1
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Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor. Commun Biol 2024; 7:203. [PMID: 38374160 PMCID: PMC10876535 DOI: 10.1038/s42003-024-05901-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.
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Affiliation(s)
- Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Júlia Ramon Mateu
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
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2
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Moreland RT, Zhang S, Barreira SN, Ryan JF, Baxevanis AD. An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi. Proteomics 2024:e2300397. [PMID: 38329168 DOI: 10.1002/pmic.202300397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The application of these novel protein structure prediction methods will serve to further position non-bilaterian species such as Mnemiopsis as powerful model systems for the study of early animal evolution and human health.
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Affiliation(s)
- R Travis Moreland
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Suiyuan Zhang
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sofia N Barreira
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Andreas D Baxevanis
- Center for Genomics and Data Science Research, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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3
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Simonson BT, Jegla M, Ryan JF, Jegla T. Functional analysis of ctenophore Shaker K + channels: N-type inactivation in the animal roots. Biophys J 2024:S0006-3495(24)00068-7. [PMID: 38291751 DOI: 10.1016/j.bpj.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/16/2023] [Accepted: 01/24/2024] [Indexed: 02/01/2024] Open
Abstract
Here we explore the evolutionary origins of fast N-type ball-and-chain inactivation in Shaker (Kv1) K+ channels by functionally characterizing Shaker channels from the ctenophore (comb jelly) Mnemiopsis leidyi. Ctenophores are the sister lineage to other animals and Mnemiopsis has >40 Shaker-like K+ channels, but they have not been functionally characterized. We identified three Mnemiopsis channels (MlShak3-5) with N-type inactivation ball-like sequences at their N termini and functionally expressed them in Xenopus oocytes. Two of the channels, MlShak4 and MlShak5, showed rapid inactivation similar to cnidarian and bilaterian Shakers with rapid N-type inactivation, whereas MlShak3 inactivated ∼100-fold more slowly. Fast inactivation in MlShak4 and MlShak5 required the putative N-terminal inactivation ball sequences. Furthermore, the rate of fast inactivation in these channels depended on the number of inactivation balls/channel, but the rate of recovery from inactivation did not. These findings closely match the mechanism of N-type inactivation first described for Drosophila Shaker in which 1) inactivation balls on the N termini of each subunit can independently block the pore, and 2) only one inactivation ball occupies the pore binding site at a time. These findings suggest classical N-type activation evolved in Shaker channels at the very base of the animal phylogeny in a common ancestor of ctenophores, cnidarians, and bilaterians and that fast-inactivating Shakers are therefore a fundamental type of animal K+ channel. Interestingly, we find evidence from functional co-expression experiments and molecular dynamics that MlShak4 and MlShak5 do not co-assemble, suggesting that Mnemiopsis has at least two functionally independent N-type Shaker channels.
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Affiliation(s)
- Benjamin T Simonson
- Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania
| | - Max Jegla
- Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL; Department of Biology, University of Florida, Gainesville, FL
| | - Timothy Jegla
- Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania.
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4
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic polyadenylation is an ancestral hallmark of early development in animals. Mol Biol Evol 2023:7191908. [PMID: 37288606 DOI: 10.1093/molbev/msad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/18/2023] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in non-animal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.
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Affiliation(s)
- Labib Rouhana
- Department of Biology, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA 02125-3393, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA
| | - Fredrik Hugosson
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA
| | - Valeria Dountcheva
- Department of Biology, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA 02125-3393, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
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5
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Lara A, Simonson BT, Ryan JF, Jegla T. Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians. Genome Biol Evol 2023; 15:6994550. [PMID: 36669828 PMCID: PMC9989356 DOI: 10.1093/gbe/evad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Ion channels are highly diverse in the cnidarian model organism Nematostella vectensis (Anthozoa), but little is known about the evolutionary origins of this channel diversity and its conservation across Cnidaria. Here, we examined the evolution of voltage-gated K+ channels in Cnidaria by comparing genomes and transcriptomes of diverse cnidarian species from Anthozoa and Medusozoa. We found an average of over 40 voltage-gated K+ channel genes per species, and a phylogenetic reconstruction of the Kv, KCNQ, and Ether-a-go-go (EAG) gene families identified 28 voltage-gated K+ channels present in the last common ancestor of Anthozoa and Medusozoa (23 Kv, 1 KCNQ, and 4 EAG). Thus, much of the diversification of these channels took place in the stem cnidarian lineage prior to the emergence of modern cnidarian classes. In contrast, the stem bilaterian lineage, from which humans evolved, contained no more than nine voltage-gated K+ channels. These results hint at a complexity to electrical signaling in all cnidarians that contrasts with the perceived anatomical simplicity of their neuromuscular systems. These data provide a foundation from which the function of these cnidarian channels can be investigated, which will undoubtedly provide important insights into cnidarian physiology.
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Affiliation(s)
- Adolfo Lara
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, Florida, USA
| | - Benjamin T Simonson
- Department of Biology and Huck Institutes for the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, Florida, USA.,Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Timothy Jegla
- Department of Biology and Huck Institutes for the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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6
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Ortiz J, Bobkov YV, DeBiasse MB, Mitchell DG, Edgar A, Martindale MQ, Moss AG, Babonis LS, Ryan JF. Independent Innexin Radiation Shaped Signaling in Ctenophores. Mol Biol Evol 2023; 40:7026321. [PMID: 36740225 PMCID: PMC9949713 DOI: 10.1093/molbev/msad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/30/2022] [Accepted: 01/25/2023] [Indexed: 02/07/2023] Open
Abstract
Innexins facilitate cell-cell communication by forming gap junctions or nonjunctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here, we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggests that this cluster has been maintained due to constraints related to gene regulation. We describe the basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.
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Affiliation(s)
| | | | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Anthony G Moss
- Biological Sciences Department, Auburn University, Auburn, AL, USA
| | - Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, FL, USA,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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7
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Steinworth BM, Martindale MQ, Ryan JF. Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement. Genome Biol Evol 2022; 15:6889381. [PMID: 36508343 PMCID: PMC9825252 DOI: 10.1093/gbe/evac172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Hox and ParaHox transcription factors are important for specifying cell fates along the primary body axes during the development of most animals. Within Cnidaria, much of the research on Hox/ParaHox genes has focused on Anthozoa (anemones and corals) and Hydrozoa (hydroids) and has concentrated on the evolution and function of cnidarian Hox genes in relation to their bilaterian counterparts. Here we analyze together the full complement of Hox and ParaHox genes from species representing all four medusozoan classes (Staurozoa, Cubozoa, Hydrozoa, and Scyphozoa) and both anthozoan classes (Octocorallia and Hexacorallia). Our results show that Hox genes involved in patterning the directive axes of anthozoan polyps are absent in the stem leading to Medusozoa. For the first time, we show spatial and temporal expression patterns of Hox and ParaHox genes in the upside-down jellyfish Cassiopea xamachana (Scyphozoa), which are consistent with diversification of medusozoan Hox genes both from anthozoans and within medusozoa. Despite unprecedented taxon sampling, our phylogenetic analyses, like previous studies, are characterized by a lack of clear homology between most cnidarian and bilaterian Hox and Hox-related genes. Unlike previous studies, we propose the hypothesis that the cnidarian-bilaterian ancestor possessed a remarkably large Hox complement and that extensive loss of Hox genes was experienced by both cnidarian and bilaterian lineages.
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Affiliation(s)
- Bailey M Steinworth
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, Florida 32080,Department of Biology, University of Florida, Gainesville, Florida 32611
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St Augustine, Florida 32080,Department of Biology, University of Florida, Gainesville, Florida 32611
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8
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Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, Reitzel AM. A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes. Genome Biol Evol 2022; 14:6717576. [PMID: 36161313 PMCID: PMC9557091 DOI: 10.1093/gbe/evac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/14/2022] Open
Abstract
Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response (“defensome”) with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.,Whitney Laboratory for Marine Bioscience, University of Florida, FL, USA
| | | | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | - John A Burt
- Water Research Center & Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, FL, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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9
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Tekle YI, Wang F, Tran H, Hayes TD, Ryan JF. The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa. Sci Rep 2022; 12:9841. [PMID: 35701521 PMCID: PMC9198077 DOI: 10.1038/s41598-022-14131-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/06/2022] [Indexed: 11/23/2022] Open
Abstract
To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium's sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.
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Affiliation(s)
- Yonas I Tekle
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA.
| | - Fang Wang
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - Hanh Tran
- Department of Biology, Spelman College, 350 Spelman Lane Southwest, Atlanta, GA, 30314, USA
| | - T Danielle Hayes
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Iowa State University, Ames, IA, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
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10
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Santander MD, Maronna MM, Ryan JF, Andrade SCS. The state of Medusozoa genomics: current evidence and future challenges. Gigascience 2022; 11:6586816. [PMID: 35579552 PMCID: PMC9112765 DOI: 10.1093/gigascience/giac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
Medusozoa is a widely distributed ancient lineage that harbors one-third of Cnidaria diversity divided into 4 classes. This clade is characterized by the succession of stages and modes of reproduction during metagenic lifecycles, and includes some of the most plastic body plans and life cycles among animals. The characterization of traditional genomic features, such as chromosome numbers and genome sizes, was rather overlooked in Medusozoa and many evolutionary questions still remain unanswered. Modern genomic DNA sequencing in this group started in 2010 with the publication of the Hydra vulgaris genome and has experienced an exponential increase in the past 3 years. Therefore, an update of the state of Medusozoa genomics is warranted. We reviewed different sources of evidence, including cytogenetic records and high-throughput sequencing projects. We focused on 4 main topics that would be relevant for the broad Cnidaria research community: (i) taxonomic coverage of genomic information; (ii) continuity, quality, and completeness of high-throughput sequencing datasets; (iii) overview of the Medusozoa specific research questions approached with genomics; and (iv) the accessibility of data and metadata. We highlight a lack of standardization in genomic projects and their reports, and reinforce a series of recommendations to enhance future collaborative research.
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Affiliation(s)
- Mylena D Santander
- Correspondence address. Mylena D. Santander, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, 277 Rua do Matão, Cidade Universitária, São Paulo 05508-090, Brazil. E-mail:
| | - Maximiliano M Maronna
- Correspondence address. Maximiliano M. Maronna, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, 101 Rua do Matão Cidade Universitária, São Paulo 05508-090, Brazil. E-mail:
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL 32080, USA,Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade São Paulo, 277 Rua do Matão, Cidade Universitária, São Paulo 05508-090, Brazil
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11
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Almazan EMP, Ryan JF, Rouhana L. Regeneration of Planarian Auricles and Reestablishment of Chemotactic Ability. Front Cell Dev Biol 2021; 9:777951. [PMID: 34901022 PMCID: PMC8662385 DOI: 10.3389/fcell.2021.777951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Detection of chemical stimuli is crucial for living systems and also contributes to quality of life in humans. Since loss of olfaction becomes more prevalent with aging, longer life expectancies have fueled interest in understanding the molecular mechanisms behind the development and maintenance of chemical sensing. Planarian flatworms possess an unsurpassed ability for stem cell-driven regeneration that allows them to restore any damaged or removed part of their bodies. This includes anteriorly-positioned lateral flaps known as auricles, which have long been thought to play a central role in chemotaxis. The contribution of auricles to the detection of positive chemical stimuli was tested in this study using Girardia dorotocephala, a North American planarian species known for its morphologically prominent auricles. Behavioral experiments staged under laboratory conditions revealed that removal of auricles by amputation leads to a significant decrease in the ability of planarians to find food. However, full chemotactic capacity is observed as early as 2 days post-amputation, which is days prior from restoration of auricle morphology, but correlative with accumulation of ciliated cells in the position of auricle regeneration. Planarians subjected to x-ray irradiation prior to auricle amputation were unable to restore auricle morphology, but were still able to restore chemotactic capacity. These results indicate that although regeneration of auricle morphology requires stem cells, some restoration of chemotactic ability can still be achieved in the absence of normal auricle morphology, corroborating with the initial observation that chemotactic success is reestablished 2-days post-amputation in our assays. Transcriptome profiles of excised auricles were obtained to facilitate molecular characterization of these structures, as well as the identification of genes that contribute to chemotaxis and auricle development. A significant overlap was found between genes with preferential expression in auricles of G. dorotocephala and genes with reduced expression upon SoxB1 knockdown in Schmidtea mediterranea, suggesting that SoxB1 has a conserved role in regulating auricle development and function. Models that distinguish between possible contributions to chemotactic behavior obtained from cellular composition, as compared to anatomical morphology of the auricles, are discussed.
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Affiliation(s)
| | - Joseph F Ryan
- Whitney Laboratory of Marine Biosciences, University of Florida, St. Augustine, FL, United States.,Department of Biology, University of Florida, Gainesville, FL, United States
| | - Labib Rouhana
- Department of Biological Sciences, Wright State University, Dayton, OH, United States
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12
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Hernandez AM, Ryan JF. Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses. Syst Biol 2021; 70:1200-1212. [PMID: 33837789 PMCID: PMC8513762 DOI: 10.1093/sysbio/syab027] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 01/25/2023] Open
Abstract
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of six-state recoding approaches by comparing the performance of analyses on recoded and non-recoded data sets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches consistently outperform six-state recoding approaches. Our results suggest that six-state recoding strategies are not effective in the face of high saturation. Furthermore, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies six-state recoding outweighs its benefits. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these consistently outperform six-state recoding. Our analyses of other recoding schemes suggest that under conditions of very high compositional heterogeneity, it may be advantageous to apply recoding using more than six states, but we caution that applying any recoding should include sufficient justification. Our results have important implications for the more than 90 published papers that have incorporated six-state recoding, many of which have significant bearing on relationships across the tree of life. [Compositional heterogeneity; Dayhoff 6-state recoding; S&R 6-state recoding; six-state amino acid recoding; substitution saturation.]
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, P.O. Box 118525, Gainesville, FL, 32611, USA
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13
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Ketchum RN, Smith EG, DeBiasse MB, Vaughan GO, McParland D, Leach WB, Al-Mansoori N, Ryan JF, Burt JA, Reitzel AM. Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient. Genome Biol Evol 2020; 12:1819-1829. [PMID: 32697837 PMCID: PMC7594579 DOI: 10.1093/gbe/evaa150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ's life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte
| | - Edward G Smith
- Department of Biological Sciences, University of North Carolina at Charlotte
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine
| | - Grace O Vaughan
- Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Dain McParland
- Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Whitney B Leach
- Department of Biological Sciences, University of North Carolina at Charlotte
| | - Noura Al-Mansoori
- Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine
| | - John A Burt
- Marine Biology Laboratory, Centre for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte
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14
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Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys SP. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nat Commun 2020; 11:3676. [PMID: 32719321 PMCID: PMC7385117 DOI: 10.1038/s41467-020-17397-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/23/2020] [Indexed: 11/09/2022] Open
Abstract
The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.
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Affiliation(s)
- Nathan J Kenny
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK. .,Faculty of Health and Life Sciences, Oxford Brookes, Oxford, OX3 0BP, UK.
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Ramón E Rivera-Vicéns
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - Alex de Mendoza
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia.,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Luis A Bezares-Calderón
- College of Life and Environmental Sciences, University of Exeter, Stocker Rd, Exeter, EX4 4QD, UK
| | - Lauren Grombacher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Lael D Barlow
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Sara Camilli
- Department of Biology, Bates College, Lewiston, ME, 04240, USA
| | - Joseph F Ryan
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL, 32080, USA
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, München, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - April L Hill
- Department of Biology, Bates College, Lewiston, ME, 04240, USA
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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15
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DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020; 12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.
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Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| | - William N Colgan
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Lincoln Harris
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
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16
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Moreland RT, Nguyen AD, Ryan JF, Baxevanis AD. The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. Database (Oxford) 2020; 2020:5834871. [PMID: 32386298 DOI: 10.1093/database/baaa029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/22/2020] [Indexed: 11/13/2022]
Abstract
Following the completion of the genome sequencing and gene prediction of Mnemiopsis leidyi, a lobate ctenophore that is native to the coastal waters of the western Atlantic Ocean, we developed and implemented the Mnemiopsis Genome Project Portal (MGP Portal), a comprehensive Web-based data portal for navigating the genome sequence and gene annotations. In the years following the first release of the MGP Portal, it has become evident that the inclusion of data from significant published studies on Mnemiopsis has been critical to its adoption as the centralized resource for this emerging model organism. With this most recent update, the Portal has significantly expanded to include in situ images, temporal developmental expression profiles and single-cell expression data. Recent enhancements also include implementations of an updated BLAST interface, new graphical visualization tools and updates to gene pages that integrate all new data types. Database URL: https://research.nhgri.nih.gov/mnemiopsis/.
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Affiliation(s)
- R Travis Moreland
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anh-Dao Nguyen
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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17
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Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan JF, Davidson B, Nishida H, Dantec C, Lemaire P. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Res 2020; 48:D668-D675. [PMID: 31680137 PMCID: PMC7145539 DOI: 10.1093/nar/gkz955] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022] Open
Abstract
ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.
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Affiliation(s)
| | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Faure
- Laboratoire d’Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier, CNRS, Montpellier, France
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | | | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Lydia Besnardeau
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kai Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | | | | | - Shigeki Fujiwara
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi-shi, Kochi, Japan
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Hugues Roest Crollius
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL 32611, USA
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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18
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DeBiasse MB, Ryan JF. Phylotocol: Promoting Transparency and Overcoming Bias in Phylogenetics. Syst Biol 2019; 68:672-678. [PMID: 30597106 PMCID: PMC6568013 DOI: 10.1093/sysbio/syy090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 11/22/2022] Open
Abstract
The integrity of science requires that the process be based on sound experimental design and objective methodology. Strategies that increase reproducibility and transparency in science protect this integrity by reducing conscious and unconscious biases. Given the large number of analysis options and the constant development of new methodologies in phylogenetics, this field is one that would particularly benefit from more transparent research design. Herein, we introduce phylotocol (fi lō ’ta kôl), an a priori protocol-driven approach in which all analyses are planned and documented at the start of a project. The phylotocol template is simple and the implementation options are flexible to reduce administrative burdens and allow researchers to adapt it to their needs without restricting scientific creativity. While the primary goal of phylotocol is to increase transparency and accountability, it has a number of auxiliary benefits including improving study design and reproducibility, enhancing collaboration and education, and increasing the likelihood of project completion. Our goal with this Point of View article is to encourage a dialog about transparency in phylogenetics and the best strategies to bring transparent research practices to our field.
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Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA.,Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
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19
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Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, Yanai I. Author Correction: The mid-developmental transition and the evolution of animal body plans. Nature 2019; 575:E3. [PMID: 31673121 DOI: 10.1038/s41586-019-1698-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Michal Levin
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Mainz, Germany
| | - Leon Anavy
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Alison G Cole
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Eitan Winter
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Natalia Mostov
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Sally Khair
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Naftalie Senderovich
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Ekaterina Kovalev
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - David H Silver
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Martin Feder
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Selene L Fernandez-Valverde
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Nagayasu Nakanishi
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia.,Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N, Ocean Shore Blvd, St Augustine, Florida, 32080-8610, USA
| | - David Simmons
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida, 32080-8610, USA
| | - Oleg Simakov
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tomas Larsson
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shang-Yun Liu
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Ayelet Jerafi-Vider
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida, 32080-8610, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida, 32080-8610, USA
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sandie M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Tamar Hashimshony
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Itai Yanai
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 32000, Israel.
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20
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Colgan W, Leanza A, Hwang A, DeBiasse MB, Llosa I, Rodrigues D, Adhikari H, Barreto Corona G, Bock S, Carillo-Perez A, Currie M, Darkoa-Larbi S, Dellal D, Gutow H, Hokama P, Kibby E, Linhart N, Moody S, Naganuma A, Nguyen D, Stanton R, Stark S, Tumey C, Velleca A, Ryan JF, Davidson B. Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements. EvoDevo 2019; 10:24. [PMID: 31632631 PMCID: PMC6790052 DOI: 10.1186/s13227-019-0137-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/13/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. RESULTS Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. CONCLUSIONS Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture.
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Affiliation(s)
| | - Alexis Leanza
- Thomas Jefferson University Sidney Kimmel Medical College, Philadelphia, USA
| | - Ariel Hwang
- University of North Carolina, Chapel Hill, USA
| | | | | | | | | | | | | | | | | | | | - Daniel Dellal
- Icahn School of Medicine at Mount Sinai, New York, USA
| | | | | | - Emily Kibby
- University of Colorado Boulder, Boulder, USA
| | | | | | | | | | | | - Sierra Stark
- University of California San Francisco, San Francisco, USA
| | | | | | - Joseph F. Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, USA
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21
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Ohdera A, Ames CL, Dikow RB, Kayal E, Chiodin M, Busby B, La S, Pirro S, Collins AG, Medina M, Ryan JF. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). Gigascience 2019; 8:giz069. [PMID: 31257419 PMCID: PMC6599738 DOI: 10.1093/gigascience/giz069] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 03/27/2019] [Accepted: 05/21/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa-the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. FINDINGS Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. CONCLUSIONS These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.
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Affiliation(s)
- Aki Ohdera
- Department of Biology, Pennsylvania State University, 326 Mueller, University Park, PA, 16801, USA
| | - Cheryl L Ames
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
| | - Ehsan Kayal
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- UPMC, CNRS, FR2424, ABiMS, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - Marta Chiodin
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Ben Busby
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
| | - Sean La
- National Center for Biotechnology Information, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894, USA
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Barnaby, British Columbia, BC, V5A 1S6, Canada
| | - Stacy Pirro
- Iridian Genomes, Inc., 6213 Swords Way, Bethesda, MD, 20817, USA
| | - Allen G Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue NW, Washington DC, 20560, USA
- National Systematics Laboratory of NOAA's Fisheries Service, 1315 East-West Highway, Silver Spring, MD, 20910, USA
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, 326 Mueller, University Park, PA, 16801, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
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22
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Abstract
Placozoa are a morphologically simplistic group of marine animals found globally in tropical and subtropical environments. They consist of two named species, Trichoplax adhaerens and more recently Hoilungia hongkongensis, both with roughly six morphologically distinct cell types. With a sequenced genome, a limited number of cell types, and a simple flattened morphology, Trichoplax is an ideal model organism from which to explore the biology of an animal with a cellular complexity analagous to that of the earliest animals. Using a new approach for identification of gene expression patterns, this research looks at the relationship of Chordin/TgfΒ signaling and the axial patterning system of Placozoa. Our results suggest that placozoans have an oral-aboral axis similar to cnidarians and that the parahoxozoan ancestor (common ancestor of Placozoa and Cnidaria) was likely radially symmetric.
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Affiliation(s)
- Timothy Q DuBuc
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL
- Kewalo Marine Laboratory and the Department of Biology, University of Hawaii, Manoa, Honolulu, HI
- Centre for Chromosome Biology, Bioscience Building, National University of Ireland Galway, Galway, Ireland
| | - Joseph F Ryan
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL
| | - Mark Q Martindale
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL
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23
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Jiang JB, Quattrini AM, Francis WR, Ryan JF, Rodríguez E, McFadden CS. A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. Gigascience 2019; 8:giz026. [PMID: 30942866 PMCID: PMC6446218 DOI: 10.1093/gigascience/giz026] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/15/2019] [Accepted: 02/28/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral "forests," which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri. FINDINGS We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256-448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models. CONCLUSIONS The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.
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Affiliation(s)
- Justin B Jiang
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711, USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711, USA
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, FL 32080, USA
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY 10024, USA
| | - Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711, USA
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24
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Abstract
Addressing the origin of axial-patterning machinery is essential for understanding the evolution of animal form. Historically, sponges, a lineage that branched off early in animal evolution, were thought to lack Hox and ParaHox genes, suggesting that these critical axial-patterning genes arose after sponges diverged. However, a recent study has challenged this long-held doctrine by claiming to identify ParaHox genes (Cdx family) in two calcareous sponge species, Sycon ciliatum and Leucosolenia complicata. We reanalyzed the main data sets in this paper and analyzed an additional data set that expanded the number of bilaterians represented and removed outgroup homeodomains. As in the previous study, our Neighbor-Joining analyses of the original data sets recovered a clade that included sponge and Cdx genes, whereas Bayesian analyses placed these sponge genes within the NKL subclass of homeodomains. Unlike the original study, only one of our two maximum-likelihood analyses was congruent with Cdx genes in sponges. Our analyses of our additional data set led to the sponge genes consistently being placed within the NKL subclass of homeodomains regardless of method or model. Our results show more support for these sponge genes belonging to the NKL subclass, and therefore imply that Hox and ParaHox genes arose after Porifera diverged from the rest of animals.
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Affiliation(s)
- Claudia C Pastrana
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine.,Department of Biology, University of Miami
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine.,Department of Biology, University of Florida
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine.,Department of Biology, University of Florida
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25
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Babonis LS, DeBiasse MB, Francis WR, Christianson LM, Moss AG, Haddock SHD, Martindale MQ, Ryan JF. Integrating Embryonic Development and Evolutionary History to Characterize Tentacle-Specific Cell Types in a Ctenophore. Mol Biol Evol 2018; 35:2940-2956. [PMID: 30169705 PMCID: PMC6278862 DOI: 10.1093/molbev/msy171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The origin of novel traits can promote expansion into new niches and drive speciation. Ctenophores (comb jellies) are unified by their possession of a novel cell type: the colloblast, an adhesive cell found only in the tentacles. Although colloblast-laden tentacles are fundamental for prey capture among ctenophores, some species have tentacles lacking colloblasts and others have lost their tentacles completely. We used transcriptomes from 36 ctenophore species to identify gene losses that occurred specifically in lineages lacking colloblasts and tentacles. We cross-referenced these colloblast- and tentacle-specific candidate genes with temporal RNA-Seq during embryogenesis in Mnemiopsis leidyi and found that both sets of candidates are preferentially expressed during tentacle morphogenesis. We also demonstrate significant upregulation of candidates from both data sets in the tentacle bulb of adults. Both sets of candidates were enriched for an N-terminal signal peptide and protein domains associated with secretion; among tentacle candidates we also identified orthologs of cnidarian toxin proteins, presenting tantalizing evidence that ctenophore tentacles may secrete toxins along with their adhesive. Finally, using cell lineage tracing, we demonstrate that colloblasts and neurons share a common progenitor, suggesting the evolution of colloblasts involved co-option of a neurosecretory gene regulatory network. Together these data offer an initial glimpse into the genetic architecture underlying ctenophore cell-type diversity.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Warren R Francis
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | | | - Anthony G Moss
- Department of Biological Sciences, Auburn University, Auburn, AL
| | | | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL
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26
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Abstract
The complete mitogenome of Echinometra sp. EZ has been described and fully annotated in this study. Phylogenetic analysis of cytochrome c oxidase subunit I (COI) from six Echinometra species confirms that our sample is E. sp. EZ. The mitogenome is 15,698 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding region with an identical organization to other Echinoidea. The E. sp. EZ mitogenome shared ∼99.1% identity to the published Echinometra mathaei mitogenome, differing by 147 SNPs. The E. sp. EZ mitogenome will serve as a resource that can be applied to disentangling the Echinometra species complex and to future population genetic studies of this ecologically important sea urchin species.
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Affiliation(s)
- Remi N Ketchum
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - John A Burt
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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27
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Abstract
Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.
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Affiliation(s)
- Alexandra M Hernandez
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, St. Augustine, FL, USA.,Department of Biology, University of Florida, Gainesville, FL, USA
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28
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Kayal E, Bentlage B, Sabrina Pankey M, Ohdera AH, Medina M, Plachetzki DC, Collins AG, Ryan JF. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evol Biol 2018. [PMCID: PMC5932825 DOI: 10.1186/s12862-018-1142-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including stinging cells, symbiosis, colonial body plans and elaborate life histories. However, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome-scale data for each major cnidarian lineage. Results Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome-scale data that includes representatives of all cnidarian classes. Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction. We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and in the functional classes of the loci they include, but resolve the same topology. We then leverage our phylogenetic resolution of Cnidaria to understand the character histories of several critical organismal traits. Ancestral state reconstruction analyses based on our phylogeny establish several notable organismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary, non-symbiotic polyp that lacked a medusa stage. In addition, Bayes factor tests strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation. Conclusions Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations. Our results add significant clarification on the cnidarian tree of life and the histories of some of these innovations. Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans), thus reviving an evolutionary hypothesis put forward more than a century ago. Electronic supplementary material The online version of this article (10.1186/s12862-018-1142-0) contains supplementary material, which is available to authorized users.
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29
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Sasson DA, Jacquez AA, Ryan JF. The ctenophore Mnemiopsis leidyi regulates egg production via conspecific communication. BMC Ecol 2018; 18:12. [PMID: 29576018 PMCID: PMC5868061 DOI: 10.1186/s12898-018-0169-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 03/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background Communication between individuals of the same species is an important aspect of mating and reproduction in most animals. In simultaneously hermaphroditic species with the ability to self-fertilize, communication with conspecifics can be essential to avoid inbreeding depression. One such behavioral adaptation observed in some simultaneous hermaphrodites is gamete trading. This behavior involves individual hermaphrodites in pairs alternating between reproducing as the male and female, and, as such, necessarily requires communication and coordination between mates. Little is known about communication in ctenophores and conspecific communication has not been described in this group; however, our previous work suggested that the ctenophore Mnemiopsis leidyi might engage in gamete trading. We tested for this possibility by constructing divided arenas (both sealed and permeable) that allowed us to measure individual egg output for paired M. leidyi. Results We found that, when not allowed to interact, size-matched individuals produced similar numbers of eggs on each side of the arena. However, if allowed to interact and exchange water, size-matched pairs produce significantly different numbers of eggs on each side of the arena, suggesting that these pairs use chemical communication to modulate reproduction in the presence of conspecifics as would be expected in gamete trading. Conclusion This finding presents exciting new possibilities for future investigations into the nature of signaling in M. leidyi. Furthermore, this first evidence of conspecific communication in Ctenophora, a group that branched off from the rest of animals more than 600 million years ago, has significant implications for the signaling ability of the last common ancestor of all animals. Electronic supplementary material The online version of this article (10.1186/s12898-018-0169-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel A Sasson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.,Department of Biology, Saint Louis University, Saint Louis, MO, USA
| | - Anya A Jacquez
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.,Department of Biology, Lewis & Clark College, Portland, OR, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA. .,Department of Biology, University of Florida, Gainesville, FL, USA.
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30
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31
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Abstract
BACKGROUND Although most extant animals have separate sexes, simultaneous hermaphrodites can be found in lineages throughout the animal kingdom. However, the sexual modes of key ancestral nodes including the last common ancestor (LCA) of all animals remain unclear. Without these data, it is difficult to infer the reproductive-state transitions that occurred early in animal evolution, and thus a broad understanding of the evolution of animal reproduction remains elusive. In this study, we use a composite phylogeny from four previously published studies, two alternative topologies (ctenophores or sponges as sister to the rest of animals), and multiple phylogenetic approaches to conduct the most extensive analysis to date of the evolution of animal sexual modes. RESULTS Our analyses clarify the sexual mode of many ancestral animal nodes and allow for sound inferences of modal transitions that have occurred in animal history. Our results also indicate that the transition from separate sexes to hermaphroditism has been more common in animal history than the reverse. CONCLUSIONS These results provide the most complete view of the evolution of animal sexual modes to date and provide a framework for future inquiries into the correlation of these transitions with genes, behaviors, and physiology. These results also suggest that mutations promoting hermaphroditism have historically been more likely to invade gonochoristic populations than vice versa.
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Affiliation(s)
- Daniel A Sasson
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
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32
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Martín-Durán JM, Ryan JF, Vellutini BC, Pang K, Hejnol A. Increased taxon sampling reveals thousands of hidden orthologs in flatworms. Genome Res 2017; 27:1263-1272. [PMID: 28400424 PMCID: PMC5495077 DOI: 10.1101/gr.216226.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/10/2017] [Indexed: 11/25/2022]
Abstract
Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages—mistakenly considered new genes—but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its “average” evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.
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Affiliation(s)
- José M Martín-Durán
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway
| | - Joseph F Ryan
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway.,Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, USA
| | - Bruno C Vellutini
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway
| | - Kevin Pang
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen 5006, Norway
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33
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Lewis Ames C, Ryan JF, Bely AE, Cartwright P, Collins AG. Erratum to: A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex. BMC Genomics 2016; 17:980. [PMID: 27894263 PMCID: PMC5126857 DOI: 10.1186/s12864-016-3305-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/16/2016] [Indexed: 11/10/2022] Open
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34
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Abstract
Here we present a report on Ctenopalooza: A meeting of ctenophorologists held at the Whitney Laboratory for Marine Bioscience in St. Augustine, FL, USA, on March 14–15, 2016. In this report, we provide a summary of each of the sessions that occurred during this two-day meeting, which touched on most of the relevant areas of ctenophore biology. The report includes some major themes regarding the future of ctenophore research that emerged during Ctenopalooza. More information can be found at the meeting Web site: http://ctenopalooza.whitney.ufl.edu.
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Battelle BA, Ryan JF, Kempler KE, Saraf SR, Marten CE, Warren WC, Minx PJ, Montague MJ, Green PJ, Schmidt SA, Fulton L, Patel NH, Protas ME, Wilson RK, Porter ML. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata). Genome Biol Evol 2016; 8:1571-89. [PMID: 27189985 PMCID: PMC4898813 DOI: 10.1093/gbe/evw100] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2016] [Indexed: 12/19/2022] Open
Abstract
Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.
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Affiliation(s)
- Barbara-Anne Battelle
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida
| | - Karen E Kempler
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida
| | - Spencer R Saraf
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida Present address: School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY
| | - Catherine E Marten
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida Present address: Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Patrick J Minx
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Michael J Montague
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Pamela J Green
- Department of Plant and Soil Sciences, School of Marine Science and Policy, Delaware Biotechnology Institute, University of Delaware
| | - Skye A Schmidt
- Department of Plant and Soil Sciences, School of Marine Science and Policy, Delaware Biotechnology Institute, University of Delaware
| | - Lucinda Fulton
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Nipam H Patel
- Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkley
| | - Meredith E Protas
- Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkley Present address: Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
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Babonis LS, Martindale MQ, Ryan JF. Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis. BMC Evol Biol 2016; 16:114. [PMID: 27216622 PMCID: PMC4877951 DOI: 10.1186/s12862-016-0683-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The evolution of novel genes is thought to be a critical component of morphological innovation but few studies have explicitly examined the contribution of novel genes to the evolution of novel tissues. Nematosomes, the free-floating cellular masses that circulate through the body cavity of the sea anemone Nematostella vectensis, are the defining apomorphy of the genus Nematostella and are a useful model for understanding the evolution of novel tissues. Although many hypotheses have been proposed, the function of nematosomes is unknown. To gain insight into their putative function and to test hypotheses about the role of lineage-specific genes in the evolution of novel structures, we have re-examined the cellular and molecular biology of nematosomes. RESULTS Using behavioral assays, we demonstrate that nematosomes are capable of immobilizing live brine shrimp (Artemia salina) by discharging their abundant cnidocytes. Additionally, the ability of nematosomes to engulf fluorescently labeled bacteria (E. coli) reveals the presence of phagocytes in this tissue. Using RNA-Seq, we show that the gene expression profile of nematosomes is distinct from that of the tentacles and the mesenteries (their tissue of origin) and, further, that nematosomes (a Nematostella-specific tissue) are enriched in Nematostella-specific genes. CONCLUSIONS Despite the small number of cell types they contain, nematosomes are distinct among tissues, both functionally and molecularly. We provide the first evidence that nematosomes comprise part of the innate immune system in N. vectensis, and suggest that this tissue is potentially an important place to look for genes associated with pathogen stress. Finally, we demonstrate that Nematostella-specific genes comprise a significant proportion of the differentially expressed genes in all three of the tissues we examined and may play an important role in novel cell functions.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA.
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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Long KA, Nossa CW, Sewell MA, Putnam NH, Ryan JF. Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis. Gigascience 2016; 5:20. [PMID: 27175279 PMCID: PMC4863316 DOI: 10.1186/s13742-016-0125-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and sand dollars), and Holothuroidea (sea cucumbers). These animals are known for their pentaradial symmetry as adults, unique water vascular system, mutable collagenous tissues, and endoskeletons of high magnesium calcite. To our knowledge, the only echinoderm species with a genome sequence available to date is Strongylocentrotus pupuratus (Echinoidea). The availability of additional echinoderm genome sequences is crucial for understanding the biology of these animals. FINDINGS Here we present assembled draft genomes of the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis from Illumina sequence data with coverages of 12.5x, 22.5x, and 21.4x, respectively. CONCLUSIONS These data provide a resource for mining gene superfamilies, identifying non-coding RNAs, confirming gene losses, and designing experimental constructs. They will be important comparative resources for future genomic studies in echinoderms.
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Affiliation(s)
- Kyle A Long
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080 USA
| | - Carlos W Nossa
- Department of Ecology and Evolutionary Biology, Rice University, P.O. Box 1892, Houston, TX 77251-1892 USA
| | - Mary A Sewell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Nicholas H Putnam
- Department of Ecology and Evolutionary Biology, Rice University, P.O. Box 1892, Houston, TX 77251-1892 USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080 USA ; Department of Biology, University of Florida, Gainesville, FL 32611-8525 USA
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Sasson DA, Ryan JF. The sex lives of ctenophores: the influence of light, body size, and self-fertilization on the reproductive output of the sea walnut, Mnemiopsis leidyi. PeerJ 2016; 4:e1846. [PMID: 27042395 PMCID: PMC4811168 DOI: 10.7717/peerj.1846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/03/2016] [Indexed: 12/31/2022] Open
Abstract
Ctenophores (comb jellies) are emerging as important animals for investigating fundamental questions across numerous branches of biology (e.g., evodevo, neuroscience and biogeography). A few ctenophore species including, most notably, Mnemiopsis leidyi, are considered as invasive species, adding to the significance of studying ctenophore ecology. Despite the growing interest in ctenophore biology, relatively little is known about their reproduction. Like most ctenophores, M. leidyi is a simultaneous hermaphrodite capable of self-fertilization. In this study, we assess the influence of light on spawning, the effect of body size on spawning likelihood and reproductive output, and the cost of self-fertilization on egg viability in M. leidyi. Our results suggest that M. leidyi spawning is more strongly influenced by circadian rhythms than specific light cues and that body size significantly impacts spawning and reproductive output. Mnemiopsis leidyi adults that spawned alone produced a lower percentage of viable embryos versus those that spawned in pairs, suggesting that self-fertilization may be costly in this species. These results provide insight into the reproductive ecology of M. leidyi and provide a fundamental resource for researchers working with them in the laboratory.
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Affiliation(s)
- Daniel A Sasson
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, United States of America; Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, United States of America; Department of Biology, University of Florida, Gainesville, Florida, United States of America
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Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, Yanai I. The mid-developmental transition and the evolution of animal body plans. Nature 2016; 531:637-641. [PMID: 26886793 PMCID: PMC4817236 DOI: 10.1038/nature16994] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 01/12/2016] [Indexed: 12/25/2022]
Abstract
Animals are grouped into ~35 'phyla' based upon the notion of distinct body plans. Morphological and molecular analyses have revealed that a stage in the middle of development--known as the phylotypic period--is conserved among species within some phyla. Although these analyses provide evidence for their existence, phyla have also been criticized as lacking an objective definition, and consequently based on arbitrary groupings of animals. Here we compare the developmental transcriptomes of ten species, each annotated to a different phylum, with a wide range of life histories and embryonic forms. We find that in all ten species, development comprises the coupling of early and late phases of conserved gene expression. These phases are linked by a divergent 'mid-developmental transition' that uses species-specific suites of signalling pathways and transcription factors. This mid-developmental transition overlaps with the phylotypic period that has been defined previously for three of the ten phyla, suggesting that transcriptional circuits and signalling mechanisms active during this transition are crucial for defining the phyletic body plan and that the mid-developmental transition may be used to define phylotypic periods in other phyla. Placing these observations alongside the reported conservation of mid-development within phyla, we propose that a phylum may be defined as a collection of species whose gene expression at the mid-developmental transition is both highly conserved among them, yet divergent relative to other species.
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Affiliation(s)
- Michal Levin
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Leon Anavy
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Alison G Cole
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Eitan Winter
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Natalia Mostov
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Sally Khair
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Naftalie Senderovich
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Ekaterina Kovalev
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - David H Silver
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Martin Feder
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | | | - Nagayasu Nakanishi
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - David Simmons
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida 32080-8610 USA
| | - Oleg Simakov
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tomas Larsson
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shang-Yun Liu
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Ayelet Jerafi-Vider
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida 32080-8610 USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Ocean Shore Blvd, St Augustine, Florida 32080-8610 USA
| | - Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sandie M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Tamar Hashimshony
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
| | - Itai Yanai
- Department of Biology, Technion - Israel Institute of Technion, Haifa 32000, Israel
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Zwarycz AS, Nossa CW, Putnam NH, Ryan JF. Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida. Genome Biol Evol 2016. [DOI: 10.1093/gbe/evv243 v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Recent phylogenomic evidence suggests that ctenophores may be the sister group to the rest of animals. This phylogenetic arrangement opens the possibility that sponges and placozoans could have lost neural cell types or that the ctenophore nervous system evolved independently. We critically review evidence to date that has been put forth in support of independent evolution of neural cell types in ctenophores. We observe a reluctance in the literature to consider a lost nervous system in sponges and placozoans and suggest that this may be due to historical bias and the commonly misconstrued concept of animal complexity. In support of the idea of loss (or modification beyond recognition), we provide hypothetical scenarios to show how sponges and placozoans may have benefitted from the loss and/or modification of their neural cell types.
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Affiliation(s)
- Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Marta Chiodin
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St Augustine, FL 32080, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA
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Zwarycz AS, Nossa CW, Putnam NH, Ryan JF. Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida. Genome Biol Evol 2015; 8:271-81. [PMID: 26659921 PMCID: PMC4758240 DOI: 10.1093/gbe/evv243] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid lineage and better understand the diversity within the group. We sequenced and assembled the genome of the common earthworm, Eisenia fetida. As a first pass at understanding the diversity within the group, we classified 363 earthworm homeoboxes and compared them with those of the leech Helobdella robusta and the polychaete Capitella teleta. We inferred many gene expansions occurring in the lineage connecting the most recent common ancestor (MRCA) of Capitella and Eisenia to the Eisenia/Helobdella MRCA. Likewise, the lineage leading from the Eisenia/Helobdella MRCA to the leech H. robusta has experienced substantial gains and losses. However, the lineage leading from Eisenia/Helobdella MRCA to E. fetida is characterized by extraordinary levels of homeobox gain. The evolutionary dynamics observed in the homeoboxes of these lineages are very likely to be generalizable to all genes. These genome expansions and losses have likely contributed to the remarkable biology exhibited in this group. These results provide a new perspective from which to understand the diversity within these lineages, show the utility of sub-draft genome assemblies for understanding genomic evolution, and provide a critical resource from which the biology of these animals can be studied.
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Affiliation(s)
- Allison S Zwarycz
- Whitney Laboratory for Marine Bioscience, University of Florida Viterbo University
| | - Carlos W Nossa
- Department of Ecology and Evolutionary Biology, Rice University
| | | | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida Department of Biology, University of Florida
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Abstract
Genome sequences are now available for hundreds of species sampled across the animal phylogeny, bringing key features of animal genome evolution into sharper focus. The field of animal evolutionary genomics has focused on identifying and classifying the diversity genomic features, reconstructing the history of evolutionary changes in animal genomes, and testing hypotheses about the evolutionary relationships of animals. The grand challenges moving forward are to connect evolutionary changes in genomes with particular evolutionary changes in phenotypes, and to determine which changes are driven by selection. This will require far greater genome sampling both across and within species, extensive phenotype data, a well resolved animal phylogeny, and advances in comparative methods.
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Affiliation(s)
- Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St., Providence, RI 02906, USA.
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
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Abstract
The Swofford–Olsen–Waddell–Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in log-likelihood between two topologies to a null distribution of differences in log-likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but it is sensitive to model misspecification, it is computationally burdensome to perform, and its implementation requires the investigator to make several decisions that each have the potential to affect the outcome of the test. We analyzed the effects of multiple factors using seven data sets to which the SOWH test was previously applied. These factors include a number of sample replicates, likelihood software, the introduction of gaps to simulated data, the use of distinct models of evolution for data simulation and likelihood inference, and a suggested test correction wherein an unresolved “zero-constrained” tree is used to simulate sequence data. To facilitate these analyses and future applications of the SOWH test, we wrote SOWHAT, a program that automates the SOWH test. We find that inadequate bootstrap sampling can change the outcome of the SOWH test. The results also show that using a zero-constrained tree for data simulation can result in a wider null distribution and higher p-values, but does not change the outcome of the SOWH test for most of the data sets tested here. These results will help others implement and evaluate the SOWH test and allow us to provide recommendations for future applications of the SOWH test. SOWHAT is available for download from https://github.com/josephryan/SOWHAT.
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Affiliation(s)
- Samuel H Church
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA;
| | - Joseph F Ryan
- Whitney Laboratory for Marine Biosciences, St. Augustine, Florida, USA; and Sars International Centre For Marine Molecular Biology, Bergen, Norway
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA
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Bracken-Grissom H, Collins AG, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien SJ, Paulay G, Putnam N, Ravasi T, Rouse GW, Ryan JF, Schulze A, Wörheide G, Adamska M, Bailly X, Breinholt J, Browne WE, Diaz MC, Evans N, Flot JF, Fogarty N, Johnston M, Kamel B, Kawahara AY, Laberge T, Lavrov D, Michonneau F, Moroz LL, Oakley T, Osborne K, Pomponi SA, Rhodes A, Santos SR, Satoh N, Thacker RW, Van de Peer Y, Voolstra CR, Welch DM, Winston J, Zhou X. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. J Hered 2014; 105:1-18. [PMID: 24336862 DOI: 10.1093/jhered/est084] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.
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Abstract
Recent evidence supports the placement of ctenophores as the most distant relative to all other animals. This revised animal tree means that either the ancestor of all animals possessed neurons (and that sponges and placozoans apparently lost them) or that ctenophores developed them independently. Differentiating between these possibilities is important not only from a historical perspective, but also for the interpretation of a wide range of neurobiological results. In this short perspective paper, I review the evidence in support of each scenario and show that the relationship between the nervous system of ctenophores and other animals is an unsolved, yet tractable problem.
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Affiliation(s)
- Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32080, USA.
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Moreland RT, Nguyen AD, Ryan JF, Schnitzler CE, Koch BJ, Siewert K, Wolfsberg TG, Baxevanis AD. A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics 2014; 15:316. [PMID: 24773765 PMCID: PMC4234515 DOI: 10.1186/1471-2164-15-316] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/31/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mnemiopsis leidyi is a ctenophore native to the coastal waters of the western Atlantic Ocean. A number of studies on Mnemiopsis have led to a better understanding of many key biological processes, and these studies have contributed to the emergence of Mnemiopsis as an important model for evolutionary and developmental studies. Recently, we sequenced, assembled, annotated, and performed a preliminary analysis on the 150-megabase genome of the ctenophore, Mnemiopsis. This sequencing effort has produced the first set of whole-genome sequencing data on any ctenophore species and is amongst the first wave of projects to sequence an animal genome de novo solely using next-generation sequencing technologies. DESCRIPTION The Mnemiopsis Genome Project Portal (http://research.nhgri.nih.gov/mnemiopsis/) is intended both as a resource for obtaining genomic information on Mnemiopsis through an intuitive and easy-to-use interface and as a model for developing customized Web portals that enable access to genomic data. The scope of data available through this Portal goes well beyond the sequence data available through GenBank, providing key biological information not available elsewhere, such as pathway and protein domain analyses; it also features a customized genome browser for data visualization. CONCLUSIONS We expect that the availability of these data will allow investigators to advance their own research projects aimed at understanding phylogenetic diversity and the evolution of proteins that play a fundamental role in metazoan development. The overall approach taken in the development of this Web site can serve as a viable model for disseminating data from whole-genome sequencing projects, framed in a way that best-serves the specific needs of the scientific community.
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Affiliation(s)
| | | | | | | | | | | | | | - Andreas D Baxevanis
- Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA.
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Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SHD, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 2013; 342:1242592. [PMID: 24337300 DOI: 10.1126/science.1242592] [Citation(s) in RCA: 436] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.
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Affiliation(s)
- Joseph F Ryan
- Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Maxwell EK, Ryan JF, Schnitzler CE, Browne WE, Baxevanis AD. MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics 2012; 13:714. [PMID: 23256903 PMCID: PMC3563456 DOI: 10.1186/1471-2164-13-714] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/30/2012] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs play a vital role in the regulation of gene expression and have been identified in every animal with a sequenced genome examined thus far, except for the placozoan Trichoplax. The genomic repertoires of metazoan microRNAs have become increasingly endorsed as phylogenetic characters and drivers of biological complexity. Results In this study, we report the first investigation of microRNAs in a species from the phylum Ctenophora. We use short RNA sequencing and the assembled genome of the lobate ctenophore Mnemiopsis leidyi to show that this species appears to lack any recognizable microRNAs, as well as the nuclear proteins Drosha and Pasha, which are critical to canonical microRNA biogenesis. This finding represents the first reported case of a metazoan lacking a Drosha protein. Conclusions Recent phylogenomic analyses suggest that Mnemiopsis may be the earliest branching metazoan lineage. If this is true, then the origins of canonical microRNA biogenesis and microRNA-mediated gene regulation may postdate the last common metazoan ancestor. Alternatively, canonical microRNA functionality may have been lost independently in the lineages leading to both Mnemiopsis and the placozoan Trichoplax, suggesting that microRNA functionality was not critical until much later in metazoan evolution.
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Affiliation(s)
- Evan K Maxwell
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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DuBuc TQ, Ryan JF, Shinzato C, Satoh N, Martindale MQ. Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor. Integr Comp Biol 2012; 52:835-41. [PMID: 22767488 PMCID: PMC4817585 DOI: 10.1093/icb/ics098] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The key developmental role of the Hox cluster of genes was established prior to the last common ancestor of protostomes and deuterostomes and the subsequent evolution of this cluster has played a major role in the morphological diversity exhibited in extant bilaterians. Despite 20 years of research into cnidarian Hox genes, the nature of the cnidarian-bilaterian ancestral Hox cluster remains unclear. In an attempt to further elucidate this critical phylogenetic node, we have characterized the Hox cluster of the recently sequenced Acropora digitifera genome. The A. digitifera genome contains two anterior Hox genes (PG1 and PG2) linked to an Eve homeobox gene and an Anthox1A gene, which is thought to be either a posterior or posterior/central Hox gene. These data show that the Hox cluster of the cnidarian-bilaterian ancestor was more extensive than previously thought. The results are congruent with the existence of an ancient set of constraints on the Hox cluster and reinforce the importance of incorporating a wide range of animal species to reconstruct critical ancestral nodes.
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Affiliation(s)
- Timothy Q. DuBuc
- *Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Joseph F. Ryan
- *Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- *Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Nori Satoh
- *Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Mark Q. Martindale
- *Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, Honolulu, HI 96813, USA; Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway; Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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