| Number of contigs | 333 | |
| Contig N50 length (Mb) | 4.7 | |
| Number of scaffolds | 81 | |
| Scaffold N50 length (Mb) | 61.1 | |
| Longest scaffold (Mb) | 64.62 | |
| INSDC
| Chromosome | Length
| GC% |
|---|---|---|---|
| 1 | 64.62 | 33.5 | |
| 2 | 63.81 | 33.0 | |
| 3 | 62.49 | 33.0 | |
| 4 | 61.76 | 34.0 | |
| 5 | 61.61 | 34.5 | |
| 6 | 61.12 | 33.0 | |
| 7 | 60.37 | 33.0 | |
| 8 | 60.21 | 33.5 | |
| 9 | 59.94 | 33.5 | |
| 10 | 54.63 | 33.0 | |
| 11 | 52.55 | 34.0 | |
| MT | 0.02 | 25.5 | |
| X1 | 54.9 | 32.5 | |
| X2 | 61.27 | 33.0 |
| Software tool | Version | Source |
|---|---|---|
| BEDTools | 2.30.0 |
|
| Blast | 2.14.0 |
|
| BlobToolKit | 4.3.7 |
|
| BUSCO | 5.4.3 |
|
| BUSCO | 5.4.3 and 5.5.0 |
|
| bwa-mem2 | 2.2.1 |
|
| Cooler | 0.8.11 |
|
| DIAMOND | 2.1.8 |
|
| fasta_windows | 0.2.4 |
|
| FastK | 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c |
|
| GoaT CLI | 0.2.5 |
|
| Hifiasm | 0.19.5-r587 |
|
| HiGlass | 1.11.6 |
|
| HiGlass | 44086069ee7d4d3f6f3f0012569789ec138f42b84aa44357826c0b6753eb28de |
|
| MerquryFK | d00d98157618f4e8d1a9190026b19b471055b22e |
|
| MitoHiFi | 3 |
|
| MultiQC | 1.14, 1.17, and 1.18 |
|
| NCBI Datasets | 15.12.0 |
|
| Nextflow | 23.04.0-5857 |
|
| PretextView | 0.2 |
|
| purge_dups | 1.2.5 |
|
| samtools | 1.16.1, 1.17, and 1.18 |
|
| sanger-tol/genomenote | 1.1.1 |
|
| sanger-tol/readmapping | 1.2.1 |
|
| Seqtk | 1.3 |
|
| Singularity | 3.9.0 |
|
| TreeVal | 1.0.0 |
|
| YaHS | 1.2a.2 |
|
- —Wellcome Trust
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Taxonomy
TopicsGenomics and Phylogenetic Studies · Spider Taxonomy and Behavior Studies · RNA and protein synthesis mechanisms
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Chelicerata; Arachnida; Araneae; Araneomorphae; Entelegynae; Orbiculariae; Araneoidea; Tetragnathidae; Tetragnatha; Tetragnatha montana ( Simon, 1874) (NCBI:txid500645).
Background
The tetragnathid Tetragnatha montana, commonly known as the silver stretch spider, was first described by Eugène Simon in 1874 and first recorded in the UK in 1895 ( British Arachnological Society, 2024; Simon, 1874; World Spider Catalog, 2024).
T. montana is one of six species of Tetragnatha found in the UK; alongside T. extensa (common long-jawed orbweb spider), T. pinicola, T. obtusa, T. nigrita and T. striata (striped long-jawed orbweb spider) ( Bee et al., 2020). Tetragnathids, or long-jawed orbweb spiders, including T. montana, are characterised by their elongated chelicerae, legs, and bodies. T. montana is Palaearctic and is widespread in central and western Europe ( World Spider Catalogue, 2024). T. montana, together with T. extensa, are the most common and widely distributed tetragnathids in the UK, although T. montana has a wider range and is more numerous in the south than the north ( Bee et al., 2020; British Arachnological Society, 2024).
T. montana spins simple orb webs in grass and bushes, usually near open water, and can also be found on trees ( Bee et al., 2020; British Arachnological Society, 2024). Like other species of this genus, T. montana pose cryptically with their legs and bodies stretched out along grass, stems, or branches to hide when alarmed.
The T. montana genome was sequenced as part of the Darwin Tree of Life Project. This chromosomal-level assembly of the T. montana genome is from a female specimen (specimen ID SAMEA7520006) collected on 29/7/2019 from Wytham Woods near Oxford, UK. The T. montana genome will provide new insights into the biology of this spider, for example how sperm competition may have shaped the mating system of this and other Tetragnatha species (e.g. Yoward & Oxford, 2014). The genome of this tetragnathid will also provide a valuable comparison to the genomes of spiders in other families to help better understand spider and arachnid genome evolution (e.g. Aase-Remedios et al., 2023).
Genome sequence report
The genome was sequenced from a female Tetragnatha montana ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, –1.33). A total of 26-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 39 missing joins or mis-joins and removed 13 haplotypic duplications, reducing the assembly length by 0.83% and the scaffold number by 11.83%, and increasing the scaffold N50 by 0.76%.
Photograph of the Tetragnatha montana (qqTetMont2) specimen used for genome sequencing.
The final assembly has a total length of 784.7 Mb in 81 sequence scaffolds with a scaffold N50 of 61.1 Mb ( Table 1). The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3. The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla. Most (99.3%) of the assembly sequence was assigned to 13 chromosomal-level scaffolds, representing 11 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). Chromosomes X 1 and X 2 were assigned by synteny to Metellina segmentata (GCA_947359465.1) ( Henriques et al., 2023). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Table 1.: Genome data for Tetragnatha montana, qqTetMont2.1.
Genome assembly of Tetragnatha montana, qqTetMont2.1: metrics.The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 784,702,176 bp assembly. The distribution of sequence lengths is shown in dark grey with the plot radius scaled to the longest sequence present in the assembly (64,617,543 bp, shown in red). . Orange and pale-orange arcs show the N50 and N90 sequence lengths (61,119,082 and 54,634,059 bp), respectively. The pale grey spiral shows the cumulative sequence count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the arachnida_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Tetragnatha_montana/dataset/GCA_963680715.1/snail.
Genome assembly of Tetragnatha montana, qqTetMont2.1: BlobToolKit GC-coverage plot.Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Tetragnatha_montana/dataset/GCA_963680715.1/blob.
Genome assembly of Tetragnatha montana, qqTetMont2.1: BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Tetragnatha_montana/dataset/GCA_963680715.1/cumulative.
Genome assembly of Tetragnatha montana, qqTetMont2.1: Hi-C contact map of the qqTetMont2.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=FrlNoy89SoiJhaaO37ENNw.
Table 2.: Chromosomal pseudomolecules in the genome assembly of Tetragnatha montana, qqTetMont2.
The estimated Quality Value (QV) of the final assembly is 62.0 with k-mer completeness of 100.0%, and the assembly has a BUSCO v completeness of 97.6% (single = 91.8%, duplicated = 5.8%), using the arachnida_odb10 reference set ( n = 2,934).
Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/500645.
Methods
Sample acquisition and nucleic acid extraction
A female Tetragnatha montana (specimen ID Ox000088, ToLID qqTetMont2) was collected from Wytham Great Wood, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude –1.33) on 2019-07-29 by netting. The specimen was collected and identified by Alistair McGregor, Lauren Sumner-Rooney, Richard Burkmar and Anna Schoenauer (Oxford Brookes University). After identification and imaging at Oxford Brookes University, the spider was barcoded and flash-frozen in liquid nitrogen at the University of Oxford.
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. The sample was prepared for DNA extraction at the WSI Tree of life Core Laboratory: the qqTetMont2 sample was weighed and dissected on dry ice ( Jay et al., 2023). Tissue from the cephalothorax was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a).
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol ( Oatley et al., 2023). The DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences Sequel IIe instrument. Hi-C data were also generated from remaining cephalothorax tissue of qqTetMont2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
Genome assembly and curation
Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and PretextView ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Final assembly evaluation
The final assembly was post-processed and evaluated with the three Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a), “sanger-tol/genomenote” ( Surana et al., 2023b), and “sanger-tol/blobtoolkit” ( Muffato et al., 2024). The pipeline sanger-tol/readmapping aligns the Hi-C reads with bwa-mem2 ( Vasimuddin et al., 2019) and combines the alignment files with SAMtools ( Danecek et al., 2021). The sanger-tol/genomenote pipeline transforms the Hi-C alignments into a contact map with BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020), which is then visualised with HiGlass ( Kerpedjiev et al., 2018). It also provides statistics about the assembly with the NCBI datasets ( Sayers et al., 2024) report, computes k-mer completeness and QV consensus quality values with FastK and MerquryFK, and a completeness assessment with BUSCO ( Manni et al., 2021).
The sanger-tol/blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads with SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database ( Bateman et al., 2023) with DIAMOND ( Buchfink et al., 2021) blastp. The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx. Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). All those outputs are combined with the blobtools suite into a blobdir for visualisation.
All three pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.
Table 3 contains a list of relevant software tool versions and sources.
Wellcome Sanger Institute – Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the ‘Darwin Tree of Life Project Sampling Code of Practice’, which can be found in full on the Darwin Tree of Life website here. By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are:
• Ethical review of provenance and sourcing of the material
• Legality of collection, transfer and use (national and international)
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
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