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Kyritsi M, Tsiolas G, Michailidou S, Koukaras K, Argiriou A. Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791. Data Brief 2023; 48:109171. [PMID: 37206897 PMCID: PMC10189087 DOI: 10.1016/j.dib.2023.109171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/29/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.
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Affiliation(s)
- Maria Kyritsi
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - George Tsiolas
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - Sofia Michailidou
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - Konstantinos Koukaras
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences / CERTH, P.O. Box 60361, Thermi, Thessaloniki 57001, Greece
- Department of Food Science and Nutrition, University of the Aegean, Lemnos 81400, Greece
- Corresponding author.
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2
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Chen T, Ren C, Wong NK, Yan A, Sun C, Fan D, Luo P, Jiang X, Zhang L, Ruan Y, Li J, Wu X, Huo D, Huang J, Li X, Wu F, E Z, Cheng C, Zhang X, Wang Y, Hu C. The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins. Proc Natl Acad Sci U S A 2023; 120:e2213512120. [PMID: 37036994 PMCID: PMC10120082 DOI: 10.1073/pnas.2213512120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 02/04/2023] [Indexed: 04/12/2023] Open
Abstract
Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.
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Affiliation(s)
- Ting Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Chunhua Ren
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Nai-Kei Wong
- Clinical Pharmacology Section, Department of Pharmacology, Shantou University Medical College, Shantou515041, China
| | - Aifen Yan
- School of Medicine, Foshan University, Foshan528225, China
| | - Caiyun Sun
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou510275, China
- Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou510275, China
| | - Dingding Fan
- EasyATGC Limited Liability Company, Shenzhen518081, China
| | - Peng Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Xiao Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Lvping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Yao Ruan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiaxi Li
- School of Medicine, Foshan University, Foshan528225, China
| | - Xiaofen Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Da Huo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jiasheng Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Xiaomin Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Feifei Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Zixuan E
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Chuhang Cheng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning530007, China
| | - Xin Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yanhong Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou510301, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning530007, China
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3
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Mashanov V, Machado DJ, Reid R, Brouwer C, Kofsky J, Janies DA. Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research. BMC Genomics 2022; 23:574. [PMID: 35953768 PMCID: PMC9367165 DOI: 10.1186/s12864-022-08750-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/08/2022] [Indexed: 12/13/2022] Open
Abstract
Background Echinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference for experimental studies of regenerative mechanisms. Results We report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,703 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration. Conclusions The sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08750-y).
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Affiliation(s)
- Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 391 Technology Way, Winston-Salem, 27101, NC, USA. .,University of North Florida, Department of Biology, 1 UNF Drive, Jacksonville, 32224, FL, USA.
| | - Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, 28223, NC, USA
| | - Robert Reid
- University of North Carolina at Charlotte, College of Computing and Informatics, North Carolina Research Campus, 150 Research Campus Drive, Kannapolis, 28081, NC, USA
| | - Cory Brouwer
- University of North Carolina at Charlotte, College of Computing and Informatics, North Carolina Research Campus, 150 Research Campus Drive, Kannapolis, 28081, NC, USA
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, 28223, NC, USA
| | - Daniel A Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, 9201 University City Blvd, Charlotte, 28223, NC, USA
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4
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Ahmed W, Gupta S, Singh D, Singh R. Insight of genetic features prevalent in three Echinoderm species (Apostichopus japonicus, Heliocedaris erythrogramma and Asterias rubens) and their evolutionary association using comparative codon pattern analysis. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Khor JM, Ettensohn CA. Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene. eLife 2022; 11:72834. [PMID: 35212624 PMCID: PMC8903837 DOI: 10.7554/elife.72834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid- and bacterial artificial chromosome-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN subcircuits, including specific transcription factor–CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell–cell fusion, providing a paradigm for extending the explanatory power of GRNs.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
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6
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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7
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Medina-Feliciano JG, Pirro S, García-Arrarás JE, Mashanov V, Ryan JF. Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration. FRONTIERS IN MARINE SCIENCE 2021; 8:603410. [PMID: 38741925 PMCID: PMC11090492 DOI: 10.3389/fmars.2021.603410] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Regeneration is one of the most fascinating and yet least understood biological processes. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Among echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species has been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 89,105 scaffolds totaling 1.1 gigabases with an N50 of 25 kilobases. Our BUSCO assessment of the genome resulted in 894 (91.4%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 51,415 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in the regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.
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Affiliation(s)
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD, United States
| | - Jose E. García-Arrarás
- Biology Department, University of Puerto Rico, Río Piedras Campus, San Juan, PR, United States
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, United States
| | - Joseph F. Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, United States
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8
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Torkian B, Hann S, Preisner E, Norman RS. BLAST-QC: automated analysis of BLAST results. ENVIRONMENTAL MICROBIOME 2020; 15:15. [PMID: 33902722 PMCID: PMC8066848 DOI: 10.1186/s40793-020-00361-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/13/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The Basic Local Alignment Search Tool (BLAST) from NCBI is the preferred utility for sequence alignment and identification for bioinformatics and genomics research. Among researchers using NCBI's BLAST software, it is well known that analyzing the results of a large BLAST search can be tedious and time-consuming. Furthermore, with the recent discussions over the effects of parameters such as '-max_target_seqs' on the BLAST heuristic search process, the use of these search options are questionable. This leaves using a stand-alone parser as one of the only options of condensing these large datasets, and with few available for download online, the task is left to the researcher to create a specialized piece of software anytime they need to analyze BLAST results. The need for a streamlined and fast script that solves these issues and can be easily implemented into a variety of bioinformatics and genomics workflows was the initial motivation for developing this software. RESULTS In this study, we demonstrate the effectiveness of BLAST-QC for analysis of BLAST results and its desirability over the other available options. Applying genetic sequence data from our bioinformatic workflows, we establish BLAST_QC's superior runtime when compared to existing parsers developed with commonly used BioPerl and BioPython modules, as well as C and Java implementations of the BLAST_QC program. We discuss the 'max_target_seqs' parameter, the usage of and controversy around the use of the parameter, and offer a solution by demonstrating the ability of our software to provide the functionality this parameter was assumed to produce, as well as a variety of other parsing options. Executions of the script on example datasets are given, demonstrating the implemented functionality and providing test-cases of the program. BLAST-QC is designed to be integrated into existing software, and we establish its effectiveness as a module of workflows or other processes. CONCLUSIONS BLAST-QC provides the community with a simple, lightweight and portable Python script that allows for easy quality control of BLAST results while avoiding the drawbacks of other options. This includes the uncertain results of applying the -max_target_seqs parameter or relying on the cumbersome dependencies of other options like BioPerl, Java, etc. which add complexity and run time when running large data sets of sequences. BLAST-QC is ideal for use in high-throughput workflows and pipelines common in bioinformatic and genomic research, and the script has been designed for portability and easy integration into whatever type of processes the user may be running.
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Affiliation(s)
- Behzad Torkian
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC, 29208, USA
| | - Spencer Hann
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC, 29208, USA
| | - Eva Preisner
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC, 29208, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, University of South Carolina, 921 Assembly Street, Columbia, SC, 29208, USA.
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9
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Chen Y, Li Y, Zhan Y, Hu W, Sun J, Zhang W, Song J, Li D, Chang Y. Identification of molecular markers for superior quantitative traits in a novel sea cucumber strain by comparative microRNA-mRNA expression profiling. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 35:100686. [PMID: 32413829 DOI: 10.1016/j.cbd.2020.100686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023]
Abstract
To investigate the adaptability of Apostichopus japonicus (A. japonicus) strain "Anyuan No. 1" in the South China Sea, field monitoring and microRNA-mRNA integrated analyses were conducted between "Anyuan No. 1" and a regular A. japonicus population from Wendeng (Shandong Province, as a control) in the Xiapu farming area in Fujian Province, China. The results showed that "Anyuan No. 1" exhibited greater body weight increase and a higher number of papillae compared to the control during two and a half months of field monitoring. Comparative microRNA (miRNA) and mRNA transcriptome analyses identified 12 differentially expressed miRNAs (DEMs) and 165 differentially expressed genes (DEGs) in "Anyuan No. 1" compared to the control. Long-chain specific acyl-CoA dehydrogenase (ACADL), transmembrane protein 251 (TMEM251), dehydrogenase/reductase SDR family protein 7-like (Dhrs7), insulin-like growth factor-binding protein 7 (IGFBP-7), CDK5 regulatory subunit-associated protein 1 (CDK5RAP1), visual pigment-like receptor peropsin, 39S ribosomal protein, miR-10, miR-153, miR-7, and miR-3529 were identified as gene and miRNA candidates correlated with superior economic traits in "Anyuan No. 1". Collectively, "Anyuan No. 1" is suitable for large-scale cultivation extension due to its better adaptability to the South China Sea area. Furthermore, we identified "miR10-ACADL" as a potential module for further molecular marker-assisted selective breeding of A. japonicus.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yingying Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
| | - Wanbin Hu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jingxian Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Dantong Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023, PR China.
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10
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Utzeri VJ, Ribani A, Bovo S, Taurisano V, Calassanzio M, Baldo D, Fontanesi L. Microscopic ossicle analyses and the complete mitochondrial genome sequence of Holothuria (Roweothuria) polii (Echinodermata; Holothuroidea) provide new information to support the phylogenetic positioning of this sea cucumber species. Mar Genomics 2019; 51:100735. [PMID: 31866382 DOI: 10.1016/j.margen.2019.100735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
Sea cucumbers (Holothuroidea) are ecologically important organisms for their bioturbation and alkalinization activities of the seabed. These species are extensively fished as they are considered luxury food. Sea cucumbers are also relevant for biomedical studies and the production of bioactive compounds. A few initiatives are recently evaluating sea cucumbers as novel aquaculture species. The aim of this study was to provide morphological and genetic information useful for the identification of Holothuria polii, the white spot sea cucumber (a common species of the Mediterranean Sea). We generated the complete sequence of the mitochondrial DNA (mtDNA) genome of this species and combined it with a detailed ossicle characterization of the sequenced specimen by scanning electron microscopic analysis. Ossicles (known also as sclerites) are anatomical features that can discriminate Holothuroidea species, including the closely related ones of the genus Holothuria. The complete mitochondrial genome was assembled, functionally annotated and then used to evaluate the phylogenetic relationship of H. polii against the other few Holothuroidea species for which the whole mtDNA was available. The 15,907 bp H. polii mtDNA sequence has the same gene order already reported for H. scabra, H. forskali and other species of the same class. Cox1 and 16S gene sequences were informative for species identification across the genus and could be used for the authentication of commercialized Holothuria spp. The mitochondrial genome sequence presented here provides the basis to a future analysis of the variability of H. polii populations in the Mediterranean region.
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Affiliation(s)
- Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Valeria Taurisano
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Matteo Calassanzio
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - David Baldo
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy.
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11
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Li Y, Wang R, Xun X, Wang J, Bao L, Thimmappa R, Ding J, Jiang J, Zhang L, Li T, Lv J, Mu C, Hu X, Zhang L, Liu J, Li Y, Yao L, Jiao W, Wang Y, Lian S, Zhao Z, Zhan Y, Huang X, Liao H, Wang J, Sun H, Mi X, Xia Y, Xing Q, Lu W, Osbourn A, Zhou Z, Chang Y, Bao Z, Wang S. Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation. Cell Discov 2018; 4:29. [PMID: 29951224 PMCID: PMC6018497 DOI: 10.1038/s41421-018-0030-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/18/2018] [Accepted: 04/08/2018] [Indexed: 12/27/2022] Open
Abstract
Echinoderms exhibit several fascinating evolutionary innovations that are rarely seen in the animal kingdom, but how these animals attained such features is not well understood. Here we report the sequencing and analysis of the genome and extensive transcriptomes of the sea cucumber Apostichopus japonicus, a species from a special echinoderm group with extraordinary potential for saponin synthesis, aestivation and organ regeneration. The sea cucumber does not possess a reorganized Hox cluster as previously assumed for all echinoderms, and the spatial expression of Hox7 and Hox11/13b potentially guides the embryo-to-larva axial transformation. Contrary to the typical production of lanosterol in animal cholesterol synthesis, the oxidosqualene cyclase of sea cucumber produces parkeol for saponin synthesis and has "plant-like" motifs suggestive of convergent evolution. The transcriptional factors Klf2 and Egr1 are identified as key regulators of aestivation, probably exerting their effects through a clock gene-controlled process. Intestinal hypometabolism during aestivation is driven by the DNA hypermethylation of various metabolic gene pathways, whereas the transcriptional network of intestine regeneration involves diverse signaling pathways, including Wnt, Hippo and FGF. Decoding the sea cucumber genome provides a new avenue for an in-depth understanding of the extraordinary features of sea cucumbers and other echinoderms.
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Affiliation(s)
- Yuli Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Ruijia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Xiaogang Xun
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Lisui Bao
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637 USA
| | - Ramesha Thimmappa
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Jun Ding
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023 China
| | - Liheng Zhang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Tianqi Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Chuang Mu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Yuqiang Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Lijie Yao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Yangfan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Shanshan Lian
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Zelong Zhao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023 China
| | - Yaoyao Zhan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Jia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Hongzhen Sun
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Xue Mi
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Yu Xia
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Wei Lu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023 China
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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12
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Staal J, Driege Y, Haegman M, Borghi A, Hulpiau P, Lievens L, Gul IS, Sundararaman S, Gonçalves A, Dhondt I, Pinzón JH, Braeckman BP, Technau U, Saeys Y, van Roy F, Beyaert R. Ancient Origin of the CARD-Coiled Coil/Bcl10/MALT1-Like Paracaspase Signaling Complex Indicates Unknown Critical Functions. Front Immunol 2018; 9:1136. [PMID: 29881386 PMCID: PMC5978004 DOI: 10.3389/fimmu.2018.01136] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/07/2018] [Indexed: 12/16/2022] Open
Abstract
The CARD–coiled coil (CC)/Bcl10/MALT1-like paracaspase (CBM) signaling complexes composed of a CARD–CC family member (CARD-9, -10, -11, or -14), Bcl10, and the type 1 paracaspase MALT1 (PCASP1) play a pivotal role in immunity, inflammation, and cancer. Targeting MALT1 proteolytic activity is of potential therapeutic interest. However, little is known about the evolutionary origin and the original functions of the CBM complex. Type 1 paracaspases originated before the last common ancestor of planulozoa (bilaterians and cnidarians). Notably in bilaterians, Ecdysozoa (e.g., nematodes and insects) lacks Bcl10, whereas other lineages have a Bcl10 homolog. A survey of invertebrate CARD–CC homologs revealed such homologs only in species with Bcl10, indicating an ancient common origin of the entire CBM complex. Furthermore, vertebrate-like Syk/Zap70 tyrosine kinase homologs with the ITAM-binding SH2 domain were only found in invertebrate organisms with CARD–CC/Bcl10, indicating that this pathway might be related to the original function of the CBM complex. Moreover, the type 1 paracaspase sequences from invertebrate organisms that have CARD–CC/Bcl10 are more similar to vertebrate paracaspases. Functional analysis of protein–protein interactions, NF-κB signaling, and CYLD cleavage for selected invertebrate type 1 paracaspase and Bcl10 homologs supports this scenario and indicates an ancient origin of the CARD–CC/Bcl10/paracaspase signaling complex. By contrast, many of the known MALT1-associated activities evolved fairly recently, indicating that unknown functions are at the basis of the protein conservation. As a proof-of-concept, we provide initial evidence for a CBM- and NF-κB-independent neuronal function of the Caenorhabditis elegans type 1 paracaspase malt-1. In conclusion, this study shows how evolutionary insights may point at alternative functions of MALT1.
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Affiliation(s)
- Jens Staal
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yasmine Driege
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mira Haegman
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Alice Borghi
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paco Hulpiau
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Unit of Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
| | - Laurens Lievens
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Ismail Sahin Gul
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Unit of Molecular Cell Biology, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
| | - Srividhya Sundararaman
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Unit of Molecular Cell Biology, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
| | - Amanda Gonçalves
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,VIB Bio Imaging Core Gent, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
| | - Ineke Dhondt
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Ghent, Belgium
| | - Jorge H Pinzón
- Department of Biology, University of Texas Arlington, Arlington, TX, United States
| | - Bart P Braeckman
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Ghent, Belgium
| | - Ulrich Technau
- Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Yvan Saeys
- Unit of Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Frans van Roy
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Unit of Molecular Cell Biology, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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13
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Zueva O, Khoury M, Heinzeller T, Mashanova D, Mashanov V. The complex simplicity of the brittle star nervous system. Front Zool 2018; 15:1. [PMID: 29434647 PMCID: PMC5796562 DOI: 10.1186/s12983-017-0247-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/11/2017] [Indexed: 12/15/2022] Open
Abstract
Background Brittle stars (Ophiuroidea, Echinodermata) have been increasingly used in studies of animal behavior, locomotion, regeneration, physiology, and bioluminescence. The success of these studies directly depends on good working knowledge of the ophiuroid nervous system. Results Here, we describe the arm nervous system at different levels of organization, including the microanatomy of the radial nerve cord and peripheral nerves, ultrastructure of the neural tissue, and localization of different cell types using specific antibody markers. We standardize the nomenclature of nerves and ganglia, and provide an anatomically accurate digital 3D model of the arm nervous system as a reference for future studies. Our results helped identify several general features characteristic to the adult echinoderm nervous system, including the extensive anatomical interconnections between the ectoneural and hyponeural components, neuroepithelial organization of the central nervous system, and the supporting scaffold of the neuroepithelium formed by radial glial cells. In addition, we provide further support to the notion that the echinoderm radial glia is a complex and diverse cell population. We also tested the suitability of a range of specific cell-type markers for studies of the brittle star nervous system and established that the radial glial cells are reliably labeled with the ERG1 antibodies, whereas the best neuronal markers are acetylated tubulin, ELAV, and synaptotagmin B. The transcription factor Brn1/2/4 – a marker of neuronal progenitors – is expressed not only in neurons, but also in a subpopulation of radial glia. For the first time, we describe putative ophiuroid proprioceptors associated with the hyponeural part of the central nervous system. Conclusions Together, our data help establish both the general principles of neural architecture common to the phylum Echinodermata and the specific ophiuroid features. Electronic supplementary material The online version of this article (10.1186/s12983-017-0247-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olga Zueva
- 1University of North Florida, FL, Jacksonville, USA
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14
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García-Arrarás JE, Lázaro-Peña MI, Díaz-Balzac CA. Holothurians as a Model System to Study Regeneration. Results Probl Cell Differ 2018; 65:255-283. [PMID: 30083924 DOI: 10.1007/978-3-319-92486-1_13] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Echinoderms possess an incredible regenerative capacity. Within this phylum, holothurians, better known as sea cucumbers, can regenerate most of their internal and external organs. While regeneration has been studied in several species, the most recent and extensive studies have been done in the species Holothuria glaberrima, the focus of most of our discussion. This chapter presents the model system and integrates the work that has been done to determine the major steps that take place, during regeneration of the intestinal and nervous system, from wound healing to the reestablishment of original function. We describe the cellular and molecular events associated with the regeneration processes and also describe the techniques that have been used, discuss the results, and explain the gaps in our knowledge that remain. We expect that the information provided here paves the road for new and young investigators to continue the study of the amazing potential of regeneration in members of the Echinodermata and how these studies will shed some light into the mechanisms that are common to many regenerative processes.
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Affiliation(s)
- José E García-Arrarás
- Department of Biology, University of Puerto Rico - Río Piedras Campus, San Juan, Puerto Rico.
| | - María I Lázaro-Peña
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Carlos A Díaz-Balzac
- Department of Medicine, University of Rochester Medical Center, Strong Memorial Hospital, Rochester, NY, USA
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15
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Buckley KM, Rast JP. An Organismal Model for Gene Regulatory Networks in the Gut-Associated Immune Response. Front Immunol 2017; 8:1297. [PMID: 29109720 PMCID: PMC5660111 DOI: 10.3389/fimmu.2017.01297] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/27/2017] [Indexed: 12/27/2022] Open
Abstract
The gut epithelium is an ancient site of complex communication between the animal immune system and the microbial world. While elements of self-non-self receptors and effector mechanisms differ greatly among animal phyla, some aspects of recognition, regulation, and response are broadly conserved. A gene regulatory network (GRN) approach provides a means to investigate the nature of this conservation and divergence even as more peripheral functional details remain incompletely understood. The sea urchin embryo is an unparalleled experimental model for detangling the GRNs that govern embryonic development. By applying this theoretical framework to the free swimming, feeding larval stage of the purple sea urchin, it is possible to delineate the conserved regulatory circuitry that regulates the gut-associated immune response. This model provides a morphologically simple system in which to efficiently unravel regulatory connections that are phylogenetically relevant to immunity in vertebrates. Here, we review the organism-wide cellular and transcriptional immune response of the sea urchin larva. A large set of transcription factors and signal systems, including epithelial expression of interleukin 17 (IL17), are important mediators in the activation of the early gut-associated response. Many of these have homologs that are active in vertebrate immunity, while others are ancient in animals but absent in vertebrates or specific to echinoderms. This larval model provides a means to experimentally characterize immune function encoded in the sea urchin genome and the regulatory interconnections that control immune response and resolution across the tissues of the organism.
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Affiliation(s)
- Katherine M Buckley
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
| | - Jonathan P Rast
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada
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16
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High-throughput targeted screening in triple-negative breast cancer cells identifies Wnt-inhibiting activities in Pacific brittle stars. Sci Rep 2017; 7:11964. [PMID: 28931883 PMCID: PMC5607299 DOI: 10.1038/s41598-017-12232-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/06/2017] [Indexed: 02/06/2023] Open
Abstract
Pro-proliferative oncogenic signaling is one of the hallmarks of cancer. Specific targeting of such signaling pathways is one of the main approaches to modern anti-cancer drug discovery, as opposed to more traditional search for general cytotoxic agents. Natural products, especially from marine sources, represent a largely untapped source of chemical diversity, which so far have mostly been screened for cytotoxicity. Here we present a pioneering pipeline of high-throughput screening of marine-based activities targeted against the Wnt signaling pathway, which is one of the key factors in oncogenic transformation, growth and metastasis in different cancers, including the devastating triple-negative breast cancer (TNBC) currently lacking any targeted therapies. This pipeline consisted of collection and characterization of numerous invertebrates during the SokhoBio expedition to the Kuril Basin in North Pacific, preparation of extracts from these specimen, and their screening in dedicated assays monitoring Wnt signaling in TNBC cells. This approach yielded a number of promising hits, including highly specific anti-Wnt activities targeting multiple levels within the Wnt pathway from Ophiura irrorata and other Pacific brittle stars.
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17
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Jo J, Oh J, Lee HG, Hong HH, Lee SG, Cheon S, Kern EMA, Jin S, Cho SJ, Park JK, Park C. Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants. Gigascience 2017; 6:1-6. [PMID: 28369350 PMCID: PMC5437941 DOI: 10.1093/gigascience/giw006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/03/2017] [Indexed: 11/14/2022] Open
Abstract
The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 Gb of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb, which is about 80.5% of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986%. The resulting draft genome assembly comprising 132 607 scaffolds with an N50 value of 10.5 kb contains a total of 21 771 predicted protein-coding genes. We identified 6.6-14.5 million heterozygous single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research.
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Affiliation(s)
- Jihoon Jo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyun-Gwan Lee
- Marine Ecological Disturbing and Harmful Organisms Research Center, Department of Oceanography, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyun-Hee Hong
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Elizabeth M A Kern
- Division of EcoScience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soyeong Jin
- Division of EcoScience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sung-Jin Cho
- Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
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18
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Oba Y, Stevani CV, Oliveira AG, Tsarkova AS, Chepurnykh TV, Yampolsky IV. Selected Least Studied but not Forgotten Bioluminescent Systems. Photochem Photobiol 2017; 93:405-415. [DOI: 10.1111/php.12704] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/15/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Yuichi Oba
- Department of Environmental Biology; Chubu University; Kasugai Japan
| | - Cassius V. Stevani
- Departamento de Química Fundamental; Instituto de Química; Universidade de São Paulo; São Paulo Brazil
| | - Anderson G. Oliveira
- Departamento de Oceanografia Física; Química e Geológica; Instituto Oceanográfico; Universidade de São Paulo; São Paulo Brazil
| | - Aleksandra S. Tsarkova
- Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Pirogov Russian National Research Medical University; Moscow Russia
| | - Tatiana V. Chepurnykh
- Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Pirogov Russian National Research Medical University; Moscow Russia
| | - Ilia V. Yampolsky
- Institute of Bioorganic Chemistry; Russian Academy of Sciences; Moscow Russia
- Pirogov Russian National Research Medical University; Moscow Russia
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19
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Cary GA, Hinman VF. Echinoderm development and evolution in the post-genomic era. Dev Biol 2017; 427:203-211. [PMID: 28185788 DOI: 10.1016/j.ydbio.2017.02.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 01/01/2023]
Abstract
The highly recognizable animals within the phylum Echinodermata encompass an enormous disparity of adult and larval body plans. The extensive knowledge of sea urchin development has culminated in the description of the exquisitely detailed gene regulatory network (GRN) that governs the specification of various embryonic territories. This information provides a unique opportunity for comparative studies in other echinoderm taxa to understand the evolution and developmental mechanisms underlying body plan change. This review focuses on recent work that has utilized new genomic resources and systems-level experiments to address questions of evolutionary developmental biology. In particular, we synthesize the results of several recent studies from various echinoderm classes that have explored the development and evolution of the larval skeleton, which is a major feature that distinguishes the two predominant larval subtypes within the Phylum. We specifically examine the ways in which GRNs can evolve, either through cis regulatory and/or protein-level changes in transcription factors. We also examine recent work comparing evolution across shorter time scales that occur within and between species of sea urchin, and highlight the kinds of questions that can be addressed by these comparisons. The advent of new genomic and transcriptomic datasets in additional species from all classes of echinoderm will continue to empower the use of these taxa for evolutionary developmental studies.
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Affiliation(s)
- Gregory A Cary
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, United States
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, United States.
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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] [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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