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Su ZH, Sasaki A, Minami H, Ozaki K. Arthropod Phylotranscriptomics With a Special Focus on the Basal Phylogeny of the Myriapoda. Genome Biol Evol 2024; 16:evae189. [PMID: 39219333 DOI: 10.1093/gbe/evae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 08/08/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Arthropoda represents the most diverse animal phylum, but clarifying the phylogenetic relationships among arthropod taxa remains challenging given the numerous arthropod lineages that diverged over a short period of time. In order to resolve the most controversial aspects of deep arthropod phylogeny, focusing on the Myriapoda, we conducted phylogenetic analyses based on ten super-matrices comprised of 751 to 1,233 orthologous genes across 64 representative arthropod species, including 28 transcriptomes that were newly generated in this study. Our findings provide unambiguous support for the monophyly of the higher arthropod taxa, Chelicerata, Mandibulata, Myriapoda, Pancrustacea, and Hexapoda, while the Crustacea are paraphyletic, with the class Remipedia supported as the lineage most closely related to hexapods. Within the Hexapoda, our results largely affirm previously proposed phylogenetic relationships among deep hexapod lineages, except that the Paraneoptera (Hemiptera, Thysanoptera, and Psocodea) was recovered as a monophyletic lineage in some analyses. The results corroborated the recently proposed phylogenetic framework of the four myriapod classes, wherein Symphyla and Pauropoda, as well as Chilopoda and Diplopoda, are each proposed to be sister taxa. The findings provide important insights into understanding the phylogeny and evolution of arthropods.
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Affiliation(s)
- Zhi-Hui Su
- JT Biohistory Research Hall, Takatsuki, Osaka 569-1125, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Ayako Sasaki
- JT Biohistory Research Hall, Takatsuki, Osaka 569-1125, Japan
| | - Hiroaki Minami
- JT Biohistory Research Hall, Takatsuki, Osaka 569-1125, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Katsuhisa Ozaki
- JT Biohistory Research Hall, Takatsuki, Osaka 569-1125, Japan
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Li W, Wang Q. Recent progress in the research of exosomes and Dscam regulated crab antiviral immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103925. [PMID: 33217412 DOI: 10.1016/j.dci.2020.103925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Crustaceans, including crab and shrimp, generally lack lymphocytes or adaptive immunity, and they rely solely on innate immunity for pathogen defense. The white spot syndrome virus (WSSV) causes the most prevalent viral disease in penaeid shrimps, which are widely cultured species in coastal waters worldwide. Numerous studies have elucidated the role of the immune system in protecting shrimps from WSSV infection for the development of safe and effective defensive strategies against WSSV. Although WSSV has a wide host range, it appears to exhibit high pathogenicity and virulence in only penaeid shrimps. Crabs are interesting models for studying immune responses after WSSV infection. Therefore, we reviewed recent information on the innate immune responses of crabs to WSSV and mainly focused on the antiviral functions of exosome-mediated apoptosis and alternatively spliced Down syndrome cell adhesion molecule. Our review may provide novel insights into antiviral management for crustaceans, especially penaeid shrimps.
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Affiliation(s)
- Weiwei Li
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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Roelofs D, Zwaenepoel A, Sistermans T, Nap J, Kampfraath AA, Van de Peer Y, Ellers J, Kraaijeveld K. Multi-faceted analysis provides little evidence for recurrent whole-genome duplications during hexapod evolution. BMC Biol 2020; 18:57. [PMID: 32460826 PMCID: PMC7251882 DOI: 10.1186/s12915-020-00789-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/06/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Gene duplication events play an important role in the evolution and adaptation of organisms. Duplicated genes can arise through different mechanisms, including whole-genome duplications (WGDs). Recently, WGD was suggested to be an important driver of evolution, also in hexapod animals. RESULTS Here, we analyzed 20 high-quality hexapod genomes using whole-paranome distributions of estimated synonymous distances (KS), patterns of within-genome co-linearity, and phylogenomic gene tree-species tree reconciliation methods. We observe an abundance of gene duplicates in the majority of these hexapod genomes, yet we find little evidence for WGD. The majority of gene duplicates seem to have originated through small-scale gene duplication processes. We did detect segmental duplications in six genomes, but these lacked the within-genome co-linearity signature typically associated with WGD, and the age of these duplications did not coincide with particular peaks in KS distributions. Furthermore, statistical gene tree-species tree reconciliation failed to support all but one of the previously hypothesized WGDs. CONCLUSIONS Our analyses therefore provide very limited evidence for WGD having played a significant role in the evolution of hexapods and suggest that alternative mechanisms drive gene duplication events in this group of animals. For instance, we propose that, along with small-scale gene duplication events, episodes of increased transposable element activity could have been an important source for gene duplicates in hexapods.
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Affiliation(s)
- Dick Roelofs
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands
- Keygene N.V, Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
| | - Arthur Zwaenepoel
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Tom Sistermans
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands
| | - Joey Nap
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands
| | - Andries A Kampfraath
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands
| | - Yves Van de Peer
- Center for Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, Center for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0028, South Africa
| | - Jacintha Ellers
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081HV, Amsterdam, The Netherlands
| | - Ken Kraaijeveld
- Origins Center, Nijenborgh 7, 9747AG, Groningen, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1090 GE, Amsterdam, The Netherlands
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Chipman AD, Edgecombe GD. Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo. Proc Biol Sci 2019; 286:20191881. [PMID: 31575373 DOI: 10.1098/rspb.2019.1881] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Segmentation is fundamental to the arthropod body plan. Understanding the evolutionary steps by which arthropods became segmented is being transformed by the integration of data from evolutionary developmental biology (evo-devo), Cambrian fossils that allow the stepwise acquisition of segmental characters to be traced in the arthropod stem-group, and the incorporation of fossils into an increasingly well-supported phylogenetic framework for extant arthropods based on genomic-scale datasets. Both evo-devo and palaeontology make novel predictions about the evolution of segmentation that serve as testable hypotheses for the other, complementary data source. Fossils underpin such hypotheses as arthropodization originating in a frontal appendage and then being co-opted into other segments, and segmentation of the endodermal midgut in the arthropod stem-group. Insights from development, such as tagmatization being associated with different modes of segment generation in different body regions, and a distinct patterning of the anterior head segments, are complemented by palaeontological evidence for the pattern of tagmatization during ontogeny of exceptionally preserved fossils. Fossil and developmental data together provide evidence for a short head in stem-group arthropods and the mechanism of its formation and retention. Future breakthroughs are expected from identification of molecular signatures of developmental innovations within a phylogenetic framework, and from a focus on later developmental stages to identify the differentiation of repeated units of different systems within segmental precursors.
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Affiliation(s)
- Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Silberman Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Bonatto Paese CL, Leite DJ, Schönauer A, McGregor AP, Russell S. Duplication and expression of Sox genes in spiders. BMC Evol Biol 2018; 18:205. [PMID: 30587109 PMCID: PMC6307133 DOI: 10.1186/s12862-018-1337-4] [Citation(s) in RCA: 12] [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: 05/30/2018] [Accepted: 12/17/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The Sox family of transcription factors is an important part of the genetic 'toolbox' of all metazoans examined to date and is known to play important developmental roles in vertebrates and insects. However, outside the commonly studied Drosophila model little is known about the repertoire of Sox family transcription factors in other arthropod species. Here we characterise the Sox family in two chelicerate species, the spiders Parasteatoda tepidariorum and Stegodyphus mimosarum, which have experienced a whole genome duplication (WGD) in their evolutionary history. RESULTS We find that virtually all of the duplicate Sox genes have been retained in these spiders after the WGD. Analysis of the expression of Sox genes in P. tepidariorum embryos suggests that it is likely that some of these genes have neofunctionalised after duplication. Our expression analysis also strengthens the view that an orthologue of vertebrate Group B1 genes, SoxNeuro, is implicated in the earliest events of CNS specification in both vertebrates and invertebrates. In addition, a gene in the Dichaete/Sox21b class is dynamically expressed in the spider segment addition zone, suggestive of an ancient regulatory mechanism controlling arthropod segmentation as recently suggested for flies and beetles. Together with the recent analysis of Sox gene expression in the embryos of other arthropods, our findings support the idea of conserved functions for some of these genes, including a potential role for SoxC and SoxD genes in CNS development and SoxF in limb development. CONCLUSIONS Our study provides a new chelicerate perspective to understanding the evolution and function of Sox genes and how the retention of duplicates of such important tool-box genes after WGD has contributed to different aspects of spider embryogenesis. Future characterisation of the function of these genes in spiders will help us to better understand the evolution of the regulation of important developmental processes in arthropods and other metazoans including neurogenesis and segmentation.
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Affiliation(s)
- Christian L Bonatto Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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Paese CLB, Schoenauer A, Leite DJ, Russell S, McGregor AP. A SoxB gene acts as an anterior gap gene and regulates posterior segment addition in a spider. eLife 2018; 7:e37567. [PMID: 30126532 PMCID: PMC6167052 DOI: 10.7554/elife.37567] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023] Open
Abstract
Sox genes encode a set of highly conserved transcription factors that regulate many developmental processes. In insects, the SoxB gene Dichaete is the only Sox gene known to be involved in segmentation. To determine if similar mechanisms are used in other arthropods, we investigated the role of Sox genes during segmentation in the spider Parasteatoda tepidariorum. While Dichaete does not appear to be involved in spider segmentation, we found that the closely related Sox21b-1 gene acts as a gap gene during formation of anterior segments and is also part of the segmentation clock for development of the segment addition zone and sequential addition of opisthosomal segments. Thus, we have found that two different mechanisms of segmentation in a non-mandibulate arthropod are regulated by a SoxB gene. Our work provides new insights into the function of an important and conserved gene family, and the evolution of the regulation of segmentation in arthropods.
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Affiliation(s)
- Christian Louis Bonatto Paese
- Laboratory of Evolutionary Developmental BiologyDepartment of Biological and Medical Sciences, Oxford Brookes UniversityOxfordUnited Kingdom
| | - Anna Schoenauer
- Laboratory of Evolutionary Developmental BiologyDepartment of Biological and Medical Sciences, Oxford Brookes UniversityOxfordUnited Kingdom
| | - Daniel J Leite
- Laboratory of Evolutionary Developmental BiologyDepartment of Biological and Medical Sciences, Oxford Brookes UniversityOxfordUnited Kingdom
| | - Steven Russell
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Alistair P McGregor
- Laboratory of Evolutionary Developmental BiologyDepartment of Biological and Medical Sciences, Oxford Brookes UniversityOxfordUnited Kingdom
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The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure. Mol Phylogenet Evol 2018; 129:60-69. [PMID: 30102976 DOI: 10.1016/j.ympev.2018.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/10/2018] [Accepted: 08/03/2018] [Indexed: 11/22/2022]
Abstract
Rhipicephalus microplus and R. decoloratus are one-host ticks that preferentially feed on cattle. They are capable of transmitting various tick-borne pathogens which may be detrimental to the agricultural and livestock industry in South Africa. Previous studies have shown that R. microplus forms five lineages in the R. microplus complex, segregating into different geographical areas based on mitochondrial markers. This study examined the phylogenetic relationship within and between R. microplus and R. decoloratus using the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes. The results showed that the nuclear ITS2 marker is informative for interspecific variation but lacks the resolution for intraspecific variation. Analysis of the mitochondrial COI gene revealed that R. microplus ticks from South Africa grouped into a clade comprised of ticks from Asia and South America. The population structure of these two tick species was also investigated using novel microsatellite markers. Population structure analyses revealed that both the R. microplus and R. decoloratus populations presented with two genetic clusters. Rhipicephalus microplus ticks from the Kwa-Zulu Natal (KZN) province belonged to cluster 1, and those from the Eastern Cape (EC) province predominantly grouped into cluster 2. No observable population structure was noted for R. decoloratus. The overlap of genetic clusters in both species could be attributed to inbreeding between the regions by unrestricted movement of cattle across provinces. Such movement promotes tick mobility, gene flow and the homogenisation of tick populations.
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A chelicerate-specific burst of nonclassical Dscam diversity. BMC Genomics 2018; 19:66. [PMID: 29351731 PMCID: PMC5775551 DOI: 10.1186/s12864-017-4420-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The immunoglobulin (Ig) superfamily receptor Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for both nervous and immune systems in insects. However, further information is required to develop a comprehensive view of Dscam diversification across the broad spectrum of Chelicerata clades, a basal branch of arthropods and the second largest group of terrestrial animals. RESULTS In this study, a genome-wide comprehensive analysis of Dscam genes across Chelicerata species revealed a burst of nonclassical Dscams, categorised into four types-mDscam, sDscamα, sDscamβ, and sDscamγ-based on their size and structure. Although the mDscam gene class includes the highest number of Dscam genes, the sDscam genes utilise alternative promoters to expand protein diversity. Furthermore, we indicated that the 5' cassette duplicate is inversely correlated with the sDscam gene duplicate. We showed differential and sDscam- biased expression of nonclassical Dscam isoforms. Thus, the Dscam isoform repertoire across Chelicerata is entirely dominated by the number and expression levels of nonclassical Dscams. Taken together, these data show that Chelicerata evolved a large conserved and lineage-specific repertoire of nonclassical Dscams. CONCLUSIONS This study showed that arthropods have a large diversified Chelicerata-specific repertoire of nonclassical Dscam isoforms, which are structurally and mechanistically distinct from those of insects. These findings provide a global framework for the evolution of Dscam diversity in arthropods and offer mechanistic insights into the diversification of the clade-specific Ig superfamily repertoire.
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Savriama Y, Gerber S, Baiocco M, Debat V, Fusco G. Development and evolution of segmentation assessed by geometric morphometrics: The centipede Strigamia maritima as a case study. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:419-428. [PMID: 28302585 DOI: 10.1016/j.asd.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 02/22/2017] [Accepted: 03/11/2017] [Indexed: 05/14/2023]
Abstract
Using the centipede model species Strigamia maritima as a subject of study, we illustrate the potential of geometric morphometrics for investigating the development and evolution of segmentation, with a specific focus on post-embryonic segmental patterning. We show how these techniques can contribute detailed descriptive data for comparative purposes, but also precious information on some features of the developmental system that are considered relevant for the evolvability of a segmented body architecture, such as developmental stability and canalization. Morphometric analyses allow to separately investigate several sources of phenotypic variation along a segmented body axis, like constitutive and random segment heteronomy, both within and among individuals. Specifically, in S. maritima, the segmental pattern of ventral sclerite shapes mirrors that of their bilateral fluctuating asymmetry and among-individual variation in associating the most anterior and most posterior segments in diverging from the central ones. Also, among segments, there seems to be a correlation between fluctuating asymmetry and shape variation among individuals, suggesting that canalization and developmental stability are somehow associated. Overall, these associations might stem from a joint influence of the segmental position on the two processes of developmental buffering.
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Affiliation(s)
- Yoland Savriama
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sylvain Gerber
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Matteo Baiocco
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131 Padova, Italy
| | - Vincent Debat
- Institut de Systématique, Évolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Giuseppe Fusco
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131 Padova, Italy.
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