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Pan W, Wang X, Ren C, Jiang X, Gong S, Xie Z, Wong NK, Li X, Huang J, Fan D, Luo P, Yang Y, Ren X, Yu S, Qin Z, Wu X, Huo D, Ma B, Liu Y, Zhang X, E Z, Liang J, Sun H, Yuan L, Liu X, Cheng C, Long H, Li J, Wang Y, Hu C, Chen T. Sea cucumbers and their symbiotic microbiome have evolved to feed on seabed sediments. Nat Commun 2024; 15:8825. [PMID: 39394205 DOI: 10.1038/s41467-024-53205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 10/01/2024] [Indexed: 10/13/2024] Open
Abstract
Sea cucumbers are predominant deposit feeders in benthic ecosystems, providing protective benefits to coral reefs by reducing disease prevalence. However, how they receive sufficient nutrition from seabed sediments remains poorly understood. Here, we investigate Holothuria leucospilota, an ecologically significant tropical sea cucumber, to elucidate digestive mechanisms underlying marine deposit-feeding. Genomic analysis reveals intriguing evolutionary adaptation characterized by an expansion of digestive carbohydrase genes and a contraction of digestive protease genes, suggesting specialization in digesting microalgae. Developmentally, two pivotal dietary shifts, namely, from endogenous nutrition to planktonic feeding, and from planktonic feeding to deposit feeding, induce changes in digestive tract enzyme profiles, with adults mainly expressing carbohydrases and lipases. A nuanced symbiotic relationship exists between gut microbiota and the host, namely, specific resident bacteria supply crucial enzymes for food digestion, while other bacteria are digested and provide assimilable nutrients. Our study further identifies Holothuroidea lineage-specific lysozymes that are restrictedly expressed in the intestines to support bacterial digestion. Overall, this work advances our knowledge of the evolutionary innovations in the sea cucumber digestive system which enable them to efficiently utilize nutrients from seabed sediments and promote food recycling within marine ecosystems.
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Affiliation(s)
- Wenjie Pan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunhua Ren
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao Jiang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenyu Xie
- Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, China
| | - Nai-Kei Wong
- Clinical Pharmacology Section, Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Xiaomin Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiasheng Huang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dingding Fan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Peng Luo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yun Yang
- Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xinyue Ren
- School of Life sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Suzhong Yu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhou Qin
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaofen Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Da Huo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bo Ma
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Zixuan E
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingxuan Liang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Lihong Yuan
- School of Life sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xujia Liu
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
| | - Chuhang Cheng
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
| | - Hao Long
- Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, China
| | - Jianlong Li
- Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, China
| | - Yanhong Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chaoqun Hu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Ting Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
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2
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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Miranda-Negrón Y, García-Arrarás JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601561. [PMID: 39005414 PMCID: PMC11244903 DOI: 10.1101/2024.07.01.601561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In holothurians, the regenerative process following evisceration involves the development of a "rudiment" or "anlage" at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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Perillo M, Sepe RM, Paganos P, Toscano A, Annunziata R. Sea cucumbers: an emerging system in evo-devo. EvoDevo 2024; 15:3. [PMID: 38368336 PMCID: PMC10874539 DOI: 10.1186/s13227-023-00220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/24/2023] [Indexed: 02/19/2024] Open
Abstract
A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used to investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As a phylum of the sister group to chordates, echinoderms extensively contributed to our knowledge of embryonic patterning, organ development and cell-type evolution. Echinoderms display a variety of larval forms with diverse shapes, making them a suitable group to compare the evolution of embryonic developmental strategies. However, because of the laboratory accessibility and the already available techniques, most studies focus on sea urchins and sea stars mainly. As a comparative approach, the field would benefit from including information on other members of this group, like the sea cucumbers (holothuroids), for which little is known on the molecular basis of their development. Here, we review the spawning and culture methods, the available morphological and molecular information, and the current state of genomic and transcriptomic resources on sea cucumbers. With the goal of making this system accessible to the broader community, we discuss how sea cucumber embryos and larvae can be a powerful system to address the open questions in evo-devo, including understanding the origins of bilaterian structures.
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Affiliation(s)
- Margherita Perillo
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA, 02543, USA.
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Rosa Maria Sepe
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Periklis Paganos
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Alfonso Toscano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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4
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Zhong S, Ma X, Jiang Y, Liu X, Zeng M, Zhao L, Huang L, Huang G, Zhao Y, Qiao Y, Chen X. The draft genome of the tropical sea cucumber Stichopus monotuberculatus (Echinodermata, Stichopodidae) reveals critical genes in fucosylated chondroitin sulfates biosynthetic pathway. Front Genet 2023; 14:1182002. [PMID: 37252657 PMCID: PMC10213396 DOI: 10.3389/fgene.2023.1182002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Shengping Zhong
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Yan Jiang
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Xujia Liu
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, China
| | - Mengqing Zeng
- Guangxi Engineering Technology Research Center for Marine Aquaculture, Guangxi Institute of Oceanology Co., Ltd., Beihai, China
| | - Longyan Zhao
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Lianghua Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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5
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Wang Q, Cao T, Wang Y, Li X, Wang Y. Genome-wide identification and comparative analysis of Dmrt genes in echinoderms. Sci Rep 2023; 13:7664. [PMID: 37169947 PMCID: PMC10175285 DOI: 10.1038/s41598-023-34819-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
The Dmrt (Doublesex-mab3-related transcription factor) gene family is a class of crucial transcription factors characterized by one or several conserved DM (Doublesex/Mab-3) domains. Dmrt family genes can participate in various physiological developmental processes, especially in sex determination/differentiation. Echinoderms are extremely important research objects in various fields, such as sex determination/differentiation and neuroscience. However, to date, the genome-wide characterization and analysis of Dmrt genes in echinoderms have not been investigated. In this study, the identification and analysis of Dmrt genes in 11 representative echinoderms were performed using bioinformatics methods. A total of 43 Dmrt genes have been found in the studied echinoderms, and the number of Dmrt genes in different species ranges from 2 to 5. The phylogenetic tree showed that all Dmrt genes from echinoderms can be subdivided into 5 classes, the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and a novel Dmrt (starfish-specific) class. Furthermore, selective pressure assessment suggested that the Dmrt genes underwent purifying selection pressure. In general, this study provides a molecular basis for echinoderm Dmrt genes and may serve as a reference for in-depth phylogenomics.
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Affiliation(s)
- Quanchao Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Key Laboratory of Ecological Warning, Protection and Restoration for Bohai Sea, Ministry of Natural Resources, Qingdao, 266061, China
| | - Tiangui Cao
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Yanxia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xiaojing Li
- Yantai Vocational College, Yantai, 264670, China
| | - Yue Wang
- Yantai Vocational College, Yantai, 264670, China.
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6
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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: 9] [Impact Index Per Article: 9.0] [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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7
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Auger NA, Medina-Feliciano JG, Quispe-Parra DJ, Colón-Marrero S, Ortiz-Zuazaga H, García-Arrarás JE. Characterization and Expression of Holothurian Wnt Signaling Genes during Adult Intestinal Organogenesis. Genes (Basel) 2023; 14:309. [PMID: 36833237 PMCID: PMC9957329 DOI: 10.3390/genes14020309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Wnt signaling has been shown to play multiple roles in regenerative processes, one of the most widely studied of which is the regeneration of the intestinal luminal epithelia. Most studies in this area have focused on self-renewal of the luminal stem cells; however, Wnt signaling may also have more dynamic functions, such as facilitating intestinal organogenesis. To explore this possibility, we employed the sea cucumber Holothuria glaberrima that can regenerate a full intestine over the course of 21 days after evisceration. We collected RNA-seq data from various intestinal tissues and regeneration stages and used these data to define the Wnt genes present in H. glaberrima and the differential gene expression (DGE) patterns during the regenerative process. Twelve Wnt genes were found, and their presence was confirmed in the draft genome of H. glaberrima. The expressions of additional Wnt-associated genes, such as Frizzled and Disheveled, as well as genes from the Wnt/β-catenin and Wnt/Planar Cell Polarity (PCP) pathways, were also analyzed. DGE showed unique distributions of Wnt in early- and late-stage intestinal regenerates, consistent with the Wnt/β-catenin pathway being upregulated during early-stages and the Wnt/PCP pathway being upregulated during late-stages. Our results demonstrate the diversity of Wnt signaling during intestinal regeneration, highlighting possible roles in adult organogenesis.
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Affiliation(s)
- Noah A. Auger
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
| | | | - David J. Quispe-Parra
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
| | - Stephanie Colón-Marrero
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
| | - Humberto Ortiz-Zuazaga
- Department of Computer Science, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
| | - José E. García-Arrarás
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
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8
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Miranda-Negrón Y, García-Arrarás JE. Radial glia and radial glia-like cells: Their role in neurogenesis and regeneration. Front Neurosci 2022; 16:1006037. [PMID: 36466166 PMCID: PMC9708897 DOI: 10.3389/fnins.2022.1006037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 01/25/2024] Open
Abstract
Radial glia is a cell type traditionally associated with the developing nervous system, particularly with the formation of cortical layers in the mammalian brain. Nonetheless, some of these cells, or closely related types, called radial glia-like cells are found in adult central nervous system structures, functioning as neurogenic progenitors in normal homeostatic maintenance and in response to injury. The heterogeneity of radial glia-like cells is nowadays being probed with molecular tools, primarily by the expression of specific genes that define cell types. Similar markers have identified radial glia-like cells in the nervous system of non-vertebrate organisms. In this review, we focus on adult radial glia-like cells in neurogenic processes during homeostasis and in response to injury. We highlight our results using a non-vertebrate model system, the echinoderm Holothuria glaberrima where we have described a radial glia-like cell that plays a prominent role in the regeneration of the holothurian central nervous system.
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Affiliation(s)
| | - José E. García-Arrarás
- Department of Biology, College of Natural Sciences, University of Puerto Rico, San Juan, Puerto Rico
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9
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Mittal V, Reid RW, Machado DJ, Mashanov V, Janies DA. EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms. BMC Genom Data 2022; 23:75. [PMID: 36274129 PMCID: PMC9590158 DOI: 10.1186/s12863-022-01090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
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Affiliation(s)
- Varnika Mittal
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA.
| | - Robert W Reid
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
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Su F, Yang H, Sun L. A Review of Histocytological Events and Molecular Mechanisms Involved in Intestine Regeneration in Holothurians. BIOLOGY 2022; 11:1095. [PMID: 35892951 PMCID: PMC9332576 DOI: 10.3390/biology11081095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
Most species of the class Holothuroidea are able to regenerate most of their internal organs following a typical evisceration process, which is a unique mechanism that allows sea cucumbers to survive in adverse environments. In this review, we compare autotomy among different type of sea cucumber and summarize the histocytological events that occur during the five stages of intestinal regeneration. Multiple cytological activities, such as apoptosis and dedifferentiation, take place during wound healing and anlage formation. Many studies have focused on the molecular regulation mechanisms that underlie regeneration, and herein we describe the techniques that have been used as well as the development-related signaling pathways and key genes that are significantly expressed during intestinal regeneration. Future analyses of the underlying mechanisms responsible for intestinal regeneration should include mapping at the single-cell level. Studies of visceral regeneration in echinoderms provide a unique perspective for understanding whole-body regeneration or appendage regeneration.
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Affiliation(s)
- Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.S.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
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11
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Medina-Feliciano JG, García-Arrarás JE. Regeneration in Echinoderms: Molecular Advancements. Front Cell Dev Biol 2021; 9:768641. [PMID: 34977019 PMCID: PMC8718600 DOI: 10.3389/fcell.2021.768641] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Which genes and gene signaling pathways mediate regenerative processes? In recent years, multiple studies, using a variety of animal models, have aimed to answer this question. Some answers have been obtained from transcriptomic and genomic studies where possible gene and gene pathway candidates thought to be involved in tissue and organ regeneration have been identified. Several of these studies have been done in echinoderms, an animal group that forms part of the deuterostomes along with vertebrates. Echinoderms, with their outstanding regenerative abilities, can provide important insights into the molecular basis of regeneration. Here we review the available data to determine the genes and signaling pathways that have been proposed to be involved in regenerative processes. Our analyses provide a curated list of genes and gene signaling pathways and match them with the different cellular processes of the regenerative response. In this way, the molecular basis of echinoderm regenerative potential is revealed, and is available for comparisons with other animal taxa.
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Kornthong N, Phanaksri T, Saetan J, Duangprom S, Lekskul B, Vivattanasarn T, Songkoomkrong S, Jattujan P, Cummins SF, Sobhon P, Suwansa-ard S. Identification and localization of growth factor genes in the sea cucumber , Holothuria scabra. Heliyon 2021; 7:e08370. [PMID: 34825084 PMCID: PMC8605306 DOI: 10.1016/j.heliyon.2021.e08370] [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: 08/11/2021] [Revised: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
The sea cucumber Holothuria scabra is both an economically important species in Asian countries and an emerging experimental model for research studies in regeneration and medicinal bioactives. Growth factors and their receptors are known to be key components that guide tissue repair and renewal, yet validation of their presence in H. scabra has not been established. We performed a targeted in silico search of H. scabra transcriptome data to elucidate conserved growth factor family and receptor genes. In total, 42 transcripts were identified, of which 9 were validated by gene cloning and sequencing. The H. scabra growth factor genes, such as bone morphogenetic protein 2A (BMP 2A), bone morphogenetic protein 5-like (BMP5-like), neurotrophin (NT) and fibroblast growth factor 18 (FGF18), were selected for further analyses, including phylogenetic comparison and spatial gene expression using RT-PCR and in situ hybridization. Expression of all genes investigated were widespread in multiple tissues. However, BMP 2A, BMP5-like and NT were found extensively in the radial nerve cord cells, while FGF18 was highly expressed in connective tissue layer of the body wall. Our identification and expression analysis of the H. scabra growth factor genes provided the molecular information of growth factors in this species which may ultimately complement the research in regenerative medicine.
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Affiliation(s)
- Napamanee Kornthong
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Teva Phanaksri
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Jirawat Saetan
- Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Supawadee Duangprom
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Buranee Lekskul
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Tipok Vivattanasarn
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Sineenart Songkoomkrong
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Prapaporn Jattujan
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathumthani, 12121, Thailand
| | - Scott F. Cummins
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore, Queensland, 4558, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, 4558, Australia
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Saowaros Suwansa-ard
- GeneCology Research Centre, University of the Sunshine Coast, Maroochydore, Queensland, 4558, Australia
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Wolff A, Hinman V. The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration. Genes (Basel) 2021; 12:1063. [PMID: 34356079 PMCID: PMC8303351 DOI: 10.3390/genes12071063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to regenerate is scattered among the metazoan tree of life. Further still, regenerative capacity varies widely within these specific organisms. Numerous organisms, all with different regenerative capabilities, have been studied at length and key similarities and disparities in how regeneration occurs have been identified. In order to get a better grasp on understanding regeneration as a whole, we must search for new models that are capable of extensive regeneration, as well as those that have been under sampled in the literature. As invertebrate deuterostomes, echinoderms fit both of these requirements. Multiple members regenerate various tissue types at all life stages, including examples of whole-body regeneration. Interrogations in two highly studied echinoderms, the sea urchin and the sea star, have provided knowledge of tissue and whole-body regeneration at various life stages. Work has begun to examine regeneration in echinoderm larvae, a potential new system for understanding regenerative mechanisms in a basal deuterostome. Here, we review the ways these two animals' larvae have been utilized as a model of regeneration.
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Affiliation(s)
- Andrew Wolff
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA;
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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