Long-read transcriptomic analysis of orb-weaving spider Araneus ventricosus indicates transcriptional diversity of spidroins

Zhou, Shi-Yi; Dong, Qinglin; Zhu, Kesen; Gao, Lei; Chen, Xin; Xiang, Hui

doi:10.1016/j.ijbiomac.2020.11.182

Cited by 6 publications

(3 citation statements)

References 37 publications

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“…The others have all relied upon long-read sequencing to some extent (Babb et al, 2017;Schwager et al, 2017;Garb et al, 2019;Kono et al, 2019;Adams et al, 2023;Wen et al, 2023). While long-read sequencing provide additional information that short reads do not, such as the details of nucleotide point mutations (Amarasinghe et al, 2020), there are many formidable challenges faced when applying long-read sequencing procedures to map whole genomes, particularly those associated with arachnid silk or venom proteins (Sańchez-Herrero et al, 2019;Amarasinghe et al, 2020;Fan et al, 2021;Sheffer et al, 2021;Zhou et al, 2021;Zhu et al, 2023). In arachnid silkomics or venomics the challenges are exacerbated by the extensive variation present in motif length, repeating patterns, and allele orders, particularly among silk and venom genes (Arakawa et al, 2002;Clarke et al, 2014;Haney et al, 2014;Rao et al, 2022).…”

Section: Interpreting the Functional Significance Of Unique Arachnid ...mentioning

confidence: 99%

Grand challenges in arachnid genetics and biomaterials

Blamires

2024

Front. Arachn. Sci.

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Section: Interpreting the Functional Significance Of Unique Arachnid ...mentioning

confidence: 99%

Grand challenges in arachnid genetics and biomaterials

Blamires

2024

Front. Arachn. Sci.

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“…Several recombinant studies have demonstrated that functional silk fibers, albeit with diminished mechanical properties, can be produced from the transgenic expression of constructs containing only the terminal and limited repetitive sequence from a single spidroin (Adrianos et al, 2013;Brooks et al, 2008;Heidebrecht et al, 2015;Saric et al, 2021;Xia et al, 2010;You et al, 2018). Second, recent advances in genomic technologies have made possible the discovery of complete silk gene sequences, which were previously inaccessible (Babb et al, 2017;Kono et al, 2019;Sheffer et al, 2021;Stellwagen and Burns, 2021;Stellwagen and Renberg, 2019;Zhou et al, 2021). Genomic comparisons coupled with our biomechanical tests will allow us to understand S1 and S2.…”

Section: Conditional Performance Of Structural Materialsmentioning

confidence: 99%

Connecting materials, performance and evolution: a case study of the glue of moth-catching spiders (Cyrtarachninae)

Díaz

Baker

Long

et al. 2022

Journal of Experimental Biology

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Morphological structures and extended phenotypes are made possible by materials that are encoded by the genome. Nearly all biomaterials are viscoelastic, which means that to understand performance, one must understand the strain rate-dependent properties of these materials in relevant ecological interactions, as the behavior of a material can vary dramatically and rapidly. Spider silks are an example of materials whose properties vary substantially intra- and inter-specifically. Here, we focus on aggregate silk, which functions as a biological adhesive. As a case study to understand how a material manifests from genome through organism to ecology, we highlight moth-specialist spiders, the Cyrtarachninae, and their glues as an ideal experimental system to investigate the relationship between genomics and ecologically variable performance of a biological material. There is a clear eco-evolutionary innovation that Cyrtarachne akirai and related species have evolved, a unique trait not found in other spiders, a glue which overcomes the scales of moths. By examining traditional orb-weavers, C. akirai and other subfamily members using biomechanical testing and genomic analysis, we argue that we can track the evolution of this novel bioadhesive and comment on the selection pressures influencing prey specialization. The importance of the ecological context of materials testing is exemplified by the poor performance of C. akirai glue on glass and the exceptional spreading ability and adhesive strength on moths. The genetic basis for these performance properties is experimentally tractable because spider silk genes are minimally pleiotropic and advances in genomic technologies now make possible the discovery of complete silk gene sequences.

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“…Marine nematodes [ 41 ], mussels [ 42 ], crabs [ 43 ], and marine fish [ 44 ] were selected as target organisms for marine environments. Soil nematodes [ 45 ], springtails [ 46 ], earthworms [ 47 ], and spiders [ 48 ] were selected as target organisms for soil environments. Neurotoxicity, reproductive toxicity, and developmental toxicity are highly complex and dependent on multiple molecular-signaling pathways.…”

Section: Introductionmentioning

confidence: 99%

Exploring the Potential Hormonal Effects of Tire Polymers (TPs) on Different Species Based on a Theoretical Computational Approach

Wang

Yang

et al. 2023

Polymers

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Tire polymers (TPs) are the most prevalent type of microplastics and are of great concern due to their potential environmental risks. This study aims to determine the toxicity of TPs with the help of molecular-dynamics simulations of their interactions with receptors and to highlight the differences in the toxicity characteristics of TPs in different environmental media (marine environment, freshwater environment, soil environment). For this purpose, five TPs—natural rubber, styrene–butadiene rubber (SBR), butadiene rubber, nitrile–butadiene rubber, and isobutylene–isoprene rubber—were analyzed. Molecular-dynamics calculations were conducted on their binding energies to neurotoxic, developmental, and reproductive receptors of various organisms to characterize the toxic effects of the five TPs. The organisms included freshwater species (freshwater nematodes, snails, shrimp, and freshwater fish), marine species (marine nematodes, mussels, crab, and marine fish), and soil species (soil nematodes, springtails, earthworms, and spiders). A multilevel empowerment method was used to determine the bio-toxicity of the TPs in various environmental media. A coupled-normalization method–principal-component analysis–factor-analysis weighting method—was used to calculate the weights of the TP toxicity (first level) categories. The results revealed that the TPs were the most biologically neurotoxic to three environmental media (20.79% and 10.57% higher compared with developmental and reproductive toxicity, respectively). Regarding the effects of TPs on organisms in various environmental media (second level), using a subjective empowerment approach, a gradual increase in toxicity was observed with increasing trophic levels due to the enrichment of TPs and the feeding behavior of organisms. TPs had the greatest influence in the freshwater-environment organisms according to the subjective empowerment approach employed to weight the three environmental media (third level). Therefore, using the minimum-value method coupled with the feature-aggregation method, the interval-deflation method coupled with the entropy-weighting method, and the standard-deviation normalization method, the three toxicity characteristics of SBR in three environmental media and four organisms were determined. SBR was found to have the greatest impact on the overall toxicity of the freshwater environment (12.38% and 9.33% higher than the marine and soil environments, respectively). The greatest contribution to neurotoxicity (26.01% and 15.95% higher than developmental and reproductive toxicity, respectively) and the greatest impact on snails and shrimp among organisms in the freshwater environment were observed. The causes of the heterogeneity of SBR’s toxicity were elucidated using amino-acid-residue analysis. SBR primarily interacted with toxic receptors through van der Waals, hydrophobic, π-π, and π-sigma interactions, and the more stable the binding, the more toxic the effect. The toxicity characteristics of TMPs to various organisms in different environments identified in this paper provide a theoretical basis for subsequent studies on the prevention and control of TMPs in the environment.

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Long-read transcriptomic analysis of orb-weaving spider Araneus ventricosus indicates transcriptional diversity of spidroins

Cited by 6 publications

References 37 publications

Grand challenges in arachnid genetics and biomaterials

Grand challenges in arachnid genetics and biomaterials

Connecting materials, performance and evolution: a case study of the glue of moth-catching spiders (Cyrtarachninae)

Exploring the Potential Hormonal Effects of Tire Polymers (TPs) on Different Species Based on a Theoretical Computational Approach

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