A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

GigaScience, Journal Year: 2021, Volume and Issue: 10(3)

Published: March 1, 2021

Abstract Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred spiders, lack of a high-quality genome limited characterization this event. Results We present chromosome-level T. constructed basis PacBio Hi-C sequencing. assembled is 2.29 Gb size scaffold N50 172.89 Mb. scaffolding assigned 98.5% bases 13 pseudo-chromosomes, BUSCO completeness analysis revealed assembly included 94.8% complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% genome. predicted 19,001 protein-coding genes, which 96.78% were supported by transcriptome-based evidence 96.32% matched protein records UniProt database. also shows substantial expansions several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, ATP-binding cassette transporters, reflecting possible genomic polyphagy. Further architecture reveals event, based 2 lines evidence: (i) large-scale duplications inter-chromosome synteny (ii) duplicated clusters Hox genes. Conclusions represents valuable resource research provides insights into species’ adaptation environment.

Language: Английский

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Chromosome-level genome of spider Pardosa pseudoannulata and cuticle protein genes in environmental stresses

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Jan. 24, 2024

Abstract Spiders are representative arthropods of adaptive radiation. The high-quality genomes have only been reported in several web weaver spider species, leaving the wandering spiders’ genomic information scarce. pond wolf spider, Pardosa pseudoannulata , is a species retrolateral titial apophysis (RTA) clade. We present chromosome-level P. pseusoannulata genome assembly 2.42 Gb size with scaffold N50 169.99 Mb. Hi-C scaffolding assigns 94.83% bases to 15 pseudo-chromosomes. repeats account for 52.79% assembly. includes 96.2% complete arthropod universal single-copy orthologs. Gene annotation predicted 24,530 protein-coding genes BUSCO score 95.8% complete. identified duplicate clusters Hox and an expanded cuticle protein gene family 243 genes. expression patterns CPR change response environmental stresses such as coldness insecticide exposure. provides valuable functional comparative studies spiders.

Language: Английский

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A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 15, 2023

Abstract The process of natural silk production in the spider major ampullate (Ma) gland endows dragline with extraordinary mechanical properties and potential for biomimetic applications. However, precise genetic roles Ma during this remain unknown. Here, we performed a systematic molecular atlas through high-quality genome assembly golden orb-weaving Trichonephila clavata multiomics approach to defining tri-sectional architecture: Tail, Sac, Duct. We uncovered hierarchical biosynthesis spidroins, organic acids, lipids, chitin sectionalized dedicated fine constitution. ordered secretion spidroins was achieved by synergetic regulation epigenetic ceRNA signatures genomic group-distributed spidroin genes. Single-cellular spatial RNA profiling identified ten cell types partitioned functional division determining organization gland. Convergence analysis manipulation further validated that architecture analogous across Arthropoda inextricably linked formation. Collectively, our study provides multidimensional data significantly expand knowledge generation ultimately benefit innovation spider-inspired fibers.

Language: Английский

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Disentangling the riddle of systemic lupus erythematosus with antiphospholipid syndrome: blood transcriptome analysis reveals a less-pronounced IFN-signature and distinct molecular profiles in venous versus arterial events

Annals of the Rheumatic Diseases, Journal Year: 2024, Volume and Issue: unknown, P. ard - 225664

Published: April 12, 2024

Systemic lupus erythematosus with antiphospholipid syndrome (SLE-APS) represents a challenging SLE endotype whose molecular basis remains unknown.

Language: Английский

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Molecular Phylogenetic Relationships Based on Mitogenomes of Spider: Insights Into Evolution and Adaptation to Extreme Environments

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT In this study, we performed a comparative analysis based on total of 255 spider mitogenomes and four outgroups, which the 39 species were assembled de novo, to explore phylogenetic relationships adaptive evolution mitogenomes. Results showed that Argyroneta aquatica had longest mitochondrial length most pronounced codon preference be UUA, followed by CCU. Codon usage frequencies similar between families in mitogenome spiders was mainly influenced natural selection pressures rather than G/C mutation bias. Our topology clearly explained evolutionary among spiders, divergence time estimates indicated originated early Devonian, two clades Mesothelae Opisthothelae separated late Carboniferous. Ancestral range trait reconstruction results supported ancestral origin Devonian Nearctic realm, with trapdoor being original trait. Selection detected positive signals ATP8 gene Desis jiaxiangi . The ND5 is convergent D. A. Positive sites may facilitate metabolic adaptation aquatic environment spiders. conclusion, our contributes better understanding taxonomic status, diversity, characteristics, environmental adaptations these

Language: Английский

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The Genome of Chenopodium ficifolium: Developing Genetic Resources and a Diploid Model System for Allotetraploid Quinoa

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

Abstract High-quality nuclear, chloroplast, and preliminary mitochondrial genomes have been assembled annotated for the B-genome diploid (BB: 2n = 2x 18) figleaf goosefoot ( Chenopodium ficifolium ). The primary objective was to advance a simplified model system genetic characterization improvement of allotetraploid (AABB: 4x 36) quinoa ), nutritionally valuable, halophytic orphan crop. In addition its diploidy favorably small genome size, C. provides shorter generational period smaller overall plant size as compared , while displaying relevant agronomic trait variations amenable gene-trait association studies. ‘Portsmouth’ nuclear sequenced using PacBio HiFi Long Read technology Hifiasm. After manual adjustments, final ChenoFicP_1.0 assembly consisted nine pseudochromosomes spanning 711.5 Mbp, 22,617 genes were identified annotated. BUSCO analyses indicated completeness 97.5%, proteome transcriptome 98.4 percent. chloroplast detected two equally represented structural haplotypes differing in orientation Short Single Copy region relative region. Phylogenetic parentage pointed an unspecified AA species away from likely maternal donor(s) during initial tetraploidization event lineage. Using new reference genome, GWAS performed on previously studied F2 population further define region(s) implicated control three key traits: days flowering, height, branch number. This analysis localized all traits 7 Mb interval pseudochromosome Cf4. contains approximately 770 genes, including FTL1 locus, thus confirming extending our prior, single-marker showing these with amplicon length polymorphism. use data develop genetics breeding serves expand knowledge germplasm resources improvement.

Language: Английский

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Darwin's bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression

Open Biology, Journal Year: 2021, Volume and Issue: 11(12)

Published: Dec. 1, 2021

Spider silk is a protein-based material whose toughness suggests possible novel applications. A particularly fascinating example of provided by Darwin's bark spider ( Caerostris darwini ) found in Madagascar. This produces extraordinarily tough silk, with an average 350 MJ m −1 and over 50% extensibility, can build river-bridging webs size 2.8 2 . Recent studies have suggested that specific spidroins expressed C. are responsible for the mechanical properties its silk. Therefore, more comprehensive investigation spidroin sequences, thread protein contents phylogenetic conservation among closely related species required. Here, we conducted genomic, transcriptomic proteomic analyses close relative extrusa variety low-molecular-weight proteins were dragline these species; all genes encoding conserved both genomes, but their The potential to produce very common genus , our results may suggest existence plasticity allowing be changed optimizing gene expression response environment.

Language: Английский

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Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(12)

Published: Nov. 3, 2023

Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes undergo subfunctionalization partition ancestral functions and/or neofunctionalization assume a function. We previously found there had been whole genome (WGD) in an ancestor arachnopulmonates, lineage including spiders scorpions but excluding other arachnids like mites, ticks, harvestmen. This WGD was evidenced by many duplicated homeobox genes, two Hox clusters, spiders. However, it unclear which paralogues originated versus smaller-scale events such as tandem duplications. Understanding this is key determining contribution arachnopulmonate evolution. Here we characterized distribution across eight chromosome-level spider genomes. most are consistent with origin WGD. also copies conserved Hox, NK, HRO, Irx, SINE all species. Consistently, observed one copy each cluster degenerated terms content organization while remained more intact. Focussing on NK cluster, evidence for between Parasteatoda tepidariorum compared their single-copy orthologues harvestman Phalangium opilio. Our study provides insights into relative contributions multiple modes repertoire during function genes.

Language: Английский

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Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates

G3 Genes Genomes Genetics, Journal Year: 2021, Volume and Issue: 11(12)

Published: Sept. 6, 2021

Abstract Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components microRNAs are frequently retained duplicates (so-called ohnologs) following WGD. not only provide the best evidence for WGD, but an opportunity study its evolutionary consequences. Although these well studied context vertebrate similar comparisons across extant arachnopulmonate orders patchy. We sequenced embryonic transcriptomes from two spider species amblypygid surveyed three important families, Hox, Wnt, frizzled, 12 existing transcriptomic genomic resources chelicerates. report retention putative ohnologs, further supporting ancestral also found consistent trajectories Hox Wnt repertoires six orders, with interorder variation specific paralogs. identified between major clades spiders better able reconstruct chronology losses spiders, amblypygids, scorpions. insights shed light on evolution toolkit arachnopulmonates, highlight importance comparative approach within lineages, substantial data future study.

Language: Английский

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Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(6), P. 2333 - 2348

Published: Feb. 19, 2022

Spiders are the most abundant venomous predators in world. Previous research related to spider venom has mostly relied on transcriptomes and proteomes, with only a few high-quality genomes available. This is far from consistent species diversity of spiders. In this study, we constructed chromosome-level genome assembly Hylyphantes graminicola, which contained 13 chromosomes, length 931.68 Mb scaffold N50 77.07 Mb. Integrating genome, transcriptome, proteome profiling, identified total 59 coding genes among nine toxin gene families. Among them, Group 7 allergen (ALL7) protein was reported for first time. Its had predicted signal peptide maintained high expression levels venom, suggesting that ALL7 plays an important role maybe type newly discovered spider. By implementing comparative genomics, found similar number main families spiders scorpion conservative evolutionary rates, indicating these could be ancient (~400 million years) conserved "basic toolkit" scorpions perform primary defence functions. Obtaining not facilitates resource application, but also can improve genomic analysis other traits, like evolution silk or behaviour.

Language: Английский

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