The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Schwager, Evelyn E.; Sharma, Prashant P.; Clarke, Thomas H.; Leite, Daniel J.; Wierschin, Torsten; Pechmann, Matthias; Akiyama-Oda, Yasuko; Esposito, Lauren A.; Bechsgaard, Jesper; Bilde, Trine; Buffry, Alexandra D.; Chao, Hsu; Dinh, Huyen; Doddapaneni, Harshavardhan; Dugan, Shannon; Eibner, Cornelius; Extavour, Cassandra G.; Funch, Peter; Garb, Jessica E.; Gonzalez, Luis Baudouin; González, Vanessa L.; Griffiths-Jones, Sam; Han, Yi; Hayashi, Cheryl Y.; Hilbrant, Maarten; Hughes, Daniel; Janßen, Ralf; Lee, Sandra L.; Maeso, Ignacio; Murali, Shwetha C.; Fonseca, Rodrigo Nunes da; Paese, Christian Louis Bonatto; Qu, Jiaxin; Ronshaugen, Matthew; Schomburg, Christoph; Schoenauer, Anna; Stollewerk, Angelika; Torres-Oliva, Montserrat; Turetzek, Natascha; Vanthournout, Bram; Werren, John H.; Wolff, Carsten; Worley, Kim C.; Bucher, Gregor; Gibbs, Richard A.; Coddington, Jonathan A.; Oda, Hiroki; Stanke, Mario; Ayoub, Nadia A.; Prpic, Nikola‐Michael; Flot, Jean‐François; Posnien, Nico; Richards, Stephen; McGregor, Alistair P.

doi:10.1101/106385

Cited by 10 publications

(14 citation statements)

References 130 publications

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“…This is an indication that recent gene duplication and loss is very low in this group, and that our results are not compromised by the deep arachnid whole-genome duplication (Schwager et al 2017). It also indicates that the individuals whose DNA was pooled for each species were quite similar (the assembler interpreted any differences at the level of allelic differences).…”

Section: Methodsmentioning

confidence: 48%

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

Maddison¹,

Evans²,

Hamilton³

et al. 2017

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We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, Onomastus (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.

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Section: Methodsmentioning

confidence: 48%

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

Maddison¹,

Evans²,

Hamilton³

et al. 2017

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“…Moreover, the distributions of these two hox clusters in T. tridentatus are very similar with its closely species, such as spider ( Parasteatoda tepidariorum ) and scorpion ( Centruroides sculpturatus ). These results indicated that hox clusters are very conservative in evolution and thus we have assembled a highly integrated genome (Figure c; Schwager et al., ). The results could further contribute to the study of specific body plan in T. tridentatus .…”

Section: Resultsmentioning

confidence: 83%

Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

Gong

Fan

Ren

et al. 2019

Molecular Ecology Resources

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Horseshoe crabs including Tachypleus tridentatus are a group of marine arthropods and living fossil species which have existed on the earth for ~500 million years. However, the genetic mechanisms underlying their unique adaptive ability are still unclear. Here, we assembled the first chromosome‐level T. tridentatus genome, and proved that this genome is of high quality with contig N50 1.69 Mb. By comparison with other arthropods, some gene families of T. tridentatus experienced significant expansion, which are related to several signaling pathways, endonuclease activities, and metabolic processes. Based on the results of comparative analysis of genomics and 27 transcriptomes from nine tissues, we found that the expanded Dscam genes are located at key hub positions of immune network. Furthermore, the Dscam genes showed higher levels of expression in the yellow connective tissue (the birthplace of blood cells with strong differentiation capability) than the other eight tissues. Besides, the Dscam genes are positively correlated with the expression of the core immunity gene, clotting factor B, which is involved in the coagulation cascade reaction. The effective and unusual immune ability endowed by the expansion and expression of Dscam genes in the horseshoe crab may be a factor that makes the species have a strong environmental adaptability within ~500 million years. The high quality chromosome level genome of a horseshoe crab and unique genomic features reported in this study provide important data resources for future studies on the evolution of marine ecological systems.

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“…Whereas tsh represses expression of the gnathal Hox genes labial ( lab ) and Sex combs reduced ( Scr ) in the trunk D. melanogaster , tio/tsh expression of both arachnids encompasses the expression domains of their lab , Deformed ( Dfd ), and Scr orthologs (Röder et al, ; Khadjeh et al, ; Sharma et al, ). In addition, whereas trunk Hox genes like Antp and Ubx maintain tsh expression in the posterior compartment of specific D. melanogaster trunk segments, homologs of neither of these genes are expressed in the prosoma of arachnids during stages corresponding to leg fate specification (Khadjeh et al, ; Schwager et al, ; Sharma et al, ; Sharma, Schwager, Extavour, & Wheeler, ). Furthermore, the limited data available on Hox gene function in arachnids (e.g., lab‐ 1, Dfd‐1 , Antp‐1 ), in addition to expression patterns of centipede posterior Hox genes in the posterior trunk (the region correspond to the appendage‐free insect abdomen), have shown that orthology of Hox genes does not correspond to homology of function between insects, centipedes, and arachnids (Hughes & Kaufman, ; Khadjeh et al, ; Pechmann et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…A single 2906‐bp fragment of P. tepidariorum tio/tsh ortholog was identified from the developmental transcriptome and genome of this species (Posnien et al, ; Schwager et al, ), using the Drosophila melanogaster tio and tsh sequences as queries. Gene specific primers were designed for a 794‐bp fragment of Ptep‐tio/tsh .…”

Section: Methodsmentioning

confidence: 99%

The evolution of selector gene function: Expression dynamics and regulatory interactions of tiptop/teashirt across Arthropoda

March

Smaby

Setton

et al. 2018

Evolution and Development

Self Cite

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The transcription factors spineless (ss) and tiptop/teashirt (tio/tsh) have been shown to be selectors of distal appendage identity in an insect, but it is unknown how they regulate one another. Here, we examined the regulatory relationships between these two determinants in the milkweed bug Oncopeltus faciatus, using maternal RNA interference (RNAi). We show that Ofas-ss RNAi embryos bear distally transformed antennal buds with heterogeneous Ofas-tio/tsh expression domains comparable to wild type legs. In the reciprocal experiment, Ofas-tio/tsh RNAi embryos bear distally transformed walking limb buds with ectopic expression of Ofas-ss in the distal leg primordia. These data suggest that Ofas-ss is required for the maintenance of Ofas-tio/tsh expression in the distal antenna, whereas Ofas-tio/tsh represses Ofas-ss in the leg primordia. To assess whether expression boundaries of tio/tsh are associated with the trunk region more generally, we surveyed the expression of one myriapod and two chelicerate tio/tsh homologs. Our expression survey suggests that tio/tsh could play a role in specifying distal appendage identity across Arthropoda, but Hox regulation of tio/tsh homologs has been evolutionarily labile.

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The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Cited by 10 publications

References 130 publications

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

Chromosomal level reference genome of Tachypleus tridentatus provides insights into evolution and adaptation of horseshoe crabs

The evolution of selector gene function: Expression dynamics and regulatory interactions of tiptop/teashirt across Arthropoda

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