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Silva FJ, Domínguez-Santos R, Latorre A, García-Ferris C. Comparative Transcriptomics of Fat Bodies between Symbiotic and Quasi-Aposymbiotic Adult Females of Blattella germanica with Emphasis on the Metabolic Integration with Its Endosymbiont Blattabacterium and Its Immune System. Int J Mol Sci 2024; 25:4228. [PMID: 38673813 PMCID: PMC11050582 DOI: 10.3390/ijms25084228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
We explored the metabolic integration of Blattella germanica and its obligate endosymbiont Blattabacterium cuenoti by the transcriptomic analysis of the fat body of quasi-aposymbiotic cockroaches, where the endosymbionts were almost entirely removed with rifampicin. Fat bodies from quasi-aposymbiotic insects displayed large differences in gene expression compared to controls. In quasi-aposymbionts, the metabolism of phenylalanine and tyrosine involved in cuticle sclerotization and pigmentation increased drastically to compensate for the deficiency in the biosynthesis of these amino acids by the endosymbionts. On the other hand, the uricolytic pathway and the biosynthesis of uric acid were severely decreased, probably because the reduced population of endosymbionts was unable to metabolize urea to ammonia. Metabolite transporters that could be involved in the endosymbiosis process were identified. Immune system and antimicrobial peptide (AMP) gene expression was also reduced in quasi-aposymbionts, genes encoding peptidoglycan-recognition proteins, which may provide clues for the maintenance of the symbiotic relationship, as well as three AMP genes whose involvement in the symbiotic relationship will require additional analysis. Finally, a search for AMP-like factors that could be involved in controlling the endosymbiont identified two orphan genes encoding proteins smaller than 200 amino acids underexpressed in quasi-aposymbionts, suggesting a role in the host-endosymbiont relationship.
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Affiliation(s)
- Francisco J. Silva
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Rebeca Domínguez-Santos
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
| | - Carlos García-Ferris
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, 46980 Paterna, Spain; (R.D.-S.); (A.L.)
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, 46020 Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, 46100 Burjassot, Spain
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Cornwallis CK, van 't Padje A, Ellers J, Klein M, Jackson R, Kiers ET, West SA, Henry LM. Symbioses shape feeding niches and diversification across insects. Nat Ecol Evol 2023; 7:1022-1044. [PMID: 37202501 PMCID: PMC10333129 DOI: 10.1038/s41559-023-02058-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/15/2023] [Indexed: 05/20/2023]
Abstract
For over 300 million years, insects have relied on symbiotic microbes for nutrition and defence. However, it is unclear whether specific ecological conditions have repeatedly favoured the evolution of symbioses, and how this has influenced insect diversification. Here, using data on 1,850 microbe-insect symbioses across 402 insect families, we found that symbionts have allowed insects to specialize on a range of nutrient-imbalanced diets, including phloem, blood and wood. Across diets, the only limiting nutrient consistently associated with the evolution of obligate symbiosis was B vitamins. The shift to new diets, facilitated by symbionts, had mixed consequences for insect diversification. In some cases, such as herbivory, it resulted in spectacular species proliferation. In other niches, such as strict blood feeding, diversification has been severely constrained. Symbioses therefore appear to solve widespread nutrient deficiencies for insects, but the consequences for insect diversification depend on the feeding niche that is invaded.
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Affiliation(s)
| | - Anouk van 't Padje
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Jacintha Ellers
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Malin Klein
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Raphaella Jackson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, section Ecology and Evolution, Vrije Universiteit, Amsterdam, the Netherlands
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, UK
| | - Lee M Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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3
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Liu JL, Zhang JW, Han W, Wang YS, He SL, Wang ZQ. Advances in the understanding of Blattodea evolution: Insights from phylotranscriptomics and spermathecae. Mol Phylogenet Evol 2023; 182:107753. [PMID: 36898488 DOI: 10.1016/j.ympev.2023.107753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
Cockroaches, an ancient and diverse group of insects on earth that originated in the Carboniferous, displays a wide array of morphology or biology diversity. The spermatheca is an organ of the insect reproductive system; the diversity of spermathecae might be the adaption to different mating and sperm storage strategies. Yet a consensus about the phylogenetic relationships among the main lineages of Blattodea and the evolution of spermatheca has not been reached until now. Here we added the transcriptome data of Anaplectidae for the first time and supplemented other family level groups (such as Blaberidae, Corydiidae) to address the pending issues. Our results showed that Blattoidea was recovered as sister to Corydioidea, which was strongly supported by molecular evidence. In Blattoidea, (Lamproblattidae + Anaplectidae) + (Cryptocercidae + Termitoidae) was strongly supported by our molecular data. In Blaberoidea, Pseudophyllodromiidae and Blaberidae were recovered to be monophyletic, while Blattellidae was found to be paraphyletic with respect to Malaccina. Ectobius sylvestris + Malaccina discoidalis formed the sister group to other Blaberoidea; Blattellidae (except Malaccina discoidalis) + Nyctiboridae was found as the sister of Blaberidae. Corydiidae was recovered to be non-monophyletic due to the embedding of Nocticola sp. Our ASR analysis of spermatheca suggested that primary spermathecae were present in the common ancestor, and it transformed at least six times during the evolutionary history of Blattodea. The evolution of spermatheca could be described as a unidirectional trend: the increased size to accommodate more sperm. Furthermore, major splits within the existing genera of cockroaches occurred in the Upper Paleogene to Neogene. Our study provides strong support for the relationship among three superfamilies and offers some new insights into the phylogeny of cockroaches. Meanwhile, this study also provides basic knowledge on the evolution of spermathecae and reproductive patterns.
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Affiliation(s)
- Jin-Lin Liu
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Jia-Wei Zhang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Han
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Yi-Shu Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Shu-Lin He
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, China
| | - Zong-Qing Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China.
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4
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Luo XX, Li QQ, Zamani A, Che YL, Wang ZQ. Redescription of Periplaneta arabica (Bey-Bienko, 1938) (Blattodea, Blattidae), with a comparative analysis of three species of Periplaneta Burmeister, 1838 (sensu stricto). Zookeys 2023; 1146:165-183. [DOI: 10.3897/zookeys.1146.90817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
The blattid cockroach Periplaneta arabica (Bey-Bienko, 1938) has been poorly understood since its original description. In this study, male and female (including nymph) of P. arabica are paired using DNA barcoding, and their morphological characters (including both external characteristics and genitalia) are described. A detailed comparative morphological study of this species and the closely related Periplaneta americana (Linnaeus, 1758) and Periplaneta lateralis Walker, 1868 was carried out to explore phylogenetically relevant characters.
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5
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Vasquez YM, Bennett GM. A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes. iScience 2022; 25:104786. [PMID: 35982793 PMCID: PMC9379567 DOI: 10.1016/j.isci.2022.104786] [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: 03/27/2022] [Revised: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 01/03/2023] Open
Abstract
Many insects depend on ancient associations with intracellular bacteria for essential nutrition. The genomes of these bacteria are often highly reduced. Although drift is a major driver of symbiont evolution, other evolutionary forces continue to influence them. To understand how ongoing molecular evolution and gene loss shape symbiont genomes, we sequenced two of the most ancient symbionts known, Sulcia and Nasuia, from 20 Hawaiian Nesophrosyne leafhoppers. We leveraged the parallel divergence of Nesophrosyne lineages throughout Hawaii as a natural experimental framework. Sulcia and Nasuia experience ongoing-but divergent-gene loss, often in a convergent fashion. Although some genes are under relaxed selection, purifying and positive selection are also important drivers of genome evolution, particularly in maintaining certain nutritional and cellular functions. Our results further demonstrate that symbionts experience dramatically different evolutionary environments, as evidenced by the finding that Sulcia and Nasuia have one of the slowest and fastest rates of molecular evolution known.
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Affiliation(s)
- Yumary M. Vasquez
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA,Corresponding author
| | - Gordon M. Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA,Corresponding author
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6
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Manthey JD, Girón JC, Hruska JP. Impact of host demography and evolutionary history on endosymbiont molecular evolution: A test in carpenter ants (genus Camponotus) and their Blochmannia endosymbionts. Ecol Evol 2022; 12:e9026. [PMID: 35795355 PMCID: PMC9251289 DOI: 10.1002/ece3.9026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Obligate endosymbioses are tight associations between symbionts and the hosts they live inside. Hosts and their associated obligate endosymbionts generally exhibit codiversification, which has been documented in taxonomically diverse insect lineages. Host demography (e.g., effective population sizes) may impact the demography of endosymbionts, which may lead to an association between host demography and the patterns and processes of endosymbiont molecular evolution. Here, we used whole-genome sequencing data for carpenter ants (Genus Camponotus; subgenera Camponotus and Tanaemyrmex) and their Blochmannia endosymbionts as our study system to address whether Camponotus demography shapes Blochmannia molecular evolution. Using whole-genome phylogenomics, we confirmed previous work identifying codiversification between carpenter ants and their Blochmannia endosymbionts. We found that Blochmannia genes have evolved at a pace ~30× faster than that of their hosts' molecular evolution and that these rates are positively associated with host rates of molecular evolution. Using multiple tests for selection in Blochmannia genes, we found signatures of positive selection and shifts in selection strength across the phylogeny. Host demography was associated with Blochmannia shifts toward increased selection strengths, but not associated with Blochmannia selection relaxation, positive selection, genetic drift rates, or genome size evolution. Mixed support for relationships between host effective population sizes and Blochmannia molecular evolution suggests weak or uncoupled relationships between host demography and Blochmannia population genomic processes. Finally, we found that Blochmannia genome size evolution was associated with genome-wide estimates of genetic drift and number of genes with relaxed selection pressures.
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Affiliation(s)
- Joseph D. Manthey
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | - Jennifer C. Girón
- Department of EntomologyPurdue UniversityWest LafayetteIndianaUSA
- Natural Science Research LaboratoryMuseum of Texas Tech UniversityLubbockTexasUSA
| | - Jack P. Hruska
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
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7
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Ametrano CG, Lumbsch HT, Di Stefano I, Sangvichien E, Muggia L, Grewe F. Should we hail the Red King? Evolutionary consequences of a mutualistic lifestyle in genomes of lichenized ascomycetes. Ecol Evol 2022; 12:e8471. [PMID: 35136549 PMCID: PMC8809443 DOI: 10.1002/ece3.8471] [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: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
The Red Queen dynamic is often brought into play for antagonistic relationships. However, the coevolutionary effects of mutualistic interactions, which predict slower evolution for interacting organisms (Red King), have been investigated to a lesser extent. Lichens are a stable, mutualistic relationship of fungi and cyanobacteria and/or algae, which originated several times independently during the evolution of fungi. Therefore, they represent a suitable system to investigate the coevolutionary effect of mutualism on the fungal genome. We measured substitution rates and selective pressure of about 2000 protein-coding genes (plus the rDNA region) in two different classes of Ascomycota, each consisting of closely related lineages of lichenized and non-lichenized fungi. Our results show that independent lichenized clades are characterized by significantly slower rates for both synonymous and non-synonymous substitutions. We hypothesize that this evolutionary pattern is connected to the lichen life cycle (longer generation time of lichenized fungi) rather than a result of different selection strengths, which is described as the main driver for the Red Kind dynamic. This first empirical evidence of slower evolution in lichens provides an important insight on how biotic cooperative interactions are able to shape the evolution of symbiotic organisms.
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Affiliation(s)
- Claudio G. Ametrano
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - H. Thorsten Lumbsch
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - Isabel Di Stefano
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
| | - Ek Sangvichien
- Department of BiologyFaculty of ScienceRamkhamhaeng UniversityBangkokThailand
| | | | - Felix Grewe
- Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science and EducationField Museum of Natural HistoryChicagoIllinoisUSA
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8
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Kinjo Y, Lo N, Martín PV, Tokuda G, Pigolotti S, Bourguignon T. Enhanced Mutation Rate, Relaxed Selection, and the "Domino Effect" are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont. Mol Biol Evol 2021; 38:3820-3831. [PMID: 34426845 PMCID: PMC8382890 DOI: 10.1093/molbev/msab159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a "domino effect" of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.
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Affiliation(s)
- Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Paula Villa Martín
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Simone Pigolotti
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
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9
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Arab DA, Lo N. Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts. J Mol Evol 2021; 89:238-248. [PMID: 33730185 DOI: 10.1007/s00239-021-10001-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such correlations between the mitochondrial genomes of cockroaches and the genomes of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of the bacterial endosymbionts Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses showed a highly significant correlation of molecular rates between the genomes of Buchnera and the mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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10
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Nalepa CA. Origin of Mutualism Between Termites and Flagellated Gut Protists: Transition From Horizontal to Vertical Transmission. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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11
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Arab DA, Bourguignon T, Wang Z, Ho SYW, Lo N. Evolutionary rates are correlated between cockroach symbionts and mitochondrial genomes. Biol Lett 2020; 16:20190702. [PMID: 31910734 DOI: 10.1098/rsbl.2019.0702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.,Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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