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Adams SA, Graham NR, Holmquist AJ, Sheffer MM, Steigerwald EC, Sahasrabudhe R, Nguyen O, Beraut E, Fairbairn C, Sacco S, Seligmann W, Escalona M, Shaffer HB, Toffelmier E, Gillespie RG. Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae). J Hered 2023; 114:395-403. [PMID: 37042574 PMCID: PMC10287146 DOI: 10.1093/jhered/esad013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 04/13/2023] Open
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.
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Affiliation(s)
- Seira A Adams
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Center for Population Biology, University of California, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Natalie R Graham
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Anna J Holmquist
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Monica M Sheffer
- Department of Biology, University of Washington, Seattle, WA, United States
- eScience Institute, University of Washington, Seattle, WA, United States
| | - Emma C Steigerwald
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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Kulkarni S, Wood HM, Hormiga G. Phylogenomics illuminates the evolution of orb webs, respiratory systems and the biogeographic history of the world's smallest orb-weaving spiders (Araneae, Araneoidea, Symphytognathoids). Mol Phylogenet Evol 2023:107855. [PMID: 37311493 DOI: 10.1016/j.ympev.2023.107855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/01/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023]
Abstract
The miniature orb weaving spiders (symphytognathoids) are a group of small spiders (< 2 mm), including the smallest adult spider Patu digua (0.37 mm in body length), that have been classified into five families. The species of one of its constituent lineages, the family Anapidae, build a remarkable diversity of webs (ranging from orbs to sheet webs and irregular tangles) and even include a webless kleptoparasitic species. Anapids are also exceptional because of the extraordinary diversity of their respiratory systems. The phylogenetic relationships of symphytognathoid families have been recalcitrant with different classes of data, such as, monophyletic with morphology and its concatenation with Sanger-based six markers, paraphyletic (including a paraphyletic Anapidae) with solely Sanger-based six markers, and polyphyletic with transcriptomes. In this study, we capitalized on a large taxonomic sampling of symphytognathoids, focusing on Anapidae, and using de novo sequenced ultraconserved elements (UCEs) combined with UCEs recovered from available transcriptomes and genomes. We evaluated the conflicting relationships using a variety of support metrics and topology tests. We found support for the phylogenetic hypothesis proposed using morphology to obtain the "symphytognathoids'' clade, Anterior Tracheal System (ANTS) Clade and monophyly of the family Anapidae. Anapidae can be divided into three major lineages, the Vichitra Clade (including Teutoniella, Holarchaea, Sofanapis and Acrobleps), the subfamily Micropholcommatinae and the Orb-weaving anapids (Owa) Clade. Biogeographic analyses reconstructed a hypothesis of multiple long-distance transoceanic dispersal events, potentially influenced by the Antarctic Circumpolar Current and West Wind Drift. In symphytognathoids, the ancestral anterior tracheal system transformed to book lungs four times and reduced book lungs five times. The posterior tracheal system was lost six times. The orb web structure was lost four times independently and transformed into sheet web once.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA; (currently) Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706, USA.
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA.
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Caetano C, Griswold CE, Michalik P, Labarque FM. Evolution and comparative morphology of raptorial feet in spiders. ARTHROPOD STRUCTURE & DEVELOPMENT 2023; 74:101255. [PMID: 37011488 DOI: 10.1016/j.asd.2023.101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 06/02/2023]
Abstract
Spiders are among the most diverse animals, which developed different morphological and behavioral traits for capturing prey. We studied the anatomy and functionality of the rare and apomorphic raptorial spider feet using 3D reconstruction modeling, among other imaging techniques. The evolutionary reconstruction of the raptorial feet (tarsus plus pretarsus) features using a composite tree of spiders, indicating that similar traits emerged three times independently in Trogloraptoridae, Gradungulinae, and Doryonychus raptor (Tetragnathidae). The characteristics defining the raptorial feet are an interlocked complex merging of the base of the elongated prolateral claw with the pretarsal sclerotized ring, with the former clasping against the tarsus. Raptorial feet even flex over robust raptorial macrosetae forming a reduced tarsal version of a catching basket to encase prey during hunting. Our results show that Celaeniini (Araneidae) and Heterogriffus berlandi (Thomisidae), taxa previously compared with raptorial spiders, lack the raptorial feet key characteristics and the tarsal-catching basket. We make predictions about the possible behavior of the abovementioned taxa that will need to be tested by observing living specimens. We conclude that multiple morphological tarsal and pretarsal micro-structures define the raptorial foot functional unit and recommend a comprehensive evaluation before assigning this configuration to any spider taxa.
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Affiliation(s)
- Carolina Caetano
- Departamento de Ecologia e Biologia Evolutiva (DEBE), Universidade Federal de São Carlos (UFSCar), campus São Carlos, Rodovia Washington Luís, Km 235, CEP, 13565-905, São Carlos, SP, Brazil; Departamento de Hidrobiologia (DHb), Universidade Federal de São Carlos (UFSCar), campus São Carlos, Rodovia Washington Luís, Km 235, CEP, 13565-905, São Carlos, SP, Brazil.
| | - Charles E Griswold
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Greifswald, Germany.
| | - Facundo M Labarque
- Departamento de Ecologia e Biologia Evolutiva (DEBE), Universidade Federal de São Carlos (UFSCar), campus São Carlos, Rodovia Washington Luís, Km 235, CEP, 13565-905, São Carlos, SP, Brazil.
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Rouhová L, Sehadová H, Pauchová L, Hradilová M, Žurovcová M, Šerý M, Rindoš M, Žurovec M. Using the multi-omics approach to reveal the silk composition in Plectrocnemia conspersa. Front Mol Biosci 2022; 9:945239. [PMID: 36060257 PMCID: PMC9432349 DOI: 10.3389/fmolb.2022.945239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
Similar to Lepidoptera, the larvae of Trichoptera are also capable of producing silk. Plectrocnemia conspersa, a predatory species belonging to the suborder Annulipalpia, builds massive silken retreats with preycapturing nets. In this study, we describe the silk glands of P. conspersa and use the multi-omics methods to obtain a complete picture of the fiber composition. A combination of silk gland-specific transcriptome and proteomic analyses of the spun-out fibers yielded 27 significant candidates whose full-length sequences and gene structures were retrieved from the publicly available genome database. About one-third of the candidates were completely novel proteins for which there are no described homologs, including a group of five pseudofibroins, proteins with a composition similar to fibroin heavy chain. The rest were homologs of lepidopteran silk proteins, although some had a larger number of paralogs. On the other hand, P. conspersa fibers lacked some proteins that are regular components in moth silk. In summary, the multi-omics approach provides an opportunity to compare the overall composition of silk with other insect species. A sufficient number of such studies will make it possible to distinguish between the basic components of all silks and the proteins that represent the adaptation of the fibers for specific purposes or environments.
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Affiliation(s)
- Lenka Rouhová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Hana Sehadová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Lucie Pauchová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Praha, Czechia
| | - Martina Žurovcová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Michal Šerý
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
| | - Michal Rindoš
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Michal Žurovec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czechia
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
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High-Density Three-Dimensional Morphometric Analyses Reveal Predation-Based Disparity and Evolutionary Modularity in Spider ‘Jaws’. Evol Biol 2022. [DOI: 10.1007/s11692-022-09576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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