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Fan Z, Wang LY, Xiao L, Tan B, Luo B, Ren TY, Liu N, Zhang ZS, Bai M. Lampshade web spider Ectatosticta davidi chromosome-level genome assembly provides evidence for its phylogenetic position. Commun Biol 2023; 6:748. [PMID: 37463957 PMCID: PMC10354039 DOI: 10.1038/s42003-023-05129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
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.
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Affiliation(s)
- Zheng Fan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lu-Yu Wang
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Lin Xiao
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bing Tan
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Bin Luo
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Tian-Yu Ren
- School of Life Sciences, Southwest University, 400700, Chongqing, China
| | - Ning Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Zhi-Sheng Zhang
- School of Life Sciences, Southwest University, 400700, Chongqing, China.
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, 150040, Harbin, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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2
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Iwasaki-Yokozawa S, Nanjo R, Akiyama-Oda Y, Oda H. Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider. BMC Biol 2022; 20:223. [PMID: 36203191 PMCID: PMC9535882 DOI: 10.1186/s12915-022-01421-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background
The process of early development varies across the species-rich phylum Arthropoda. Owing to the limited research strategies for dissecting lineage-specific processes of development in arthropods, little is known about the variations in early arthropod development at molecular resolution. The Theridiidae spider, Parasteatoda tepidariorum, has its genome sequenced and could potentially contribute to dissecting early embryonic processes. Results We present genome-wide identification of candidate genes that exhibit locally restricted expression in germ disc forming stage embryos of P. tepidariorum, based on comparative transcriptomes of isolated cells from different regions of the embryo. A subsequent pilot screen by parental RNA interference identifies three genes required for body axis formation. One of them is a GATA-like gene that has been fast evolving after duplication and divergence from a canonical GATA family gene. This gene is designated fuchi nashi (fuchi) after its knockdown phenotypes, where the cell movement toward the formation of a germ disc was reversed. fuchi expression occurs in cells outside a forming germ disc and persists in the endoderm. Transcriptome and chromatin accessibility analyses of fuchi pRNAi embryos suggest that early fuchi activity regulates chromatin state and zygotic gene activation to promote endoderm specification and pattern formation. We also show that there are many uncharacterized genes regulated by fuchi. Conclusions Our genome-based research using an arthropod phylogenetically distant from Drosophila identifies a lineage-specific, fast-evolving gene with key developmental roles in one of the earliest, genome-wide regulatory events, and allows for molecular exploration of the developmental variations in early arthropod embryos. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01421-0.
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Affiliation(s)
- Sawa Iwasaki-Yokozawa
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan
| | - Ryota Nanjo
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan.,Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.
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3
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Baudouin-Gonzalez L, Schoenauer A, Harper A, Blakeley G, Seiter M, Arif S, Sumner-Rooney L, Russell S, Sharma PP, McGregor AP. The Evolution of Sox Gene Repertoires and Regulation of Segmentation in Arachnids. Mol Biol Evol 2021; 38:3153-3169. [PMID: 33755150 PMCID: PMC8661403 DOI: 10.1093/molbev/msab088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Sox family of transcription factors regulates many processes during metazoan development, including stem cell maintenance and nervous system specification. Characterizing the repertoires and roles of these genes can therefore provide important insights into animal evolution and development. We further characterized the Sox repertoires of several arachnid species with and without an ancestral whole-genome duplication and compared their expression between the spider Parasteatoda tepidariorum and the harvestman Phalangium opilio. We found that most Sox families have been retained as ohnologs after whole-genome duplication and evidence for potential subfunctionalization and/or neofunctionalization events. Our results also suggest that Sox21b-1 likely regulated segmentation ancestrally in arachnids, playing a similar role to the closely related SoxB gene, Dichaete, in insects. We previously showed that Sox21b-1 is required for the simultaneous formation of prosomal segments and sequential addition of opisthosomal segments in P. tepidariorum. We studied the expression and function of Sox21b-1 further in this spider and found that although this gene regulates the generation of both prosomal and opisthosomal segments, it plays different roles in the formation of these tagmata reflecting their contrasting modes of segmentation and deployment of gene regulatory networks with different architectures.
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Affiliation(s)
- Luis Baudouin-Gonzalez
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Anna Schoenauer
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Amber Harper
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Grace Blakeley
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Michael Seiter
- Unit Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Saad Arif
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
| | | | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom.,Centre for Functional Genomics, Oxford Brookes University, Oxford, United Kingdom
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4
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Akiyama-Oda Y, Oda H. Hedgehog signaling controls segmentation dynamics and diversity via msx1 in a spider embryo. SCIENCE ADVANCES 2020; 6:eaba7261. [PMID: 32917677 PMCID: PMC11206446 DOI: 10.1126/sciadv.aba7261] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
Hedgehog (Hh) signaling plays fundamental roles in animal body patterning. Understanding its mechanistic complexity requires simple tractable systems that can be used for these studies. In the early spider embryo, Hh signaling mediates the formation of overall anterior-posterior polarity, yet it remains unclear what mechanisms link the initial Hh signaling activity with body axis segmentation, in which distinct periodic stripe-forming dynamics occur depending on the body region. We performed genome-wide searches for genes that transcriptionally respond to altered states of Hh signaling. Characterization of genes negatively regulated by Hh signaling suggested that msx1, encoding a conserved transcription factor, functions as a key segmentation gene. Knockdown of msx1 prevented all dynamic processes causing spatial repetition of stripes, including temporally repetitive oscillations and bi-splitting, and temporally nonrepetitive tri-splitting. Thus, Hh signaling controls segmentation dynamics and diversity via msx1 These genome-wide data from an invertebrate illuminate novel mechanistic features of Hh-based patterning.
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Affiliation(s)
- Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, Japan.
- Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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Oda H, Akiyama-Oda Y. The common house spider Parasteatoda tepidariorum. EvoDevo 2020; 11:6. [PMID: 32206294 PMCID: PMC7082966 DOI: 10.1186/s13227-020-00152-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
The common house spider Parasteatoda tepidariorum, belonging to the Chelicerata in the phylum Arthropoda, has emerged as an experimental system for studying mechanisms of development from an evolutionary standpoint. In this article, we review the distinct characteristics of P. tepidariorum, the major research questions relevant to this organism, and the available key methods and resources. P. tepidariorum has a relatively short lifecycle and, once mated, periodically lays eggs. The morphogenetic field of the P. tepidariorum embryo is cellular from an early stage and exhibits stepwise symmetry-breaking events and stripe-forming processes that are associated with body axes formation and segmentation, respectively, before reaching the arthropod phylotypic stage. Self-regulatory capabilities of the embryonic field are a prominent feature in P. tepidariorum. The mechanisms and logic underlying the evolvability of heritable patterning systems at the phylum level could be one of the major avenues of research investigated using this animal. The sequenced genome reveals whole genome duplication (WGD) within chelicerates, which offers an invertebrate platform for investigating the potential roles of WGD in animal diversification and evolution. The development and evolution of lineage-specific organs, including the book lungs and the union of spinnerets and silk glands, are attractive subjects of study. Studies using P. tepidariorum can benefit from the use of parental RNA interference, microinjection applications (including cell labeling and embryonic RNA interference), multicolor fluorescence in situ hybridization, and laser ablation as well as rich genomic and transcriptomic resources. These techniques enable functional gene discoveries and the uncovering of cellular and molecular insights.![]()
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Affiliation(s)
- Hiroki Oda
- 1Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125 Japan.,2Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka Japan
| | - Yasuko Akiyama-Oda
- 1Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125 Japan.,3Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka Japan
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6
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Oda H, Iwasaki-Yokozawa S, Usui T, Akiyama-Oda Y. Experimental duplication of bilaterian body axes in spider embryos: Holm's organizer and self-regulation of embryonic fields. Dev Genes Evol 2020; 230:49-63. [PMID: 30972574 PMCID: PMC7128006 DOI: 10.1007/s00427-019-00631-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/20/2019] [Indexed: 12/20/2022]
Abstract
Bilaterally symmetric body plans of vertebrates and arthropods are defined by a single set of two orthogonal axes, the anterior-posterior (or head-tail) and dorsal-ventral axes. In vertebrates, and especially amphibians, complete or partial doubling of the bilaterian body axes can be induced by two different types of embryological manipulations: transplantation of an organizer region or bi-sectioning of an embryo. Such axis doubling relies on the ability of embryonic fields to flexibly respond to the situation and self-regulate toward forming a whole body. This phenomenon has facilitated experimental efforts to investigate the mechanisms of vertebrate body axes formation. However, few studies have addressed the self-regulatory capabilities of embryonic fields associated with body axes formation in non-vertebrate bilaterians. The pioneer spider embryologist Åke Holm reported twinning of spider embryos induced by both types of embryological manipulations in 1952; yet, his experiments have not been replicated by other investigators, and access to spider or non-vertebrate twins has been limited. In this review, we provide a historical background on twinning experiments in spiders, and an overview of current twinning approaches in familiar spider species and related molecular studies. Moreover, we discuss the benefits of the spider model system for a deeper understanding of the ancestral mechanisms of body axes formation in arthropods, as well as in bilaterians.
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Affiliation(s)
- Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
| | - Sawa Iwasaki-Yokozawa
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
| | | | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
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7
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Leite DJ, Baudouin-Gonzalez L, Iwasaki-Yokozawa S, Lozano-Fernandez J, Turetzek N, Akiyama-Oda Y, Prpic NM, Pisani D, Oda H, Sharma PP, McGregor AP. Homeobox Gene Duplication and Divergence in Arachnids. Mol Biol Evol 2020; 35:2240-2253. [PMID: 29924328 PMCID: PMC6107062 DOI: 10.1093/molbev/msy125] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterized and compared the homeobox repertoires in a range of arachnids. We found that many families and clusters of these genes are duplicated in all studied arachnopulmonates (Parasteatoda tepidariorum, Pholcus phalangioides, Centruroides sculpturatus, and Mesobuthus martensii) compared with nonarachnopulmonate arachnids (Phalangium opilio, Neobisium carcinoides, Hesperochernes sp., and Ixodes scapularis). To assess divergence in the roles of homeobox ohnologs, we analyzed the expression of P. tepidariorum homeobox genes during embryogenesis and found pervasive changes in the level and timing of their expression. Furthermore, we compared the spatial expression of a subset of P. tepidariorum ohnologs with their single copy orthologs in P. opilio embryos. We found evidence for likely subfunctionlization and neofunctionalization of these genes in the spider. Overall our results show a high level of retention of homeobox genes in spiders and scorpions post-WGD, which is likely to have made a major contribution to their developmental evolution and diversification through pervasive subfunctionlization and neofunctionalization, and paralleling the outcomes of WGD in vertebrates.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Luís Baudouin-Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | | | - Jesus Lozano-Fernandez
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Natascha Turetzek
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University, Göttingen, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, Takatsuki, Osaka, Japan.,Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Nikola-Michael Prpic
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University, Göttingen, Germany
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Hiroki Oda
- JT Biohistory Research Hall, Takatsuki, Osaka, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
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8
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Oda H, Akiyama-Oda Y. Dataset on gene expressions affected by simultaneous knockdown of Hedgehog and Dpp signaling components in embryos of the spider Parasteatoda tepidariorum. Data Brief 2020; 28:105088. [PMID: 32226819 PMCID: PMC7096682 DOI: 10.1016/j.dib.2019.105088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/14/2019] [Accepted: 12/24/2019] [Indexed: 01/08/2023] Open
Abstract
Simultaneous, parental RNA interference (pRNAi) mediated knockdown of Hedgehog and Decapentaplegic (Dpp) signaling components, Pt-patched (Pt-ptc) and Pt-dpp, respectively, exhibited serious defects in the formation of the major embryonic axes in the model spider Parasteatoda tepidariorum. This paper describes a dataset of a custom oligonucleotide two-color microarray analysis that was carried out to compare the transcript expression levels between untreated (normal) and Pt-ptc + Pt-dpp double pRNAi embryos at late stage 5. Array spots that showed the intensity ratio of [Pt-ptc + Pt-dpp double pRNAi]/[normal] <0.6 were categorized as positive. The expressions of most, not all, of the transcripts related to the positive array spots were examined in embryos by whole-mount in situ hybridization. Some of the stained embryos showed distinct patterns of gene expression. The data presented may be useful for characterizing the mechanisms of embryonic patterning in spider embryos.
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Affiliation(s)
- Hiroki Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Laboratory of Biohistory, Department of Biological Sciences, Graduate School of Science, Osaka University, Japan
| | - Yasuko Akiyama-Oda
- Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
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