1
|
Chen J, Deng L, Wang X, Zhong C, Xia X, Liu H. Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters. mSystems 2024:e0017624. [PMID: 39105582 DOI: 10.1128/msystems.00176-24] [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: 02/05/2024] [Accepted: 07/07/2024] [Indexed: 08/07/2024] Open
Abstract
Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus Sagittula, an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (nifHDK) for nitrogen fixation, and the nifH gene was actively transcribed in situ. Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S2O32-). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters. IMPORTANCE Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to Sagittula as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.
Collapse
Affiliation(s)
- Jiawei Chen
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lixia Deng
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiao Wang
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Cheng Zhong
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, China
| |
Collapse
|
2
|
Wang H, He K, Zhang H, Zhang Q, Cao L, Li J, Zhong Z, Chen H, Zhou L, Lian C, Wang M, Chen K, Qian PY, Li C. Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing. eLife 2024; 12:RP88294. [PMID: 39102287 PMCID: PMC11299980 DOI: 10.7554/elife.88294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024] Open
Abstract
Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill's structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host-symbiont interaction and the bivalves' environmental adaption mechanisms.
Collapse
Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan LaboratoryQingdaoChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Kai He
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou UniversityGuangzhouChina
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Jing Li
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
3
|
Wang H, Xiao H, Feng B, Lan Y, Fung CW, Zhang H, Yan G, Lian C, Zhong Z, Li J, Wang M, Wu AR, Li C, Qian PY. Single-cell RNA-seq reveals distinct metabolic "microniches" and close host-symbiont interactions in deep-sea chemosynthetic tubeworm. SCIENCE ADVANCES 2024; 10:eadn3053. [PMID: 39047091 PMCID: PMC11268408 DOI: 10.1126/sciadv.adn3053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Vestimentiferan tubeworms that thrive in deep-sea chemosynthetic ecosystems rely on a single species of sulfide-oxidizing gammaproteobacterial endosymbionts housed in a specialized symbiotic organ called trophosome as their primary carbon source. While this simple symbiosis is remarkably productive, the host-symbiont molecular interactions remain unelucidated. Here, we applied an approach for deep-sea in situ single-cell fixation in a cold-seep tubeworm, Paraescarpia echinospica. Single-cell RNA sequencing analysis and further molecular characterizations of both the trophosome and endosymbiont indicate that the tubeworm maintains two distinct metabolic "microniches" in the trophosome by controlling the availability of chemosynthetic gases and metabolites, resulting in oxygenated and hypoxic conditions. The endosymbionts in the oxygenated niche actively conduct autotrophic carbon fixation and are digested for nutrients, while those in the hypoxic niche conduct anaerobic denitrification, which helps the host remove ammonia waste. Our study provides insights into the molecular interactions between animals and their symbiotic microbes.
Collapse
Affiliation(s)
- Hao Wang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan Laboratory, Qingdao, China
| | - Hongxiu Xiao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Buhan Feng
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Cheuk Wang Fung
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Huan Zhang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Guoyong Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chao Lian
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Zhaoshan Zhong
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Jing Li
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Minxiao Wang
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
| | - Angela Ruohao Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chaolun Li
- Institute of Oceanology, Chinese Academy of Science, Qingdao, China
- South China Sea Institute of Oceanology, Chinese Academy of Science, Guanzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| |
Collapse
|
4
|
Zhou Y, Liu H, Feng C, Lu Z, Liu J, Huang Y, Tang H, Xu Z, Pu Y, Zhang H. Genetic adaptations of sea anemone to hydrothermal environment. SCIENCE ADVANCES 2023; 9:eadh0474. [PMID: 37862424 PMCID: PMC10588955 DOI: 10.1126/sciadv.adh0474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/20/2023] [Indexed: 10/22/2023]
Abstract
Hydrothermal vent habitats are characterized by high hydrostatic pressure, darkness, and the continuous release of toxic metal ions into the surrounding environment where sea anemones and other invertebrates thrive. Nevertheless, the understanding of metazoan metal ion tolerances and environmental adaptations remains limited. We assembled a chromosome-level genome for the vent sea anemone, Alvinactis idsseensis sp. nov. Comparative genomic analyses revealed gene family expansions and gene innovations in A. idsseensis sp. nov. as a response to high concentrations of metal ions. Impressively, the metal tolerance proteins MTPs is a unique evolutionary response to the high concentrations of Fe2+ and Mn2+ present in the environments of these anemones. We also found genes associated with high concentrations of polyunsaturated fatty acids that may respond to high hydrostatic pressure and found sensory and circadian rhythm-regulated genes that were essential for adaptations to darkness. Overall, our results provide insights into metazoan adaptation to metal ions, high pressure, and darkness in hydrothermal vents.
Collapse
Affiliation(s)
- Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Helu Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710129, China
| | - Zaiqing Lu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Yanan Huang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Tang
- Department of Respiratory Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou, Hainan 570102, China
| | - Zehui Xu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujin Pu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| |
Collapse
|
5
|
Perez M, Aroh O, Sun Y, Lan Y, Juniper SK, Young CR, Angers B, Qian PY. Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes. Mol Biol Evol 2023; 40:msad172. [PMID: 37494294 PMCID: PMC10414810 DOI: 10.1093/molbev/msad172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.
Collapse
Affiliation(s)
- Maeva Perez
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Oluchi Aroh
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Chinese Academy of Sciences, Institute of Oceanology, Qingdao, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| | - Stanley Kim Juniper
- School of Earth and Ocean Sciences, University of Victoria, Victoria, Canada
| | | | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montréal, Canada
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China
| |
Collapse
|
6
|
Liu J, Zhou Y, Pu Y, Zhang H. A chromosome-level genome assembly of a deep-sea starfish (Zoroaster cf. ophiactis). Sci Data 2023; 10:506. [PMID: 37528102 PMCID: PMC10394057 DOI: 10.1038/s41597-023-02397-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Understanding of adaptation and evolution of organisms in the deep sea requires more genomic resources. Zoroaster cf. ophiactis is a sea star in the family Zoroasteridae occurring exclusively in the deep sea. In this study, a chromosome-level genome assembly for Z. cf. ophiactis was generated by combining Nanopore long-read, Illumina short-read, and Hi-C sequencing data. The final assembly was 1,002.0 Mb in length, with a contig N50 of 376 Kb and a scaffold N50 of 40.4 Mb, and included 22 pseudo-chromosomes, covering 92.3% of the assembly. Completeness analysis evaluated with BUSCO revealed that 95.91% of the metazoan conserved genes were complete. Additionally, 39,426 protein-coding genes were annotated for this assembly. This chromosome-level genome assembly represents the first high-quality genome for the deep-sea Asteroidea, and will provide a valuable resource for future studies on evolution and adaptation of deep-sea echinoderms.
Collapse
Affiliation(s)
- Jun Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yujin Pu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibin Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
| |
Collapse
|
7
|
Moggioli G, Panossian B, Sun Y, Thiel D, Martín-Zamora FM, Tran M, Clifford AM, Goffredi SK, Rimskaya-Korsakova N, Jékely G, Tresguerres M, Qian PY, Qiu JW, Rouse GW, Henry LM, Martín-Durán JM. Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms. Nat Commun 2023; 14:2814. [PMID: 37198188 DOI: 10.1038/s41467-023-38521-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies. Genome compaction and extensive gene losses distinguish the heterotrophic symbiosis of the bone-eating worm Osedax frankpressi from the chemoautotrophic symbiosis of deep-sea Vestimentifera. Osedax's endosymbionts complement many of the host's metabolic deficiencies, including the loss of pathways to recycle nitrogen and synthesise some amino acids. Osedax's endosymbionts possess the glyoxylate cycle, which could allow more efficient catabolism of bone-derived nutrients and the production of carbohydrates from fatty acids. Unlike in most Vestimentifera, innate immunity genes are reduced in O. frankpressi, which, however, has an expansion of matrix metalloproteases to digest collagen. Our study supports that distinct nutritional interactions influence host genome evolution differently in highly specialised symbioses.
Collapse
Affiliation(s)
- Giacomo Moggioli
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Balig Panossian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Yanan Sun
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Daniel Thiel
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Martin Tran
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Alexander M Clifford
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Nadezhda Rimskaya-Korsakova
- Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Zoology and Evolutionary Research, Erbertstr. 1, 07743, Jena, Germany
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Martin Tresguerres
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| |
Collapse
|
8
|
Shi H, Ruan L, Chen Z, Liao Y, Wu W, Liu L, Xu X. Sulfur, sterol and trehalose metabolism in the deep-sea hydrocarbon seep tubeworm Lamellibrachia luymesi. BMC Genomics 2023; 24:175. [PMID: 37020304 PMCID: PMC10077716 DOI: 10.1186/s12864-023-09267-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Lamellibrachia luymesi dominates cold sulfide-hydrocarbon seeps and is known for its ability to consume bacteria for energy. The symbiotic relationship between tubeworms and bacteria with particular adaptations to chemosynthetic environments has received attention. However, metabolic studies have primarily focused on the mechanisms and pathways of the bacterial symbionts, while studies on the animal hosts are limited. RESULTS Here, we sequenced the transcriptome of L. luymesi and generated a transcriptomic database containing 79,464 transcript sequences. Based on GO and KEGG annotations, we identified transcripts related to sulfur metabolism, sterol biosynthesis, trehalose synthesis, and hydrolysis. Our in-depth analysis identified sulfation pathways in L. luymesi, and sulfate activation might be an important detoxification pathway for promoting sulfur cycling, reducing byproducts of sulfide metabolism, and converting sulfur compounds to sulfur-containing organics, which are essential for symbiotic survival. Moreover, sulfide can serve directly as a sulfur source for cysteine synthesis in L. luymesi. The existence of two pathways for cysteine synthesis might ensure its participation in the formation of proteins, heavy metal detoxification, and the sulfide-binding function of haemoglobin. Furthermore, our data suggested that cold-seep tubeworm is capable of de novo sterol biosynthesis, as well as incorporation and transformation of cycloartenol and lanosterol into unconventional sterols, and the critical enzyme involved in this process might have properties similar to those in the enzymes from plants or fungi. Finally, trehalose synthesis in L. luymesi occurs via the trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) pathways. The TPP gene has not been identified, whereas the TPS gene encodes a protein harbouring conserved TPS/OtsA and TPP/OtsB domains. The presence of multiple trehalases that catalyse trehalose hydrolysis could indicate the different roles of trehalase in cold-seep tubeworms. CONCLUSIONS We elucidated several molecular pathways of sulfate activation, cysteine and cholesterol synthesis, and trehalose metabolism. Contrary to the previous analysis, two pathways for cysteine synthesis and the cycloartenol-C-24-methyltransferase gene were identified in animals for the first time. The present study provides new insights into particular adaptations to chemosynthetic environments in L. luymesi and can serve as the basis for future molecular studies on host-symbiont interactions and biological evolution.
Collapse
Affiliation(s)
- Hong Shi
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China.
| | - Lingwei Ruan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China.
- College of Marine Biology, Xiamen ocean vocational college, 361100, Xiamen, People's Republic of China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, People's Republic of China.
| | - Zimeng Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
| | - Yifei Liao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
- School of Advanced Manufacturing, Fuzhou University, Fuzhou, 362200, People's Republic of China
| | - Wenhao Wu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, People's Republic of China
| | - Linmin Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
| | - Xun Xu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, No. 178 Daxue Road, Xiamen, Fujian, 361005, People's Republic of China
| |
Collapse
|
9
|
Guo Y, Meng L, Wang M, Zhong Z, Li D, Zhang Y, Li H, Zhang H, Seim I, Li Y, Jiang A, Ji Q, Su X, Chen J, Fan G, Li C, Liu S. Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biol 2023; 21:51. [PMID: 36882766 PMCID: PMC9993606 DOI: 10.1186/s12915-023-01551-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution. RESULTS We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta. CONCLUSIONS Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.
Collapse
Affiliation(s)
- Yang Guo
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingfeng Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Denghui Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Yuli Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Aijun Jiang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qianyue Ji
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xiaoshan Su
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,College of Marine Science, University of Chinese Academy of Sciences, Qingdao, 266400, China. .,South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China. .,Qingdao Key Laboratory of Marine Genomics, BGI-qingdao, Qingdao, China.
| |
Collapse
|
10
|
Wang M, Ruan L, Liu M, Liu Z, He J, Zhang L, Wang Y, Shi H, Chen M, Yang F, Zeng R, He J, Guo C, Chen J. The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment. BMC Genomics 2023; 24:72. [PMID: 36774470 PMCID: PMC9921365 DOI: 10.1186/s12864-023-09166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated. RESULT We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae. CONCLUSION Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.
Collapse
Affiliation(s)
- Muhua Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Lingwei Ruan
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Meng Liu
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Zixuan Liu
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Jian He
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China ,grid.12981.330000 0001 2360 039XChina-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Long Zhang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Yuanyuan Wang
- grid.12981.330000 0001 2360 039XState Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Hong Shi
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Mingliang Chen
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Feng Yang
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Runying Zeng
- grid.453137.70000 0004 0406 0561State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005 China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Changjun Guo
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China. .,China-ASEAN Belt and Road Joint Laboratory On Mariculture Technology, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Ministry of Natural Resources, Fujian Key Laboratory of Marine Genetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, 361005, China. .,Fujian Key Laboratory On Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| |
Collapse
|
11
|
Lu G, Zhang Z, Wang WX. Metal bioaccumulation and transfer in benthic species based on isotopic signatures of individual amino acids in South China Sea cold seep environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120822. [PMID: 36481461 DOI: 10.1016/j.envpol.2022.120822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/29/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Cold seeps are deep-sea 'oases' with dense and dominant coexisting populations of large mussels and tubeworms under extreme environments. Under such natural source of high metal concentrations, the present study investigated the metal bioaccumulation and transfer with trophic positions in six benthic species by the isotopic δ15N and δ13C signatures in the active Haima cold seep, South China Sea. Comparing the isotopic signatures of bulk-tissue and amino acids by compound-specific isotopic analysis (CSIA-AA), we found that the bulk trophic (TPB) values in the benthos except mussels were significantly higher than those of CSIA-based TPGlu-Phe values. The estimated CSIA-based TPGlu-Phe values showed a relatively compressed food chain with much changeable and unique amino acid isotopic heterogeneity, followed slim tubeworms (1.20)<mussels (1.38)<clams (1.52)<brittle stars (1.82)<giant tubeworms (2.16)<shrimps (2.31). All species accumulated relatively high concentrations of Fe, Zn, Cu, and Cr, especially for Zn in clams. Pearson correlation analysis showed that most metals had no significant relationship between their bioaccumulation and trophic positions, whereas Hg showed a significantly positive bioaccumulation through trophic transfer in such a compressed food chain. Water exposure was a major metal source rather than bacterial assimilation for most metals in the cold seep higher consumers. Hyperaccumulation of specific metals in some tissues of different benthos indicated different metal overflows in the Haima cold seep (As and Ni for tubeworms, Zn and Cd for clam gills, Ag and Cu for mussel gills). This study demonstrated high metal adaptations in different species and stable isotopic characteristics of amino acid metabolism in a natural high metal source of an active deep-sea cold seep, which is important for deep-sea development and environmental protection.
Collapse
Affiliation(s)
- Guangyuan Lu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Research Center for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 51807, China
| | - Zhongyi Zhang
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Wen-Xiong Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Research Center for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 51807, China; School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.
| |
Collapse
|
12
|
Li Y, Xue Y, Peng Z, Zhang L. Immune diversity in lophotrochozoans, with a focus on recognition and effector systems. Comput Struct Biotechnol J 2023; 21:2262-2275. [PMID: 37035545 PMCID: PMC10073891 DOI: 10.1016/j.csbj.2023.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/11/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Lophotrochozoa is one of the most species-rich but immunologically poorly explored phyla. Although lack of acquired response in a narrow sense, lophotrochozoans possess various genetic mechanisms that enhance the diversity and specificity of innate immune system. Here, we review the recent advances of comparative immunology studies in lophotrochozoans with focus on immune recognition and effector systems. Haemocytes and coelomocytes are general important yet understudied player. Comparative genomics studies suggest expansion and functional divergence of lophotrochozoan immune reorganization systems is not as "homogeneous and simple" as we thought including the large-scale expansion and molecular divergence of pattern recognition receptors (PRRs) (TLRs, RLRs, lectins, etc.) and signaling adapters (MyD88s etc.), significant domain recombination of immune receptors (RLR, NLRs, lectins, etc.), extensive somatic recombination of fibrinogenrelated proteins (FREPs) in snails. Furthermore, there are repeatedly identified molecular mechanisms that generate immune effector diversity, including high polymorphism of antimicrobial peptides and proteins (AMPs), reactive oxygen and nitrogen species (RONS) and cytokines. Finally, we argue that the next generation omics tools and the recently emerged genome editing technicism will revolutionize our understanding of innate immune system in a comparative immunology perspective.
Collapse
Affiliation(s)
- Yongnan Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao Agricultural University, Qingdao, China
| | - Zhangjie Peng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
- Corresponding author at: CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| |
Collapse
|
13
|
Seudre O, Martín-Zamora FM, Rapisarda V, Luqman I, Carrillo-Baltodano AM, Martín-Durán JM. The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia. Genome Biol Evol 2022; 14:evac139. [PMID: 36099507 PMCID: PMC9539403 DOI: 10.1093/gbe/evac139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia-a large clade of invertebrate animals including molluscs and annelids-are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterize the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids. The genome of O. fusiformis contains at least a single ortholog for 20 of the 22 Fox gene classes that are ancestral to Bilateria, including an ortholog of the recently discovered foxT class. Temporal and spatial expression dynamics reveal a conserved role of Fox genes in gut formation, mesoderm patterning, and apical organ and cilia formation in Annelida and Spiralia. Moreover, we uncover an ancestral expansion of foxQ2 genes in Spiralia, represented by 11 paralogs in O. fusiformis. Notably, although all foxQ2 copies have apical expression in O. fusiformis, they show variable spatial domains and staggered temporal activation, which suggest cooperation and sub-functionalization among foxQ2 genes for the development of apical fates in this annelid. Altogether, our study informs the evolution and developmental roles of Fox genes in Annelida and Spiralia generally, providing the basis to explore how regulatory changes in Fox gene expression might have contributed to developmental and morphological diversification in Spiralia.
Collapse
Affiliation(s)
- Océane Seudre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Valentina Rapisarda
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Imran Luqman
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| |
Collapse
|
14
|
Zhong S, Ma X, Jiang Y, Qiao Y, Zhao L, Huang L, Huang G, Zhao Y, Liu Y, Chen X. The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula. Front Genet 2022; 13:910344. [PMID: 35937983 PMCID: PMC9354978 DOI: 10.3389/fgene.2022.910344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shengping Zhong
- 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
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| | - 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
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Longyan Zhao
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Lianghua Huang
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Guoqiang Huang
- 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
| | - Yonghong Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
- *Correspondence: Shengping Zhong, ; Yonghong Liu, ; Xiuli Chen,
| |
Collapse
|
15
|
Zhang L, He J, Tan P, Gong Z, Qian S, Miao Y, Zhang HY, Tu G, Chen Q, Zhong Q, Han G, He J, Wang M. The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to a deep-sea reducing environment. Commun Biol 2022; 5:224. [PMID: 35273345 PMCID: PMC8913654 DOI: 10.1038/s42003-022-03176-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by lacking oxygen and photosynthesis-derived nutrients. Most animals acquire nutrition in cold seeps or hydrothermal vents by maintaining epi- or endosymbiotic relationship with chemoautotrophic microorganisms. Although several seep- and vent-dwelling animals hosting symbiotic microbes have been well-studied, the genomic basis of adaptation to deep-sea reducing environment in nonsymbiotic animals is still lacking. Here, we report a high-quality genome of Chiridota heheva Pawson & Vance, 2004, which thrives by extracting organic components from sediment detritus and suspended material, as a reference for nonsymbiotic animal's adaptation to deep-sea reducing environments. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion. Moreover, several hypoxia-related genes (Pyruvate Kinase M2, PKM2; Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase, LHPP; Poly(A)-specific Ribonuclease Subunit PAN2, PAN2; and Ribosomal RNA Processing 9, RRP9) were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.
Collapse
Affiliation(s)
- Long Zhang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jian He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Peipei Tan
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhen Gong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shiyu Qian
- School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Yuanyuan Miao
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Han-Yu Zhang
- Hainan Key Laboratory of Marine Georesource and Prospecting, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Guangxian Tu
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qi Chen
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Qiqi Zhong
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China
| | - Guanzhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jianguo He
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| | - Muhua Wang
- State Key Laboratory for Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519000, China. .,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, 525435, China.
| |
Collapse
|
16
|
de Oliveira AL, Mitchell J, Girguis P, Bright M. Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome. Mol Biol Evol 2021; 39:6454105. [PMID: 34893862 PMCID: PMC8789280 DOI: 10.1093/molbev/msab347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.
Collapse
Affiliation(s)
| | - Jessica Mitchell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Austria
| |
Collapse
|
17
|
Filée J, Farhat S, Higuet D, Teysset L, Marie D, Thomas-Bulle C, Hourdez S, Jollivet D, Bonnivard E. Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution. Mob DNA 2021; 12:24. [PMID: 34715903 PMCID: PMC8556966 DOI: 10.1186/s13100-021-00252-0] [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: 06/10/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00252-0.
Collapse
Affiliation(s)
- Jonathan Filée
- Laboratoire Evolution, Genomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, 11794-5000, USA
| | - Dominique Higuet
- Institut de Systématique, Evolution, Biodiversité (ISYEB) - Sorbonne Université, Muséum National d'Histoire Naturel, CNRS, EPHE, Université des Antilles, 7 quai Saint Bernard, 75252, Paris Cedex 05, France
| | - Laure Teysset
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & small RNA Biology", F-75005, Paris, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Camille Thomas-Bulle
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Stephane Hourdez
- UMR8222 LECOB CNRS-Sorbonne Université, Observatoire Océanologique de Banyuls, 1 avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France.
| |
Collapse
|
18
|
Sun Y, Sun J, Yang Y, Lan Y, Ip JCH, Wong WC, Kwan YH, Zhang Y, Han Z, Qiu JW, Qian PY. Genomic signatures supporting the symbiosis and formation of chitinous tube in the deep-sea tubeworm Paraescarpia echinospica. Mol Biol Evol 2021; 38:4116-4134. [PMID: 34255082 PMCID: PMC8476170 DOI: 10.1093/molbev/msab203] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Vestimentiferan tubeworms are iconic animals that present as large habitat-forming chitinized tube bushes in deep-sea chemosynthetic ecosystems. They are gutless and depend entirely on their endosymbiotic sulfide-oxidizing chemoautotrophic bacteria for nutrition. Information on the genomes of several siboglinid endosymbionts has improved our understanding of their nutritional supplies. However, the interactions between tubeworms and their endosymbionts remain largely unclear due to a paucity of host genomes. Here, we report the chromosome-level genome of the vestimentiferan tubeworm Paraescarpia echinospica. We found that the genome has been remodeled to facilitate symbiosis through the expansion of gene families related to substrate transfer and innate immunity, suppression of apoptosis, regulation of lysosomal digestion, and protection against oxidative stress. Furthermore, the genome encodes a programmed cell death pathway that potentially controls the endosymbiont population. Our integrated genomic, transcriptomic, and proteomic analyses uncovered matrix proteins required for the formation of the chitinous tube and revealed gene family expansion and co-option as evolutionary mechanisms driving the acquisition of this unique supporting structure for deep-sea tubeworms. Overall, our study provides novel insights into the host’s support system that has enabled tubeworms to establish symbiosis, thrive in deep-sea hot vents and cold seeps, and produce the unique chitinous tubes in the deep sea.
Collapse
Affiliation(s)
- Yanan Sun
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Sun
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yi Yang
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yi Lan
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yick Hang Kwan
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yanjie Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhuang Han
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Corresponding authors: E-mails: ;
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Corresponding authors: E-mails: ;
| |
Collapse
|
19
|
Aroh O, Halanych KM. Genome-wide characterization of LTR retrotransposons in the non-model deep-sea annelid Lamellibrachia luymesi. BMC Genomics 2021; 22:466. [PMID: 34157969 PMCID: PMC8220671 DOI: 10.1186/s12864-021-07749-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background Long Terminal Repeat retrotransposons (LTR retrotransposons) are mobile genetic elements composed of a few genes between terminal repeats and, in some cases, can comprise over half of a genome’s content. Available data on LTR retrotransposons have facilitated comparative studies and provided insight on genome evolution. However, data are biased to model systems and marine organisms, including annelids, have been underrepresented in transposable elements studies. Here, we focus on genome of Lamellibrachia luymesi, a vestimentiferan tubeworm from deep-sea hydrocarbon seeps, to gain knowledge of LTR retrotransposons in a deep-sea annelid. Results We characterized LTR retrotransposons present in the genome of L. luymesi using bioinformatic approaches and found that intact LTR retrotransposons makes up about 0.1% of L. luymesi genome. Previous characterization of the genome has shown that this tubeworm hosts several known LTR-retrotransposons. Here we describe and classify LTR retrotransposons in L. luymesi as within the Gypsy, Copia and Bel-pao superfamilies. Although, many elements fell within already recognized families (e.g., Mag, CSRN1), others formed clades distinct from previously recognized families within these superfamilies. However, approximately 19% (41) of recovered elements could not be classified. Gypsy elements were the most abundant while only 2 Copia and 2 Bel-pao elements were present. In addition, analysis of insertion times indicated that several LTR-retrotransposons were recently transposed into the genome of L. luymesi, these elements had identical LTR’s raising possibility of recent or ongoing retrotransposon activity. Conclusions Our analysis contributes to knowledge on diversity of LTR-retrotransposons in marine settings and also serves as an important step to assist our understanding of the potential role of retroelements in marine organisms. We find that many LTR retrotransposons, which have been inserted in the last few million years, are similar to those found in terrestrial model species. However, several new groups of LTR retrotransposons were discovered suggesting that the representation of LTR retrotransposons may be different in marine settings. Further study would improve understanding of the diversity of retrotransposons across animal groups and environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07749-1.
Collapse
Affiliation(s)
- Oluchi Aroh
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, College of Science and Mathematics, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA.
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, College of Science and Mathematics, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA
| |
Collapse
|
20
|
Brzechffa C, Goffredi SK. Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:104-111. [PMID: 33196140 DOI: 10.1111/1758-2229.12909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Relationships fueled by sulfide between deep-sea invertebrates and bacterial symbionts are well known, yet the diverse overlapping factors influencing symbiont specificity are complex. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analysed for three co-occurring species each of Bathymodiolus mussels and vestimentiferan tubeworms, from three deep methane seeps off the west coast of Costa Rica. The bacterial internal transcribed spacer gene was analysed via direct and barcoded amplicon sequencing to reveal fine-scale symbiont diversity. Each of the three mussel species (B. earlougheri, B. billschneideri and B. nancyschneideri) hosted genetically distinct thiotrophic endosymbionts, despite living nearly side-by-side in their habitat, suggesting that host identity is crucial in driving symbiont specificity. The dominant thiotrophic symbiont of co-occurring tubeworms Escarpia spicata and Lamellibrachia (L. barhami and L. donwalshi), on the other hand, was identical regardless of host species or sample location, suggesting lack of influence by either factor on symbiont selectivity in this group of animals. These findings highlight the specific, yet distinct, influences on the environmental acquisition of symbionts in two foundational invertebrates with similar lifestyles, and provide a rapid, precise method of examining symbiont identities.
Collapse
|
21
|
Lan Y, Sun J, Chen C, Sun Y, Zhou Y, Yang Y, Zhang W, Li R, Zhou K, Wong WC, Kwan YH, Cheng A, Bougouffa S, Van Dover CL, Qiu JW, Qian PY. Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis. Nat Commun 2021; 12:1165. [PMID: 33608555 PMCID: PMC7895826 DOI: 10.1038/s41467-021-21450-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 01/07/2021] [Indexed: 01/31/2023] Open
Abstract
Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host-symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.
Collapse
Affiliation(s)
- Yi Lan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa Prefecture, Japan
| | - Yanan Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yadong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Yi Yang
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Weipeng Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Kun Zhou
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai Chuen Wong
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yick Hang Kwan
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Aifang Cheng
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Salim Bougouffa
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Cindy Lee Van Dover
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, United States
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
| |
Collapse
|
22
|
Du L, Cai S, Liu J, Liu R, Zhang H. The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae). PLoS One 2020; 15:e0242541. [PMID: 33253261 PMCID: PMC7703994 DOI: 10.1371/journal.pone.0242541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022] Open
Abstract
Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.
Collapse
Affiliation(s)
- Lvpei Du
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanya Cai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ruoyu Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| |
Collapse
|
23
|
Liu R, Wang K, Liu J, Xu W, Zhou Y, Zhu C, Wu B, Li Y, Wang W, He S, Feng C, Zhang H. De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps. Genome Biol Evol 2020; 12:905-910. [PMID: 32467969 PMCID: PMC7313663 DOI: 10.1093/gbe/evaa100] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2017] [Indexed: 12/12/2022] Open
Abstract
Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.
Collapse
Affiliation(s)
- Ruoyu Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Jun Liu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Wenjie Xu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenglong Zhu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Baosheng Wu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongxin Li
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chenguang Feng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Haibin Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| |
Collapse
|
24
|
Li Y, Tassia MG, Waits DS, Bogantes VE, David KT, Halanych KM. Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biol 2019; 17:91. [PMID: 31739792 PMCID: PMC6862839 DOI: 10.1186/s12915-019-0713-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/24/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored. RESULTS Here, we present and characterize adaptations of the cold seep-dwelling tubeworm Lamellibrachia luymesi, one of the longest-lived solitary invertebrates. We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. Contrary to previous analyses, the sulfide binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored, and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm's unique life history which are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 mya for vestimentiferans. CONCLUSIONS Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extend to other chemosynthetic symbiotic systems.
Collapse
Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St, New Haven, CT, 06511, USA.
| | - Michael G Tassia
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Damien S Waits
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Viktoria E Bogantes
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kyle T David
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.
| |
Collapse
|