Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae) - PubMed (original) (raw)

. 2023 Jun 22;114(4):395-403.

doi: 10.1093/jhered/esad013.

Seira A Adams 1 2 3, Anna J Holmquist 1, Monica M Sheffer 4 5, Emma C Steigerwald 1 6, Ruta Sahasrabudhe 7, Oanh Nguyen 7, Eric Beraut 8, Colin Fairbairn 8, Samuel Sacco 8, William Seligmann 8, Merly Escalona 9, H Bradley Shaffer 10 11, Erin Toffelmier 10 11, Rosemary G Gillespie 1

Affiliations

Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae)

Seira A Adams et al. J Hered. 2023.

Abstract

Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.

Keywords: CCGP; California Conservation Genomics Project; arachnid; spider genome.

© The American Genetic Association. 2023.

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Figures

Fig. 1.

Fig. 1.

A) Ventral view of a Tetragnatha versicolor spider on a web over water. B) A dorsal view of a T. versicolor female. C) A representative riparian habitat of T. versicolor in Tehama County, California.

Fig. 2.

Fig. 2.

Visual overview of Tetragnatha versicolor genome assembly metrics. A) K-mer spectrum output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome and the k-mer profile matches that of high heterozygosity. K-mers at lower coverage and high frequency correspond to differences between haplotypes, whereas the higher coverage and low frequency k-mers correspond to the similarities between haplotypes. B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the T. versicolor primary assembly (qqTetVers1.0.p). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly; the dark vs. light blue area around it shows mean, maximum and minimum GC vs AT content at 0.1% intervals (Challis et al. 2020). C and D) HiC Contact maps for the primary (2C) and alternate (2D) genome assembly generated with PretextSnapshot. Hi-C contact maps translate proximity of genomic regions in 3-D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between 2 of such regions. Scaffolds are separated by black lines and higher density of the lines may correspond to higher levels of fragmentation.

References

    1. Abdennur N, Mirny LA.. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. doi: 10.1093/bioinformatics/btz540 -DOI -PMC -PubMed
    1. Adams, SA. Chemical cues in species recognition and reproductive isolation of Tetragnatha spiders (Araneae: Tetragnathidae) [Doctoral dissertation]. UC Berkeley; 2022.
    1. Akamatsu F, Toda H, Okino T.. Food source of riparian spiders analyzed by using stable isotope ratios. Ecol Res. 2004;19(6):655–662.
    1. Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F.. MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. doi: 10.1111/1755-0998.13160 -DOI -PMC -PubMed
    1. Barrion AT, Litsinger JA.. The spider fauna of Philippine rice agroecosystems. II. Wetland. Philipp Entomol. 1984;6(1):11–37.

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