1
|
Zhao R, Yang Y, Li S, Chen S, Ding J, Wu Y, Qu M, Di Y. Comparative study of integrated bio-responses in deep-sea and nearshore mussels upon abiotic condition changes: Insight into distinct regulation and adaptation. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106610. [PMID: 38879901 DOI: 10.1016/j.marenvres.2024.106610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/16/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
Deep-sea mussels, one of the dominant species in most deep-sea ecosystems, have long been used as model organisms to investigate the adaptations and symbiotic relationships of deep-sea macrofauna under laboratory conditions due to their ability to survive under atmospheric pressure. However, the impact of additional abiotic conditions beyond pressure, such as temperature and light, on their physiological characteristics remains unknown. In this study, deep-sea mussels (Gigantidas platifrons) from cold seep of the South China Sea, along with nearshore mussels (Mytilus coruscus) from the East China Sea, were reared in unfavorable abiotic conditions for up to 8 days. Integrated biochemical indexes including antioxidant defense, immune ability and energy metabolism were investigated in the gill and digestive gland, while cytotoxicity was determined in hemocytes of both types of mussels. The results revealed mild bio-responses in two types of mussels in the laboratory, represented by the effective antioxidant defense with constant total antioxidant capability level and malondialdehyde content. There were also disparate adaptations in deep-sea and nearshore mussels. In deep-sea mussels, significantly increased immune response and energy reservation were observed in gills, together with the elevated cytotoxicity in hemocytes, implying the more severe biological adaptation was required, mainly due to the symbiotic bacteria loss under laboratory conditions. On the contrary, insignificant biological responses were exhibited in nearshore mussels except for the increased energy consumption, indicating the trade-off strategy to use more energy to deal with potential stress. Overall, this comparative study highlights the basal bio-responses of deep-sea and nearshore mussels out of their native environments, providing evidence that short-term culture of both mussels under easily achievable laboratory conditions would not dramatically alter their biological status. This finding will assist in broadening the application of deep-sea mussels as model organism in future research regardless of the specialized research equipment.
Collapse
Affiliation(s)
- Ruoxuan Zhao
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Yingli Yang
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Shuimei Li
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Siyu Chen
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Jiawei Ding
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Yusong Wu
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Mengjie Qu
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Yanan Di
- Ocean College, Zhejiang University, Zhoushan, 316000, China.
| |
Collapse
|
2
|
Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [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: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
Collapse
Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
| |
Collapse
|
3
|
Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
Collapse
Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
4
|
Lin YT, Ip JCH, He X, Gao ZM, Perez M, Xu T, Sun J, Qian PY, Qiu JW. Scallop-bacteria symbiosis from the deep sea reveals strong genomic coupling in the absence of cellular integration. THE ISME JOURNAL 2024; 18:wrae048. [PMID: 38531780 PMCID: PMC10999363 DOI: 10.1093/ismejo/wrae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/06/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024]
Abstract
Previous studies have revealed tight metabolic complementarity between bivalves and their endosymbiotic chemosynthetic bacteria, but little is known about their interactions with ectosymbionts. Our analysis of the ectosymbiosis between a deep-sea scallop (Catillopecten margaritatus) and a gammaproteobacterium showed that bivalves could be highly interdependent with their ectosymbionts as well. Our microscopic observation revealed abundant sulfur-oxidizing bacteria (SOB) on the surfaces of the gill epithelial cells. Microbial 16S rRNA gene amplicon sequencing of the gill tissues showed the dominance of the SOB. An analysis of the SOB genome showed that it is substantially smaller than its free-living relatives and has lost cellular components required for free-living. Genomic and transcriptomic analyses showed that this ectosymbiont relies on rhodanese-like proteins and SOX multienzyme complex for energy generation, mainly on the Calvin-Benson-Bassham (CBB) cycle and peripherally on a phosphoenolpyruvate carboxylase for carbon assimilation. Besides, the symbiont encodes an incomplete tricarboxylic acid (TCA) cycle. Observation of the scallop's digestive gland and its nitrogen metabolism pathways indicates it does not fully rely on the ectosymbiont for nutrition. Analysis of the host's gene expression provided evidence that it could offer intermediates for the ectosymbiont to complete its TCA cycle and some amino acid synthesis pathways using exosomes, and its phagosomes, endosomes, and lysosomes might be involved in harvesting nutrients from the symbionts. Overall, our study prompts us to rethink the intimacy between the hosts and ectosymbionts in Bivalvia and the evolution of chemosymbiosis in general.
Collapse
Affiliation(s)
- Yi-Tao Lin
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, 999077, China
| | - Jack Chi-Ho Ip
- Science Unit, Lingnan University, Hong Kong SAR, 999077, China
| | - Xing He
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Zhao-Ming Gao
- Deep-sea Science Division, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Maeva Perez
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, 999077, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, 999077, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, 999077, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, 999077, China
| |
Collapse
|
5
|
Zhang W, Zhang Y, Shi X, Wang S, Bao Y. Hemoglobin wonders: a fascinating gas transporter dive into molluscs. Crit Rev Biochem Mol Biol 2023; 58:132-157. [PMID: 38189101 DOI: 10.1080/10409238.2023.2299381] [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: 08/22/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb's potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
Collapse
Affiliation(s)
- Weifeng Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Yang Zhang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xizhi Shi
- School of Marine Science, Ningbo University, Ningbo, China
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China and National Laboratory for Marine Science and Technology (LMBB & LMFSFPP), Qingdao, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
| |
Collapse
|
6
|
Li Y, He X, Lin Y, Li YX, Kamenev GM, Li J, Qiu JW, Sun J. Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment. Mol Ecol Resour 2023; 23:1853-1867. [PMID: 37486074 DOI: 10.1111/1755-0998.13846] [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: 04/07/2023] [Revised: 06/16/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Previous studies have deciphered the genomic basis of host-symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae-a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep-sea and shallow-water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free-living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well-adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen-adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.
Collapse
Affiliation(s)
- Yunlong Li
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Xing He
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Yuxuan Lin
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi-Xuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Gennady M Kamenev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
| | - Jiying Li
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| |
Collapse
|
7
|
Law STS, Yu Y, Nong W, So WL, Li Y, Swale T, Ferrier DEK, Qiu J, Qian P, Hui JHL. The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes. Proc Biol Sci 2023; 290:20231563. [PMID: 37876192 PMCID: PMC10598428 DOI: 10.1098/rspb.2023.1563] [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: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Members of the phylum Cnidaria include sea anemones, corals and jellyfish, and have successfully colonized both marine and freshwater habitats throughout the world. The understanding of how cnidarians adapt to extreme environments such as the dark, high-pressure deep-sea habitat has been hindered by the lack of genomic information. Here, we report the first chromosome-level deep-sea cnidarian genome, of the anemone Actinernus sp., which was 1.39 Gbp in length and contained 44 970 gene models including 14 806 tRNA genes and 30 164 protein-coding genes. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, NK cluster and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. In addition to this striking arrangement of homeobox genes, analyses of microRNAs revealed cnidarian-specific complements that are distinctive for nested clades of these animals, presumably reflecting the progressive evolution of the gene regulatory networks in which they are embedded. Also, compared with other sea anemones, circadian rhythm genes were lost in Actinernus sp., which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian thus reveals some of the likely molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment. It also deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular, specifically from the viewpoint of key developmental control genes like the homeobox-encoding genes, where we find an array of genes that until now has only been hypothesized to have existed in the ancient ancestor that pre-dated both the cnidarians and bilaterians.
Collapse
Affiliation(s)
- Sean Tsz Sum Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Thomas Swale
- Dovetail Genomics, LLC, Scotts Valley, CA 95066, USA
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jianwen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| |
Collapse
|
8
|
Hui M, Zhang Y, Wang A, Sha Z. The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents. Animals (Basel) 2023; 13:3313. [PMID: 37958068 PMCID: PMC10648102 DOI: 10.3390/ani13213313] [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: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.
Collapse
Affiliation(s)
- Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.H.); (A.W.)
- Laoshan Laboratory, Qingdao 266237, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China;
| | - Aiyang Wang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.H.); (A.W.)
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.H.); (A.W.)
- Laoshan Laboratory, Qingdao 266237, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| |
Collapse
|
9
|
Nicolini F, Ghiselli F, Luchetti A, Milani L. Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View. Genome Biol Evol 2023; 15:evad181. [PMID: 37850870 PMCID: PMC10588774 DOI: 10.1093/gbe/evad181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.
Collapse
Affiliation(s)
- Filippo Nicolini
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| |
Collapse
|
10
|
Yin X, Li X, Li Q, Wang B, Zheng L. Complete genome analysis reveals environmental adaptability of sulfur-oxidizing bacterium Thioclava nitratireducens M1-LQ-LJL-11 and symbiotic relationship with deep-sea hydrothermal vent Chrysomallon squamiferum. Mar Genomics 2023; 71:101058. [PMID: 37478643 DOI: 10.1016/j.margen.2023.101058] [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: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/23/2023]
Abstract
One sulfur-oxidizing bacterium Thioclava sp. M1-LQ-LJL-11 was isolated from the gill of Chrysomallon squamiferum collected from 2700 m deep hydrothermal named Longqi on the southwest Indian Ocean ridge. In order to understand its survival mechanism in hydrothermal extreme environment and symbiotic relationship with its host, the complete genome of strain M1-LQ-LJL-11 was sequenced and analyzed. A total of 6117 Mb of valid data was obtained, including 4096 coding genes, 61 non coding genes, including 9 rRNAs (among them, there are 3 in 23S rRNA, 3 in 5S rRNA, and 3 in 16S rRNA.), 52 tRNAs and 35 genomic islands. Strain M1-LQ-LJL-11 contains one chromosome and two plasmids. In the genome annotation information of the strain, we found 28 genes including cys sox, sor, sqr, tst related to sulfur metabolism and 17 metal resistance genes. Interestingly, a pair of quorum sensing system which probably regulating biofilm formation located in chromosome was found. These genes are critical for self-adaptation against severe environment as well as host survival. This study provides a basis understanding for the adaptive strategies of deep-sea hydrothermal bacteria and symbiotic relationship with its host in extreme environments through gene level.
Collapse
Affiliation(s)
- Xin Yin
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China
| | - Xiang Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Qian Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Bingshu Wang
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China
| | - Li Zheng
- School of Advanced Manufacturing, Fuzhou University, Jinjiang 362200, China; Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China.
| |
Collapse
|
11
|
Gao ZM, Xu T, Chen HG, Lu R, Tao J, Wang HB, Qiu JW, Wang Y. Early genome erosion and internal phage-symbiont-host interaction in the endosymbionts of a cold-seep tubeworm. iScience 2023; 26:107033. [PMID: 37389180 PMCID: PMC10300362 DOI: 10.1016/j.isci.2023.107033] [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: 11/30/2022] [Revised: 03/11/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Endosymbiosis with chemosynthetic Gammaproteobacteria is widely recognized as an adaptive mechanism of siboglinid tubeworms, yet evolution of these endosymbionts and their driving forces remain elusive. Here, we report a finished endosymbiont genome (HMS1) of the cold-seep tubeworm Sclerolinum annulatum. The HMS1 genome is small in size, with abundant prophages and transposable elements but lacking gene sets coding for denitrification, hydrogen oxidization, oxidative phosphorylation, vitamin biosynthesis, cell pH and/or sodium homeostasis, environmental sensing, and motility, indicative of early genome erosion and adaptive evolution toward obligate endosymbiosis. Unexpectedly, a prophage embedded in the HMS1 genome undergoes lytic cycle. Highly expressed ROS scavenger and LexA repressor genes indicate that the tubeworm host likely activates the lysogenic phage into lytic cycle through the SOS response to regulate endosymbiont population and harvest nutrients. Our findings indicate progressive evolution of Sclerolinum endosymbionts toward obligate endosymbiosis and expand the knowledge about phage-symbiont-host interaction in deep-sea tubeworms.
Collapse
Affiliation(s)
- Zhao-Ming Gao
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China
| | - Ting Xu
- 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
| | - Hua-Guan Chen
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rui Lu
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jun Tao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 511458, China
| | - Hong-Bin Wang
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou 511458, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518000, China
| |
Collapse
|
12
|
Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol 2023; 21:145. [PMID: 37365567 DOI: 10.1186/s12915-023-01632-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics. RESULTS We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived ~ 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads. CONCLUSIONS We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes.
Collapse
Affiliation(s)
- Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Filippo Nicolini
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
- Fano Marine Center, Department of Biological, Geological and Environmental Sciences, University of Bologna, Viale Adriatico 1/N, 61032, Fano, Italy
| | - Simone Subacchi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniela Pasquale
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Andrea Luchetti
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| |
Collapse
|
13
|
Ip JCH, Ho MH, Chan BKK, Qiu JW. A draft genome assembly of reef-building octocoral Heliopora coerulea. Sci Data 2023; 10:381. [PMID: 37316548 DOI: 10.1038/s41597-023-02291-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
Coral reefs are under existential threat from climate change and anthropogenic impacts. Genomic studies have enhanced our knowledge of resilience and responses of some coral species to environmental stress, but reference genomes are lacking for many coral species. The blue coral Heliopora is the only reef-building octocoral genus and exhibits optimal growth at a temperature close to the bleaching threshold of scleractinian corals. Local and high-latitude expansions of Heliopora coerulea were reported in the last decade, but little is known about the molecular mechanisms underlying its thermal resistance. We generated a draft genome of H. coerulea with an assembled size of 429.9 Mb, scaffold N50 of 1.42 Mb and BUSCO completeness of 94.9%. The genome contains 239.1 Mb repetitive sequences, 27,108 protein coding genes, 6,225 lncRNAs, and 79 miRNAs. This reference genome provides a valuable resource for in-depth studies on the adaptive mechanisms of corals under climate change and the evolution of skeleton in cnidarian.
Collapse
Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| | - Ming-Hay Ho
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
| |
Collapse
|
14
|
Shu Y, Wang Y, Wei Z, Gao N, Wang S, Li C, Xing Q, Hu X, Zhang X, Zhang Y, Zhang W, Bao Z, Ding W. A bacterial symbiont in the gill of the marine scallop Argopecten irradians irradians metabolizes dimethylsulfoniopropionate. MLIFE 2023; 2:178-189. [PMID: 38817626 PMCID: PMC10989825 DOI: 10.1002/mlf2.12072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/23/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Microbial lysis of dimethylsulfoniopropionate (DMSP) is a key step in marine organic sulfur cycling and has been recently demonstrated to play an important role in mediating interactions between bacteria, algae, and zooplankton. To date, microbes that have been found to lyse DMSP are largely confined to free-living and surface-attached bacteria. In this study, we report for the first time that a symbiont (termed "Rhodobiaceae bacterium HWgs001") in the gill of the marine scallop Argopecten irradians irradians can lyse and metabolize DMSP. Analysis of 16S rRNA gene sequences suggested that HWgs001 accounted for up to 93% of the gill microbiota. Microscopic observations suggested that HWgs001 lived within the gill tissue. Unlike symbionts of other bivalves, HWgs001 belongs to Alphaproteobacteria rather than Gammaproteobacteria, and no genes for carbon fixation were identified in its small genome. Moreover, HWgs001 was found to possess a dddP gene, responsible for the lysis of DMSP to acrylate. The enzymatic activity of dddP was confirmed using the heterologous expression, and in situ transcription of the gene in scallop gill tissues was demonstrated using reverse-transcription PCR. Together, these results revealed a taxonomically and functionally unique symbiont, which represents the first-documented DMSP-metabolizing symbiont likely to play significant roles in coastal marine ecosystems.
Collapse
Affiliation(s)
- Yi Shu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Yongming Wang
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
| | - Ning Gao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Shuyan Wang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Chun‐Yang Li
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Xiao‐Hua Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Yu‐Zhong Zhang
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Weipeng Zhang
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic InstitutionOcean University of ChinaSanyaChina
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and BreedingOcean University of ChinaQingdaoChina
- College of Marine Life SciencesOcean University of ChinaQingdaoChina
| |
Collapse
|
15
|
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
|
16
|
Lin YT, Xu T, Ip JCH, Sun Y, Fang L, Luan T, Zhang Y, Qian PY, Qiu JW, Qian PY, Qiu JW. Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis. Zool Res 2023; 44:106-125. [PMID: 36419378 PMCID: PMC9841196 DOI: 10.24272/j.issn.2095-8137.2022.279] [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] [Indexed: 11/23/2022] Open
Abstract
Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.
Collapse
Affiliation(s)
- Yi-Tao Lin
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yanan Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ling Fang
- Instrumental Analysis & Research Center, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China,Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China,E-mail:
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China,
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
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
|
18
|
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
|
19
|
Han W, Liu L, Wang J, Wei H, Li Y, Zhang L, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L, Zhang L, Wang S. Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nat Ecol Evol 2022; 6:1891-1906. [PMID: 36280781 DOI: 10.1038/s41559-022-01898-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. The long-term undifferentiation of molluscan sex chromosomes is potentially sustained by the unexpected intertwined regulation of reversible sex-biased genes, together with the lack of sexual dimorphism and occasional sex chromosome turnover. The pleiotropic constraint of regulation of reversible sex-biased genes is widely present in ancient homomorphic sex chromosomes and might be resolved in heteromorphic sex chromosomes through gene duplication followed by subfunctionalization. The evolutionary dynamics of sex chromosomes suggest a mechanism for 'inheritance' turnover of sex-determining genes that is mediated by translocation of a sex-determining enhancer. On the basis of these findings, we propose an evolutionary model for the long-term preservation of homomorphic sex chromosomes.
Collapse
Affiliation(s)
- Wentao Han
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liangjie Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huilan Wei
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lijing Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenyi Guo
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yajuan Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tian Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Qiang Xing
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ya Shu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tong Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yaxin Yang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiwei Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruojiao Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiachen Yu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jia Lv
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shanshan Lian
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoli Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Lingling Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
20
|
Takeuchi T, Suzuki Y, Watabe S, Nagai K, Masaoka T, Fujie M, Kawamitsu M, Satoh N, Myers EW. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Res 2022; 29:dsac035. [PMID: 36351462 PMCID: PMC9646362 DOI: 10.1093/dnares/dsac035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 07/30/2023] Open
Abstract
Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.
Collapse
Affiliation(s)
| | - Yoshihiko Suzuki
- Present address: Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Sagamihara, Kanagawa, Japan
| | - Kiyohito Nagai
- Pearl Research Institute, K. MIKIMOTO & CO., LTD, Shima, Mie, Japan
| | - Tetsuji Masaoka
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Tamaki, Mie, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eugene W Myers
- Algorithms for Eco and Evo Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| |
Collapse
|
21
|
Yao G, Zhang H, Xiong P, Jia H, He M. Effects of scale worm parasitism on interactions between the symbiotic gill microbiome and gene regulation in deep sea mussel hosts. Front Microbiol 2022; 13:940766. [PMID: 36046021 PMCID: PMC9421265 DOI: 10.3389/fmicb.2022.940766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Diverse adaptations to the challenging deep sea environment are expected to be found across all deep sea organisms. Scale worms Branchipolynoe pettiboneae are believed to adapt to the deep sea environment by parasitizing deep sea mussels; this biotic interaction is one of most known in the deep sea chemosynthetic ecosystem. However, the mechanisms underlying the effects of scale worm parasitism on hosts are unclear. Previous studies have revealed that the microbiota plays an important role in host adaptability. Here, we compared gill-microbiota, gene expression and host-microorganism interactions in a group of deep sea mussels (Gigantidas haimaensis) parasitized by scale worm (PA group) and a no parasitic control group (NPA group). The symbiotic microorganism diversity of the PA group significantly decreased than NPA group, while the relative abundance of chemoautotrophic symbiotic bacteria that provide the host with organic carbon compounds significantly increased in PA. Interestingly, RNA-seq revealed that G. haimaensis hosts responded to B. pettiboneaei parasitism through significant upregulation of protein and lipid anabolism related genes, and that this parasitism may enhance host mussel nutrient anabolism but inhibit the host’s ability to absorb nutrients, thus potentially helping the parasite obtain nutrients from the host. In an integrated analysis of the interactions between changes in the microbiota and host gene dysregulation, we found an agreement between the microbiota and transcriptomic responses to B. pettiboneaei parasitism. Together, our findings provide new insights into the effects of parasite scale worms on changes in symbiotic bacteria and gene expression in deep sea mussel hosts. We explored the potential role of host-microorganism interactions between scale worms and deep sea mussels, and revealed the mechanisms through which scale worm parasitism affects hosts in deep sea chemosynthetic ecosystem.
Collapse
Affiliation(s)
- Gaoyou Yao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hua Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
| | - Panpan Xiong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Huixia Jia
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Maoxian He,
| |
Collapse
|
22
|
Shimizu K, Takeuchi T, Negishi L, Kurumizaka H, Kuriyama I, Endo K, Suzuki M. Evolution of EGF-like and Zona pellucida domains containing shell matrix proteins in mollusks. Mol Biol Evol 2022; 39:6633355. [PMID: 35796746 PMCID: PMC9290575 DOI: 10.1093/molbev/msac148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several types of shell matrix proteins (SMPs) have been identified in molluskan shells. Their diversity is the consequence of various molecular processes, including domain shuffling and gene duplication. However, the evolutionary origin of most SMPs remains unclear. In this study, we investigated the evolutionary process EGF-like and zona pellucida (ZP) domains containing SMPs. Two types of the proteins (EGF-like protein (EGFL) and EGF-like and ZP domains containing protein (EGFZP)) were found in the pearl oyster, Pinctada fucata. In contrast, only EGFZP was identified in the gastropods. Phylogenetic analysis and genomic arrangement studies showed that EGFL and EGFZP formed a clade in bivalves, and their encoding genes were localized in tandem repeats on the same scaffold. In P. fucata, EGFL genes were expressed in the outer part of mantle epithelial cells are related to the calcitic shell formation. However, in both P. fucata and the limpet Nipponacmea fuscoviridis, EGFZP genes were expressed in the inner part of the mantle epithelial cells are related to aragonitic shell formation. Furthermore, our analysis showed that in P. fucata, the ZP domain interacts with eight SMPs that have various functions in the nacreous shell mineralization. The data suggest that the ZP domain can interact with other SMPs, and EGFL evolution in pterimorph bivalves represents an example of neo-functionalization that involves the acquisition of a novel protein through gene duplication.
Collapse
Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie 517-0404, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| |
Collapse
|
23
|
Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea. Genes (Basel) 2022; 13:genes13050903. [PMID: 35627288 PMCID: PMC9140397 DOI: 10.3390/genes13050903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/06/2022] [Accepted: 05/14/2022] [Indexed: 02/04/2023] Open
Abstract
The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31–1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate.
Collapse
|
24
|
Yuan J, Zhang X, Kou Q, Sun Y, Liu C, Li S, Yu Y, Zhang C, Jin S, Xiang J, Li X, Li F. Genome of a giant isopod, Bathynomus jamesi, provides insights into body size evolution and adaptation to deep-sea environment. BMC Biol 2022; 20:113. [PMID: 35562825 PMCID: PMC9107163 DOI: 10.1186/s12915-022-01302-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022] Open
Abstract
Background The deep-sea may be regarded as a hostile living environment, due to low temperature, high hydrostatic pressure, and limited food and light. Isopods, a species-rich group of crustaceans, are widely distributed across different environments including the deep sea and as such are a useful model for studying adaptation, migration, and speciation. Similar to other deep-sea organisms, giant isopods have larger body size than their shallow water relatives and have large stomachs and fat bodies presumably to store organic reserves. In order to shed light on the genetic basis of these large crustaceans adapting to the oligotrophic environment of deep-sea, the high-quality genome of a deep-sea giant isopod Bathynomus jamesi was sequenced and assembled. Results B. jamesi has a large genome of 5.89 Gb, representing the largest sequenced crustacean genome to date. Its large genome size is mainly attributable to the remarkable proliferation of transposable elements (84%), which may enable high genome plasticity for adaptive evolution. Unlike its relatives with small body size, B. jamesi has expanded gene families related to pathways of thyroid and insulin hormone signaling that potentially contribute to its large body size. Transcriptomic analysis showed that some expanded gene families related to glycolysis and vesicular transport were specifically expressed in its digestive organs. In addition, comparative genomics and gene expression analyses in six tissues suggested that B. jamesi has inefficient lipid degradation, low basal metabolic rate, and bulk food storage, suggesting giant isopods adopt a more efficient mechanism of nutrient absorption, storage, and utilization to provide sustained energy supply for their large body size. Conclusions Taken together, the giant isopod genome may provide a valuable resource for understanding body size evolution and adaptation mechanisms of macrobenthic organisms to deep-sea environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01302-6.
Collapse
Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qi Kou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin, 300457, China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xinzheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Department of Marine Organism Taxonomy & Phylogeny, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| |
Collapse
|
25
|
Yan G, Lan Y, Sun J, Xu T, Wei T, Qian PY. Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences. iScience 2022; 25:104092. [PMID: 35402864 PMCID: PMC8983377 DOI: 10.1016/j.isci.2022.104092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/13/2022] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
Precise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.
Collapse
Affiliation(s)
- Guoyong Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi Lan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tong Wei
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Corresponding author
| |
Collapse
|
26
|
Perez M, Breusing C, Angers B, Beinart RA, Won YJ, Young CR. Divergent paths in the evolutionary history of maternally transmitted clam symbionts. Proc Biol Sci 2022; 289:20212137. [PMID: 35259985 PMCID: PMC8905170 DOI: 10.1098/rspb.2021.2137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.
Collapse
Affiliation(s)
- Maëva Perez
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montreal, Canada
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | | |
Collapse
|
27
|
Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot JF, Allam B. Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 2022; 23:192. [PMID: 35260071 PMCID: PMC8905726 DOI: 10.1186/s12864-021-08262-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences. RESULTS Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves. CONCLUSIONS The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.
Collapse
Affiliation(s)
- Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Emmanuelle Pales Espinosa
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Arnaud Tanguy
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Isabelle Boutet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Nadège Guiglielmoni
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, Avenue F.D. Roosevelt 50, B-1050, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels - (IB)2, B-1050, Brussels, Belgium
| | - Bassem Allam
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, 100 Nicolls Road, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
| |
Collapse
|
28
|
McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM. The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol. G3 (BETHESDA, MD.) 2022; 12:6460334. [PMID: 34897429 PMCID: PMC9210306 DOI: 10.1093/g3journal/jkab423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
Collapse
Affiliation(s)
- Michael A McCartney
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sophie Mallez
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angelico Obille
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | | | - Adam Herman
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | - Eli D Sone
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.,Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4 Canada.,Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Kevin A T Silverstein
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA.,Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
29
|
Liu H, Zha S, Zhang W, Yuan W, Lin Z, Bao Y. Genome-wide identification and characteristic analysis of PGRP gene family in Tegillarca granosa reveals distinct immune response of the invasive pathogen. FISH & SHELLFISH IMMUNOLOGY 2022; 121:232-238. [PMID: 35031474 DOI: 10.1016/j.fsi.2022.01.015] [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: 10/18/2021] [Revised: 12/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
The peptidoglycan recognition proteins (PGRPs) are conserved innate immune molecular in invertebrates and vertebrates, which play important roles in immune system by recognize the peptidoglycans of bacterial cell walls. Although PGRPs have been extensively characterized in insects, a systematic analysis of PGRPs in bivalves is lacking. In the present study, the phylogenic relationships, gene structures and expression profiles of PGRPs in marine bivalves were analyzed. The results indicated that the most PGRPs of bivalves were predicted to degrade the peptidoglycans and prevent excessive immunostimulation of bacteria. In addition, the results of the present study showed that the protein diversity of PGRPs in most marine bivalves was mainly generated by the alternative splicing of genes, however the alternative splicing of PGRP gene family was absent in Tegillarca granosa. The differences of PGRPs might be related to the genetic and environmental differences of marine bivalves. Spatiotemporal expression profiling in T. granosa suggested that PGRPs play important roles in the immune response of invasive pathogens. The present study describes a comprehensive view of PGRPs in the blood clam T. granosa and provides a foundation for functional characterization of this gene family in innate immune of marine bivalves.
Collapse
Affiliation(s)
- Hongxing Liu
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Shanjie Zha
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Weifeng Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; School of Marine Science, Ningbo University, Ningbo, 315100, China
| | - Wenbin Yuan
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; School of Marine Science, Ningbo University, Ningbo, 315100, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China.
| |
Collapse
|
30
|
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
|
31
|
Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
32
|
Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| |
Collapse
|
33
|
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
|
34
|
Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
Collapse
|
35
|
Jackson D, Maltz MR, Freund HL, Borneman J, Aronson E. Environment and Diet Influence the Bacterial Microbiome of Ambigolimax valentianus, an Invasive Slug in California. INSECTS 2021; 12:575. [PMID: 34201881 PMCID: PMC8307491 DOI: 10.3390/insects12070575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022]
Abstract
Ambigolimax valentianus is an invasive European terrestrial gastropod distributed throughout California. It is a serious pest of gardens, plant nurseries, and greenhouses. We evaluated the bacterial microbiome of whole slugs to capture a more detailed picture of bacterial diversity and composition in this host. We concentrated on the influences of diet and environment on the Ambigolimax valentianus core bacterial microbiome as a starting point for obtaining valuable information to aid in future slug microbiome studies. Ambigolimax valentianus were collected from two environments (gardens or reared from eggs in a laboratory). DNA from whole slugs were extracted and next-generation 16S rRNA gene sequencing was performed. Slug microbiomes differed between environmental sources (garden- vs. lab-reared) and were influenced by a sterile diet. Lab-reared slugs fed an unsterile diet harbored greater bacterial species than garden-reared slugs. A small core microbiome was present that was shared across all slug treatments. This is consistent with our hypothesis that a core microbiome is present and will not change due to these treatments. Findings from this study will help elucidate the impacts of slug-assisted bacterial dispersal on soils and plants, while providing valuable information about the slug microbiome for potential integrated pest research applications.
Collapse
Affiliation(s)
- Denise Jackson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Natural Science Division, Porterville College, Porterville, CA 93257, USA
| | - Mia R. Maltz
- Center for Conservation Biology, University of California, Riverside, CA 92521, USA;
- Division of Biomedical Sciences, University of California, Riverside, CA 92521, USA
| | - Hannah L. Freund
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA 92521, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
| | - Emma Aronson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Center for Conservation Biology, University of California, Riverside, CA 92521, USA;
| |
Collapse
|
36
|
Ip JCH, Qiu JW, Chan BKK. Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia). Heliyon 2021; 7:e07291. [PMID: 34189321 PMCID: PMC8220330 DOI: 10.1016/j.heliyon.2021.e07291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Members of the infraclass Cirripedia, commonly called barnacles, are unique among the subphylum Crustacea in that they exhibit a biphasic life cycle with a planktonic larval stage and a sessile adult stage. Understanding their unique sessile life and mechanisms of attachment are hampered by the lack of genomic resources. Here, we present a 746 Mb genome assembly of Lepas anserifera – the first sequenced stalked barnacle genome. We estimate that Cirripedia first arose ~495 million years ago (MYA) and further diversified since Mesozoic. A demographic analysis revealed remarkable population changes of the barnacle in relation to sea-level fluctuations in the last 2 MYA. Comparative genomic analyses revealed the expansion of a number of developmental related genes families in barnacle genomes, such as Br–C, PCP20 and Lola, which are potentially important for the evolution of metamorphosis, cuticle development and central nervous system. Phylogenetic analysis and tissue expression profiling showed the possible roles of gene duplication, functional diversification and co-option in shaping the genomic evolution of barnacles. Overall, our study provides not only a valuable draft genome for comparative genomic analysis of crustacean evolution, but also facilitates studies of biofouling control.
Collapse
Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology and Hong Kong Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong.,Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong.,Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
37
|
Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
| |
Collapse
|