Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position

Abstract

The spider of Ectatosticta davidi, belonging to the lamp-shade web spider family, Hypochilidae, which is closely related to Hypochilidae and Filistatidae and recovered as sister of the rest Araneomorphs spiders. Here we show the final assembled genome of E. davidi with 2.16 Gb in 15 chromosomes. Then we confirm the evolutionary position of Hypochilidae. Moreover, we find that the GMC gene family exhibit high conservation throughout the evolution of true spiders. We also find that the MaSp genes of E. davidi may represent an early stage of MaSp and MiSp genes in other true spiders, while CrSp shares a common origin with AgSp and PySp but differ from MaSp. Altogether, this study contributes to addressing the limited availability of genomic sequences from Hypochilidae spiders, and provides a valuable resource for investigating the genomic evolution of spiders.

Fig. 1. The genome fetures of Ectatosticta davidi .

a The Hi-C assisted assembly of E. davidi. b Distribution of chromosomal elements of E. davidi. The inner ring contains a picture of E. davidi. The outer rings of the circle represent means bellow, respectively: Chr chromosomes, Gene distribution of genes, GC GC content, SINE short interspersed nuclear element, LINE long interspersed nuclear elements, LTR long terminal repeat, DNA DNA transposable elements. c–e Synteny analysis between E. davidi, T. antipodiana, and L. elegans. Red lines between the two species was as the sample of the interchromosomal rearrangements.

Fig. 2. Phylogenetic and expansion gene family analyses of E. davidi.

Phylogenetic relationship between E. davidi and other representative Arachnida species. The divergence times among different species are shown at the bottom. Node values indicate gene families showing expansion (blue), contraction (red), and rapid evolution (black in brackets).

Fig. 3. GMC gene family analysis in E. davidi.

a Phylogenetic tree of GMC gene family in E. davidi and other representative Arachnida species. Ag (A. gambiae), Am (A. mellifera), Anig (A. niger), Aory (A. oryzae), Cele (C. elegans), Dm (D. melanogaster), Ecol (E. coli), Pama (P. amagasakiense), Tc (T. castaneum). Red star represents E. davidi. b Phylogenetic tree of GMC gene family in E. davidi and other representative spider species. The species include A. bruennichi, C. darwini, C. extrusa, N. pilipes, P. tepidariorum, S. dumicolals, S. mimosarum, T. antipodiana, and T. clavipes. The outgroup species is Scorpiones C. sculpturatus.

Fig. 4. Phylogenetic analysis of IR/iGluR and P450 gene families in E. davidi.

a Phylogenetic tree of IR/iGluR gene family in E. davidi and D. melanogaster. b Phylogenetic tree of P450 gene family in E. davidi and D. melanogaster.

Fig. 5. Spider silk gene analysis in E. davidi.

a Phylogenetic analysis of spider silk gene in E. davidi. The N-terminal domains of silk genes in the species (such as E. davidi, T. antipodiana, P. tepidariorum, and L. elegans) were used for Maximum-likelihood (ML) phylogenetic tree. b Repeat regions of spider silk genes in E. davidi. c The spidroin N-terminal domains of the E. davidi gene Ectatosticta_davidi_00014990 bear close resemblance to CrSp sequence of some Mesothelae species including Liphistiidae (H. kimurai, H. yanbaruensis, R. nishihirai), Eresidae (Stegodyphus sp.), and Uloboridae (O. sybotides).

Fig. 6. Phylogenetic analysis and protein domain structure of toxin gene families in E. davidi, H. graminicola, and T. antipodiana.

a Phylogenetic analysis and protein domain structure of ACE toxin gene family. b Phylogenetic analysis and protein domain structure of AK toxin gene family. c Phylogenetic analysis and protein domain structure of ALL7 toxin gene family. d Phylogenetic analysis and protein domain structure of SMase-4 toxin gene family. e Phylogenetic analysis and protein domain structure of CRISPs toxin gene family. Red star represent the toxin genes of E. davidi. Green circle represent the toxin genes of H. graminicola. Blue triangle represent the toxin genes of T. antipodiana. The pink, yellow, purple, sky blue, green and red rectangle respectively represent the Angiotensin-converting enzyme domain, Flavin containing amine oxidopinkuctase domain, Group 7 allergen domain, Cysteine-rich secretory protein domain, ATP:guanido phosphotransferase domain, Glycerophosphoryl diester phosphodiesterase domain.