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Kulkarni S, Wood HM, Hormiga G. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 2023; 39:479-532. [PMID: 37787157 DOI: 10.1111/cla.12557] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, 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, DC, 20052, USA
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Kallal RJ, Kulkarni SS, Dimitrov D, Benavides LR, Arnedo MA, Giribet G, Hormiga G. Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics 2021; 37:298-316. [PMID: 34478199 DOI: 10.1111/cla.12439] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long-standing hypotheses. Likewise, the evolution of spider webs-perhaps their most emblematic attribute-is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira-Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree-of-life. Overall, we provide the most comprehensive spider tree-of-life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Siddharth S Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, Bergen, 5020, Norway
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Miquel A Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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3
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Kulkarni S, Kallal RJ, Wood H, Dimitrov D, Giribet G, Hormiga G. Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life. Mol Biol Evol 2021; 38:891-903. [PMID: 32986823 PMCID: PMC7947752 DOI: 10.1093/molbev/msaa251] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), noncoding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Noncoding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low-occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low-occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.
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Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, Washington, DC
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Robert J Kallal
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Hannah Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, Washington, DC
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Fu S, Duan Y, Wang S, Ren Y, Bu W. Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages. INSECTS 2021; 12:insects12030226. [PMID: 33807991 PMCID: PMC7999114 DOI: 10.3390/insects12030226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary Riptortus pedestris is a widely distributed pest insect in East Asia that causes considerable economic losses. In this study, we applied the Illumina HiSeq6000 platform to construct and sequence the transcriptome libraries of R. pedestris during all life stages. First, a total of 60,058 unigenes were assembled from raw data, and then annotated and classified with various databases. Furthermore, different numbers of differentially expressed genes were calculated by pairwise comparisons of all life stages, and some of these DEGs were associated with various functions by GO and KEGG analysis. Additionally, a total number of 35,158 SSRs and 715,604 SNPs were identified from all the transcriptome libraries. Finally, we analyzed ten wing formation-related signaling pathways, and detected the molecular and expression characterization of five wing development-related genes by qRT-PCR for all developmental stages of R. pedestris. Collectively, all these data may pave the avenue for exploring the developmental processes of hemimetabolous insects and pest management. Abstract Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.
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dos Santos-Pinto JRA, Esteves FG, Sialana FJ, Ferro M, Smidak R, Rares LC, Nussbaumer T, Rattei T, Bilban M, Bacci Júnior M, Palma MS, Lübec G. A proteotranscriptomic study of silk-producing glands from the orb-weaving spiders. Mol Omics 2019; 15:256-270. [DOI: 10.1039/c9mo00087a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A proteotranscriptomic approach provides a biochemical basis for understanding the intricate spinning process and complex structural features of spider silk proteins.
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Affiliation(s)
| | - Franciele Grego Esteves
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | | | - Milene Ferro
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | - Roman Smidak
- Department of Pharmaceutical Chemistry
- University of Vienna
- Austria
| | - Lucaciu Calin Rares
- Division of Computational System Biology
- Department of Microbiology and Ecosystem Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Thomas Nussbaumer
- Division of Computational System Biology
- Department of Microbiology and Ecosystem Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Thomas Rattei
- Division of Computational System Biology
- Department of Microbiology and Ecosystem Science
- University of Vienna
- 1090 Vienna
- Austria
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics
- Medical University of Vienna
- Vienna
- Austria
| | - Maurício Bacci Júnior
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | - Mario Sergio Palma
- Center of the Study of Social Insects
- Department of Biology
- Institute of Biosciences of Rio Claro
- São Paulo State University
- Rio Claro
| | - Gert Lübec
- Paracelsus Medical University
- A 5020 Salzburg
- Austria
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Diniz MRV, Paiva ALB, Guerra-Duarte C, Nishiyama MY, Mudadu MA, de Oliveira U, Borges MH, Yates JR, Junqueira-de-Azevedo IDL. An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches. PLoS One 2018; 13:e0200628. [PMID: 30067761 PMCID: PMC6070231 DOI: 10.1371/journal.pone.0200628] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/29/2018] [Indexed: 01/23/2023] Open
Abstract
Phoneutria nigriventer is one of the largest existing true spiders and one of the few considered medically relevant. Its venom contains several neurotoxic peptides that act on different ion channels and chemical receptors of vertebrates and invertebrates. Some of these venom toxins have been shown as promising models for pharmaceutical or biotechnological use. However, the large diversity and the predominance of low molecular weight toxins in this venom have hampered the identification and deep investigation of the less abundant toxins and the proteins with high molecular weight. Here, we combined conventional and next-generation cDNA sequencing with Multidimensional Protein Identification Technology (MudPIT), to obtain an in-depth panorama of the composition of P. nigriventer spider venom. The results from these three approaches showed that cysteine-rich peptide toxins are the most abundant components in this venom and most of them contain the Inhibitor Cysteine Knot (ICK) structural motif. Ninety-eight sequences corresponding to cysteine-rich peptide toxins were identified by the three methodologies and many of them were considered as putative novel toxins, due to the low similarity to previously described toxins. Furthermore, using next-generation sequencing we identified families of several other classes of toxins, including CAPs (Cysteine Rich Secretory Protein-CRiSP, antigen 5 and Pathogenesis-Related 1-PR-1), serine proteinases, TCTPs (translationally controlled tumor proteins), proteinase inhibitors, metalloproteinases and hyaluronidases, which have been poorly described for this venom. This study provides an overview of the molecular diversity of P. nigriventer venom, revealing several novel components and providing a better basis to understand its toxicity and pharmacological activities.
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MESH Headings
- Amino Acid Sequence
- Animals
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- High-Throughput Nucleotide Sequencing
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Peptides/metabolism
- Proteomics
- Sequence Alignment
- Sequence Analysis, DNA
- Spider Venoms/metabolism
- Spiders/genetics
- Spiders/metabolism
- Toxins, Biological/genetics
- Toxins, Biological/metabolism
- Transcriptome
- Tumor Protein, Translationally-Controlled 1
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Affiliation(s)
- Marcelo R. V. Diniz
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ana L. B. Paiva
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Clara Guerra-Duarte
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Milton Y. Nishiyama
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Ursula de Oliveira
- Laboratório Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | - Márcia H. Borges
- Laboratório de Toxinologia Molecular, Diretoria de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - John R. Yates
- Department of Chemical Physiology and Molecular and Cellular Neurobiology, The Scripps Research Institute, La Jolla, California, United States of America
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Kallal RJ, Fernández R, Giribet G, Hormiga G. A phylotranscriptomic backbone of the orb-weaving spider family Araneidae (Arachnida, Araneae) supported by multiple methodological approaches. Mol Phylogenet Evol 2018; 126:129-140. [PMID: 29635025 DOI: 10.1016/j.ympev.2018.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/05/2018] [Accepted: 04/06/2018] [Indexed: 01/01/2023]
Abstract
The orb-weaving spider family Araneidae is extremely diverse (>3100 spp.) and its members can be charismatic terrestrial arthropods, many of them recognizable by their iconic orbicular snare web, such as the common garden spiders. Despite considerable effort to better understand their backbone relationships based on multiple sources of data (morphological, behavioral and molecular), pervasive low support remains in recent studies. In addition, no overarching phylogeny of araneids is available to date, hampering further comparative work. In this study, we analyze the transcriptomes of 33 taxa, including 19 araneids - 12 of them new to this study - representing most of the core family lineages, to examine the relationships within the family using genomic-scale datasets resulting from various methodological treatments, namely ortholog selection and gene occupancy as a measure of matrix completion. Six matrices were constructed to assess these effects by varying orthology inference method and gene occupancy threshold. Orthology methods used are the benchmarking tool BUSCO and the tree-based method UPhO; three gene occupancy thresholds (45%, 65%, 85%) were used to assess the effect of missing data. Gene tree and species tree-based methods (including multi-species coalescent and concatenation approaches, as well as maximum likelihood and Bayesian inference) were used totalling 17 analytical treatments. The monophyly of Araneidae and the placement of core araneid lineages were supported, together with some previously unsound backbone divergences; these include high support for Zygiellinae as the earliest diverging subfamily (followed by Nephilinae), the placement of Gasteracanthinae as sister group to Cyclosa and close relatives, and close relationships between the Araneus + Neoscona clade and Cyrtophorinae + Argiopinae clade. Incongruences were relegated to short branches in the clade comprising Cyclosa and its close relatives. We found congruence between most of the completed analyses, with minimal topological effects from occupancy/missing data and orthology assessment. The resulting number of genes by certain combinations of orthology and occupancy thresholds being analyzed had the greatest effect on the resulting trees, with anomalous outcomes recovered from analysis of lower numbers of genes.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA.
| | - Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA; Bioinformatics and Genomics Unit, Center for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA
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Li R, Yan Z, Wang J, Song Q, Wang Z. De novo characterization of venom apparatus transcriptome of Pardosa pseudoannulata and analysis of its gene expression in response to Bt protein. BMC Biotechnol 2017; 17:73. [PMID: 29115956 PMCID: PMC5678584 DOI: 10.1186/s12896-017-0392-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/30/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pardosa pseudoannulata is a prevailing spider species, and has been regarded as an important bio-control agent of insect pests in farmland of China. However, the available genomic and transcriptomic databases of P. pseudoannulata and their venom are limited, which severely hampers functional genomic analysis of P. pseudoannulata. Recently high-throughput sequencing technology has been proved to be an efficient tool for profiling the transcriptome of relevant non-target organisms exposed to Bacillus thuringiensis (Bt) protein through food webs. Results In this study, the transcriptome of the venom apparatus was analyzed. A total of 113,358 non-redundant unigenes were yielded, among which 34,041 unigenes with complete or various length encoding regions were assigned biological function annotations and annotated with gene ontology and karyotic orthologous group terms. In addition, 3726 unigenes involved in response to stimulus and 720 unigenes associated with immune-response pathways were identified. Furthermore, we investigated transcriptomic changes in the venom apparatus using tag-based DGE technique. A total of 1724 differentially expressed genes (DEGs) were detected, while 75 and 372 DEGs were functionally annotated with KEGG pathways and GO terms, respectively. qPCR analyses were performed to verify the DEGs directly or indirectly related to immune and stress responses, including genes encoding heat shock protein, toll-like receptor, GST and NADH dehydrogenase. Conclusion This is the first study conducted to specifically investigate the venom apparatus of P. pseudoannulata in response to Bt protein exposure through tritrophic chain. A substantial fraction of transcript sequences was generated by high-throughput sequencing of the venom apparatus of P. pseudoannulata. Then a comparative transcriptome analysis showing a large number of candidate genes involved in immune response were identified by the tag-based DGE technology. This transcriptome dataset will provide a comprehensive sequence resource for furture molecular genetic research of the venom apparatus of P. pseudoannulata. Electronic supplementary material The online version of this article (10.1186/s12896-017-0392-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Li
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China.,Department of Biosciences, Hunan University of Arts and Science, Changde, 415000, China
| | - Zhenzhen Yan
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China
| | - Juan Wang
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Zhi Wang
- College of Bioscience & Biotechnology, Hunan Agriculture University, Changsha, 410128, China.
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Carlson DE, Hedin M. Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes. PLoS One 2017; 12:e0174102. [PMID: 28379977 PMCID: PMC5381867 DOI: 10.1371/journal.pone.0174102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/04/2017] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.
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Affiliation(s)
- David E. Carlson
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, United States of America
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Fang Z, Shao J, Weng Q. De novo transcriptome analysis of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) genes in latently infected Se301 cells. Virol Sin 2016; 31:425-436. [PMID: 27770381 DOI: 10.1007/s12250-016-3791-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/22/2016] [Indexed: 11/25/2022] Open
Abstract
Cells of the P8-Se301-C1 strain are Spodoptera exigua cell clones that each harbor a partial version of the S. exigua multiple nucleopolyhedrovirus (SeMNPV) genome and which are resistant to homologous SeMNPV infections. The cells produce no viral progeny, suggesting that the infection is a latent-like viral infection. To investigate the SeMNPV genes harbored in the P8-Se301-C1 cells, the de novo transcriptomes of P8-Se301-C1 cells and S. exigua Se301 cells were analyzed and compared. A total of 54,569,296 reads were obtained from the P8-Se301-C1 cells that yielded 112,565 final unigenes with a mean length of 1,093 nt. A total of 56,865,504 reads were obtained from the Se301 cells that yielded 102,996 final unigenes with a mean length of 1,082 nt. Ten SeMNPV gene transcripts (se5, se7, se8, se12, se43, se45, se89, se90, se124, and se126) were detected in the P8-Se301-C1 cells by RNA-Seq but not in the Se301 cells, which was verified by RTPCR. 5'/3' RACE analyses showed that the 3'- or 5'-end sequences of the viral transcripts are aligned to the host gene sequences in P8-Se301-C1 cells, suggesting that the SeMNPV genes may integrate into and be transcribed with the host genes in the P8-Se301-C1 cells. Furthermore, six additional viral gene transcripts, se11, se42, se44, se88, se91, and se127 (incorporated into chimeric fusion transcripts in the P8-Se301-C1 cells), were detected in the RACE analyses. Taken together, sixteen SeMNPV transcripts were identified in the P8-Se301-C1 cell strain. This study provides information to develop the understanding of baculovirus latent infections and superinfection exclusion.
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Affiliation(s)
- Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
| | - Jingxu Shao
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
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11
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Ballesteros JA, Hormiga G. A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology. Mol Biol Evol 2016; 33:2117-34. [PMID: 27189539 DOI: 10.1093/molbev/msw069] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO.
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Affiliation(s)
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University
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Kono N, Nakamura H, Ito Y, Tomita M, Arakawa K. Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Mol Ecol Resour 2015; 16:662-72. [PMID: 26561354 DOI: 10.1111/1755-0998.12485] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022]
Abstract
With advances in high-throughput sequencing technologies, de novo transcriptome sequencing and assembly has become a cost-effective method to obtain comprehensive genetic information of a species of interest, especially in nonmodel species with large genomes such as spiders. However, high-quality RNA is essential for successful sequencing, and sample preservation conditions require careful consideration for the effective storage of field-collected samples. To this end, we report a streamlined feasibility study of various storage conditions and their effects on de novo transcriptome assembly results. The storage parameters considered include temperatures ranging from room temperature to -80°C; preservatives, including ethanol, RNAlater, TRIzol and RNAlater-ICE; and sample submersion states. As a result, intact RNA was extracted and assembly was successful when samples were preserved at low temperatures regardless of the type of preservative used. The assemblies as well as the gene expression profiles were shown to be robust to RNA degradation, when 30 million 150-bp paired-end reads are obtained. The parameters for sample storage, RNA extraction, library preparation, sequencing and in silico assembly considered in this work provide a guideline for the study of field-collected samples of spiders.
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Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hiroyuki Nakamura
- Spiber Inc., Mizukami 234-1, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Yusuke Ito
- Spiber Inc., Mizukami 234-1, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
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