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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.
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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
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Breusing C, Johnson SB, Vrijenhoek RC, Young CR. Host hybridization as a potential mechanism of lateral symbiont transfer in deep-sea vesicomyid clams. Mol Ecol 2019; 28:4697-4708. [PMID: 31478269 PMCID: PMC7004080 DOI: 10.1111/mec.15224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Deep-sea vesicomyid clams live in mutualistic symbiosis with chemosynthetic bacteria that are inherited through the maternal germ line. On evolutionary timescales, strictly vertical transmission should lead to cospeciation of host mitochondrial and symbiont lineages; nonetheless, examples of incongruent phylogenies have been reported, suggesting that symbionts are occasionally horizontally transmitted between host species. The current paradigm for vesicomyid clams holds that direct transfers cause host shifts or mixtures of symbionts. An alternative hypothesis suggests that hybridization between host species might explain symbiont transfers. Two clam species, Archivesica gigas and Phreagena soyoae, frequently co-occur at deep-sea hydrocarbon seeps in the eastern Pacific Ocean. Although the two species typically host gammaproteobacterial symbiont lineages marked by divergent 16S rRNA phylotypes, we identified a number of clams with the A. gigas mitotype that hosted symbionts with the P. soyoae phylotype. Demographic inference models based on genome-wide SNP data and three Sanger sequenced gene markers provided evidence that A. gigas and P. soyoae hybridized in the past, supporting the hypothesis that hybridization might be a viable mechanism of interspecific symbiont transfer. These findings provide new perspectives on the evolution of vertically transmitted symbionts and their hosts in deep-sea chemosynthetic environments.
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Affiliation(s)
- Corinna Breusing
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,National Oceanography Centre, Southampton, UK
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Liu H, Cai S, Liu J, Zhang H. Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep-sea habitats. Ecol Evol 2018; 8:7261-7272. [PMID: 30151147 PMCID: PMC6106168 DOI: 10.1002/ece3.4153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 11/06/2022] Open
Abstract
Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide-rich deep-sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein-coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves.
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Affiliation(s)
- Helu Liu
- Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Shanya Cai
- Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Jun Liu
- Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Haibin Zhang
- Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanyaChina
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Ozawa G, Shimamura S, Takaki Y, Takishita K, Ikuta T, Barry JP, Maruyama T, Fujikura K, Yoshida T. Ancient Occasional Host Switching of Maternally Transmitted Bacterial Symbionts of Chemosynthetic Vesicomyid Clams. Genome Biol Evol 2018; 9:2226-2236. [PMID: 28922872 PMCID: PMC5604134 DOI: 10.1093/gbe/evx166] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 11/22/2022] Open
Abstract
Vesicomyid clams in deep-sea chemosynthetic ecosystems harbor sulfur-oxidizing bacteria in their gill epithelial cells. These symbionts, which are vertically transmitted, are species-specific and thought to have cospeciated with their hosts. However, recent studies indicate incongruent phylogenies between some vesicomyid clams and their symbionts, suggesting that symbionts are horizontally transmitted. To more precisely understand the evolution of vesicomyid clams and their symbionts, we compared the evolution of vesicomyid clams and their symbionts through phylogenetic analyses using multi-gene data sets. Many clades in the phylogenetic trees of 13 host species (Abyssogena mariana, Ab. phaseoliformis, Akebiconcha kawamurai, Calyptogena fausta, C. laubieri, C. magnifica, C. nautilei, C. pacifica, Isorropodon fossajaponicum, Phreagena kilmeri, Ph. okutanii, Ph. soyoae, and Pliocardia stearnsii) and their symbionts were well resolved. Six of the 13 host-symbiont pairs (C. fausta, C. magnifica, C. pacifica, Ph. kilmeri, Ph. okutanii, and Ph. soyoae, and their respective symbionts) showed topological congruence. However, the remaining seven pairs (Ak. kawamurai, Ab mariana, Ab. phaseoliformis, C. laubieri, C. nautilei, I. fossajaponicum, and Pl. stearnsii and their corresponding symbionts) showed incongruent topologies, which were supported by the approximately unbiased and Bayes factor tests. Coevolution analyses indicated that six pairs cospeciated, whereas host switching events occurred in the remaining seven pairs. Markedly, multiple host switching events may have occurred in the lineages from the common ancestral symbiont of C. pacifica and C. fausta. Our phylogenetic and coevolution analyses provide additional evidence for host switching during the evolution of vesicomyids.
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Affiliation(s)
- Genki Ozawa
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan.,Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, Japan
| | - Shigeru Shimamura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Tetsuro Ikuta
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - James P Barry
- Monterey Bay Aquarium Research Institute, Moss Landing, Monterey, California
| | - Tadashi Maruyama
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Katsunori Fujikura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan.,Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, Japan
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Shimamura S, Kaneko T, Ozawa G, Matsumoto MN, Koshiishi T, Takaki Y, Kato C, Takai K, Yoshida T, Fujikura K, Barry JP, Maruyama T. Correction: Loss of genes related to Nucleotide Excision Repair (NER) and implications for reductive genome evolution in symbionts of deep-sea vesicomyid clams. PLoS One 2017; 12:e0176805. [PMID: 28441433 PMCID: PMC5404858 DOI: 10.1371/journal.pone.0176805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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