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Langleib M, Calvelo J, Costábile A, Castillo E, Tort JF, Hoffmann FG, Protasio AV, Koziol U, Iriarte A. Evolutionary analysis of species-specific duplications in flatworm genomes. Mol Phylogenet Evol 2024; 199:108141. [PMID: 38964593 DOI: 10.1016/j.ympev.2024.108141] [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: 12/09/2023] [Revised: 06/15/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.
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Affiliation(s)
- Mauricio Langleib
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Alicia Costábile
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Estela Castillo
- Laboratorio de Biología Parasitaria, Instituto de Higiene, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - José F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, United States of America; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, United States of America
| | - Anna V Protasio
- Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, United Kingdom
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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2
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Zhong J, Zhang J, Zhang Y, Ge Y, He W, Liang C, Gao Y, Zhu Z, Machado RAR, Zhou W. Heat stress reprograms herbivory-induced defense responses in potato plants. BMC PLANT BIOLOGY 2024; 24:677. [PMID: 39014327 PMCID: PMC11253553 DOI: 10.1186/s12870-024-05404-x] [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: 11/29/2023] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
Climate change is predicted to increase the occurrence of extreme weather events such as heatwaves, which may thereby impact the outcome of plant-herbivore interactions. While elevated temperature is known to directly affect herbivore growth, it remains largely unclear if it indirectly influences herbivore performance by affecting the host plant they feed on. In this study, we investigated how transient exposure to high temperature influences plant herbivory-induced defenses at the transcript and metabolic level. To this end, we studied the interaction between potato (Solanum tuberosum) plants and the larvae of the potato tuber moth (Phthorimaea operculella) under different temperature regimes. We found that P. operculella larvae grew heavier on leaves co-stressed by high temperature and insect herbivory than on leaves pre-stressed by herbivory alone. We also observed that high temperature treatments altered phylotranscriptomic patterns upon herbivory, which changed from an evolutionary hourglass pattern, in which transcriptomic responses at early and late time points after elicitation are more variable than the ones in the middle, to a vase pattern. Specifically, transcripts of many herbivory-induced genes in the early and late defense stage were suppressed by HT treatment, whereas those in the intermediate stage peaked earlier. Additionally, we observed that high temperature impaired the induction of jasmonates and defense compounds upon herbivory. Moreover, using jasmonate-reduced (JA-reduced, irAOC) and -elevated (JA-Ile-elevated, irCYP94B3s) potato plants, we showed that high temperature suppresses JA signaling mediated plant-induced defense to herbivore attack. Thus, our study provides evidences on how temperature reprograms plant-induced defense to herbivores.
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Affiliation(s)
- Jian Zhong
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Jinyi Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yadong Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yang Ge
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenjing He
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengjuan Liang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchatel, Neuchatel, 2000, Switzerland
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
- Hainan Institute, Zhejiang University, Sanya, 572000, China.
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3
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Ma F, Zheng C. Single-cell phylotranscriptomics of developmental and cell type evolution. Trends Genet 2024; 40:495-510. [PMID: 38490933 DOI: 10.1016/j.tig.2024.02.005] [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: 11/23/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
Single-cell phylotranscriptomics is an emerging tool to reveal the molecular and cellular mechanisms of evolution. We summarize its utility in studying the hourglass pattern of ontogenetic evolution and for understanding the evolutionary history of cell types. The developmental hourglass model suggests that the mid-embryonic stage is the most conserved period of development across species, which is supported by morphological and molecular studies. Single-cell phylotranscriptomic analysis has revealed previously underappreciated heterogeneity in transcriptome ages among lineages and cell types throughout development, and has identified the lineages and tissues that drive the whole-organism hourglass pattern. Single-cell transcriptome age analyses also provide important insights into the origin of germ layers, the different selective forces on tissues during adaptation, and the evolutionary relationships between cell types.
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Affiliation(s)
- Fuqiang Ma
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
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4
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Wu J, Tang W, Li Z, Chakraborty A, Zhou C, Li F, He S. Duplications and Losses of the Detoxification Enzyme Glycosyltransferase 1 Are Related to Insect Adaptations to Plant Feeding. Int J Mol Sci 2024; 25:6080. [PMID: 38892266 PMCID: PMC11173166 DOI: 10.3390/ijms25116080] [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: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Insects have developed sophisticated detoxification systems to protect them from plant secondary metabolites while feeding on plants to obtain necessary nutrients. As an important enzyme in the system, glycosyltransferase 1 (GT1) conjugates toxic compounds to mitigate their harm to insects. However, the evolutionary link between GT1s and insect plant feeding remains elusive. In this study, we explored the evolution of GT1s across different insect orders and feeding niches using publicly available insect genomes. GT1 is widely present in insect species; however, its gene number differs among insect orders. Notably, plant-sap-feeding species have the highest GT1 gene numbers, whereas blood-feeding species display the lowest. GT1s appear to be associated with insect adaptations to different plant substrates in different orders, while the shift to non-plant feeding is related to several losses of GT1s. Most large gene numbers are likely the consequence of tandem duplications showing variations in collinearity among insect orders. These results reveal the potential relationships between the evolution of GT1s and insect adaptation to plant feeding, facilitating our understanding of the molecular mechanisms underlying insect-plant interactions.
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Affiliation(s)
- Jinyu Wu
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Wanjiang Tang
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Zhengyang Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Amrita Chakraborty
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic;
| | - Cao Zhou
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Fei Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Shulin He
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
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5
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Li C, Yang Z, Xu X, Meng L, Liu S, Yang D. Conserved and specific gene expression patterns in the embryonic development of tardigrades. Evol Dev 2024; 26:e12476. [PMID: 38654704 DOI: 10.1111/ede.12476] [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: 09/06/2023] [Revised: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
Tardigrades, commonly known as water bears, are enigmatic organisms characterized by their remarkable resilience to extreme environments despite their simple and compact body structure. To date, there is still much to understand about their evolutionary and developmental features contributing to their special body plan and abilities. This research provides preliminary insights on the conserved and specific gene expression patterns during embryonic development of water bears, focusing on the species Hypsibius exemplaris. The developmental dynamic expression analysis of the genes with various evolutionary age grades indicated that the mid-conserved stage of H. exemplaris corresponds to the period of ganglia and midgut development, with the late embryonic stage showing a transition from non-conserved to conserved state. Additionally, a comparison with Drosophila melanogaster highlighted the absence of certain pathway nodes in development-related pathways, such as Maml and Hairless, which are respectively the transcriptional co-activator and co-repressor of NOTCH regulated genes. We also employed Weighted Gene Co-expression Network Analysis (WGCNA) to investigate the expression patterns of tardigrade-specific genes during embryo development. Our findings indicated that the module containing the highest proportion of tardigrade-specific genes (TSGs) exhibits high expression levels before the mid-conserved stage, potentially playing a role in glutathione and lipid metabolism. These functions may be associated to the ecdysone synthesis and storage cell formation, which is unique to tardigrades.
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Affiliation(s)
- Chaoran Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhixiang Yang
- School of Life Sciences, Hebei University, Baoding, China
| | - Xiaofang Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Lingling Meng
- School of Life Sciences, Hebei University, Baoding, China
| | - Shihao Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Dong Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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Schmutzer M, Dasmeh P, Wagner A. Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation. J Mol Evol 2024; 92:104-120. [PMID: 38470504 PMCID: PMC10978624 DOI: 10.1007/s00239-024-10161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
Virtually all enzymes catalyse more than one reaction, a phenomenon known as enzyme promiscuity. It is unclear whether promiscuous enzymes are more often generalists that catalyse multiple reactions at similar rates or specialists that catalyse one reaction much more efficiently than other reactions. In addition, the factors that shape whether an enzyme evolves to be a generalist or a specialist are poorly understood. To address these questions, we follow a three-pronged approach. First, we examine the distribution of promiscuity in empirical enzymes reported in the BRENDA database. We find that the promiscuity distribution of empirical enzymes is bimodal. In other words, a large fraction of promiscuous enzymes are either generalists or specialists, with few intermediates. Second, we demonstrate that enzyme biophysics is not sufficient to explain this bimodal distribution. Third, we devise a constraint-based model of promiscuous enzymes undergoing duplication and facing selection pressures favouring subfunctionalization. The model posits the existence of constraints between the catalytic efficiencies of an enzyme for different reactions and is inspired by empirical case studies. The promiscuity distribution predicted by our constraint-based model is consistent with the empirical bimodal distribution. Our results suggest that subfunctionalization is possible and beneficial only in certain enzymes. Furthermore, the model predicts that conflicting constraints and selection pressures can cause promiscuous enzymes to enter a 'frustrated' state, in which competing interactions limit the specialisation of enzymes. We find that frustration can be both a driver and an inhibitor of enzyme evolution by duplication and subfunctionalization. In addition, our model predicts that frustration becomes more likely as enzymes catalyse more reactions, implying that natural selection may prefer catalytically simple enzymes. In sum, our results suggest that frustration may play an important role in enzyme evolution.
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Affiliation(s)
- Michael Schmutzer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pouria Dasmeh
- Center for Human Genetics, Philipps University of Marburg, Marburg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Santa Fe Institute, Santa Fe, NM, USA.
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7
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Stevens DM, Moreno-Pérez A, Weisberg AJ, Ramsing C, Fliegmann J, Zhang N, Madrigal M, Martin G, Steinbrenner A, Felix G, Coaker G. Natural variation of immune epitopes reveals intrabacterial antagonism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558511. [PMID: 37790530 PMCID: PMC10543004 DOI: 10.1101/2023.09.21.558511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Plants and animals detect biomolecules termed Microbe-Associated Molecular Patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multi-copy MAMPs on immune induction is unknown. Here we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in both Arabidopsis and tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple Cold Shock Proteins and 46% carry a non-immunogenic form. We uncovered a new mechanism for immune evasion, intrabacterial antagonism, where a non-immunogenic Cold Shock Protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation.
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Affiliation(s)
- Danielle M. Stevens
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis CA 95616, USA
- Department of Plant Pathology, University of California, Davis, Davis CA 95616, USA
| | - Alba Moreno-Pérez
- Department of Plant Pathology, University of California, Davis, Davis CA 95616, USA
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis OR, USA
| | - Charis Ramsing
- Department of Plant Pathology, University of California, Davis, Davis CA 95616, USA
| | - Judith Fliegmann
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Ning Zhang
- Boyce Thompson Institute for Plant Research, Ithaca NY, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca NY, USA
| | - Melanie Madrigal
- Department of Plant Pathology, University of California, Davis, Davis CA 95616, USA
| | - Gregory Martin
- Boyce Thompson Institute for Plant Research, Ithaca NY, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca NY, USA
| | - Adam Steinbrenner
- University of Washington, Department of Biology, Box 351800, Seattle, WA, 98195, USA
| | - Georg Felix
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis CA 95616, USA
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8
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Ortega-Sanz I, Bocigas C, Melero B, Rovira J. Phase variation modulates the multi-phenotypes displayed by clinical Campylobacter jejuni strains. Food Microbiol 2024; 117:104397. [PMID: 37918995 DOI: 10.1016/j.fm.2023.104397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/15/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
The high incidence and prevalence of Campylobacter spp. in the food supply chain entail the importance to understand their mechanisms developed to withstand harsh environmental conditions encountered. Different stress conditions and phenotypic approaches were evaluated to study the behaviour of five clinical C. jejuni isolates with different genotypes, including the tolerance to oxygen and the oxidants hydrogen peroxide and cumene hydroperoxide, the motility and the ability to form biofilm on polystyrene and stainless steel at different temperatures and atmospheres. Whole Genome Sequencing was performed to analyse the occurrence of 216 genes involved in these mechanisms plus phase variation. The isolates showed high tolerance to oxygen and peroxide stress with different swimming motility performances and biofilm formation abilities. Aerotolerance was related with a reduced sensitive to peroxide stress and a loss of motility that promotes biofilm formation depending on the material surface. Comparative genomics did not reveal any clear gene pattern, although phase variation occurring during host infection was observed to be crucial for the modulation of the different survival mechanisms adopted by the bacteria. These findings reveal that the bacteria can combine diverse and complex strategies in an efficient manner to survive and persist in the environment.
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Affiliation(s)
- Irene Ortega-Sanz
- Department of Biotechnology and Food Science, University of Burgos, Burgos, Spain
| | - Carolina Bocigas
- Department of Biotechnology and Food Science, University of Burgos, Burgos, Spain
| | - Beatriz Melero
- Department of Biotechnology and Food Science, University of Burgos, Burgos, Spain
| | - Jordi Rovira
- Department of Biotechnology and Food Science, University of Burgos, Burgos, Spain.
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9
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Yao A, Kohtsuka H, Miura T. Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella). Mar Genomics 2024; 73:101086. [PMID: 38365348 DOI: 10.1016/j.margen.2024.101086] [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: 12/01/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/18/2024]
Abstract
The harlequin sandsmelt (Parapercis pulchella) is a female-to-male sex change fish in which functional females possess ovotestes that consist of both ovarian and testicular tissues. These features indicate that this species could be an excellent model for studying the flexibility of sex differentiation in vertebrates. However, genetic resources in this species have so far been limited. Therefore, in this study, the reference transcriptome of this fish was constructed through RNA-sequencing, de novo transcriptome assembly, superTranscripts construction, and functional annotations. To obtain as many genes as possible, RNA was extracted from various tissues (brains, gills, hearts, livers, guts, and gonads) and various sexual stages (females, individuals during sex change, and males) and then subjected to sequencing and downstream analyses. As a result, 91,884 representative transcripts with 32,627 protein-coding sequences were generated. 72.2% of protein-coding sequences (23,566 sequences) were functionally annotated. Also, our analysis shows that the superTranscripts method effectively removes redundant sequences from raw-assembled data compared with other strategies. The resultant dataset is a valuable resource for future molecular developmental studies on sex change in P. pulchella.
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Affiliation(s)
- Akifumi Yao
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Hisanori Kohtsuka
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Toru Miura
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa 238-0225, Japan.
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Layoun P, López-Pérez M, Haro-Moreno JM, Haber M, Thrash JC, Henson MW, Kavagutti VS, Ghai R, Salcher MM. Flexible genomic island conservation across freshwater and marine Methylophilaceae. THE ISME JOURNAL 2024; 18:wrad036. [PMID: 38365254 PMCID: PMC10872708 DOI: 10.1093/ismejo/wrad036] [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: 12/12/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
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Affiliation(s)
- Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
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11
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Lei L, Gordon SP, Liu L, Sade N, Lovell JT, Rubio Wilhelmi MDM, Singan V, Sreedasyam A, Hestrin R, Phillips J, Hernandez BT, Barry K, Shu S, Jenkins J, Schmutz J, Goodstein DM, Thilmony R, Blumwald E, Vogel JP. The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum. G3 (BETHESDA, MD.) 2023; 14:jkad245. [PMID: 37883711 PMCID: PMC10755203 DOI: 10.1093/g3journal/jkad245] [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: 06/26/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.
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Affiliation(s)
- Li Lei
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sean P Gordon
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lifeng Liu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nir Sade
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - John T Lovell
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Rachel Hestrin
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jeremy Phillips
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bryan T Hernandez
- Crop Improvement and Genetics Research Unit, USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - David M Goodstein
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Roger Thilmony
- Crop Improvement and Genetics Research Unit, USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - John P Vogel
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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12
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Frank ET, Kesner L, Liberti J, Helleu Q, LeBoeuf AC, Dascalu A, Sponsler DB, Azuma F, Economo EP, Waridel P, Engel P, Schmitt T, Keller L. Targeted treatment of injured nestmates with antimicrobial compounds in an ant society. Nat Commun 2023; 14:8446. [PMID: 38158416 PMCID: PMC10756881 DOI: 10.1038/s41467-023-43885-w] [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: 05/26/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Infected wounds pose a major mortality risk in animals. Injuries are common in the ant Megaponera analis, which raids pugnacious prey. Here we show that M. analis can determine when wounds are infected and treat them accordingly. By applying a variety of antimicrobial compounds and proteins secreted from the metapleural gland to infected wounds, workers reduce the mortality of infected individuals by 90%. Chemical analyses showed that wound infection is associated with specific changes in the cuticular hydrocarbon profile, thereby likely allowing nestmates to diagnose the infection state of injured individuals and apply the appropriate antimicrobial treatment. This study demonstrates that M. analis ant societies use antimicrobial compounds produced in the metapleural glands to treat infected wounds and reduce nestmate mortality.
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Affiliation(s)
- Erik T Frank
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland.
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, D-97074, Würzburg, Germany.
| | - Lucie Kesner
- Department of Fundamental Microbiology, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Joanito Liberti
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
- Department of Fundamental Microbiology, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Quentin Helleu
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, F-75005, Paris, France
| | - Adria C LeBoeuf
- Department of Biology, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Andrei Dascalu
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Douglas B Sponsler
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, D-97074, Würzburg, Germany
| | - Fumika Azuma
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, 904-0495, Japan
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, 904-0495, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 02138, USA
| | - Patrice Waridel
- Protein Analysis Facility, Génopode, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, D-97074, Würzburg, Germany
| | - Laurent Keller
- Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland.
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13
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Ullrich KK, Glytnasi NE. oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data. Bioinformatics 2023; 39:btad657. [PMID: 37952198 PMCID: PMC10663984 DOI: 10.1093/bioinformatics/btad657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/22/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
SUMMARY For model species, single-cell RNA-based cell atlases are available. A good cell atlas includes all major stages in a species' ontogeny, and soon, they will be standard even for nonmodel species. Here, we propose a Python package called oggmap, which allows for the easy extraction of an orthomap (gene ages per orthogroup) for any given query species from OrthoFinder and other gene family data resources, like homologous groups from eggNOG or PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic species which can be further used to calculate gene age-weighted expression data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited to one transcriptome evolutionary index, oggmap can visualize the individual gene category (e.g. age class, nucleotide diversity bin) and their corresponding expression profiles to investigate scRNA-based cell type assignments in an evolutionary context. AVAILABILITY AND IMPLEMENTATION oggmap source code is available at https://github.com/kullrich/oggmap, documentation is available at https://oggmap.readthedocs.io/en/latest/. oggmap can be installed via PyPi or directly used via a docker container.
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Affiliation(s)
- Kristian K Ullrich
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Nikoleta E Glytnasi
- Max Planck Research Group: Dynamics of Social Behavior, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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14
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Wang L, Zheng Y, Sun Y, Mao S, Li H, Bo X, Li C, Chen H. TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development. Commun Biol 2023; 6:901. [PMID: 37660148 PMCID: PMC10475079 DOI: 10.1038/s42003-023-05283-2] [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: 09/07/2022] [Accepted: 08/24/2023] [Indexed: 09/04/2023] Open
Abstract
Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their influence on early embryo development remain elusive. Here, we developed a computational framework named TimeTalk from integrated public time-course mouse scRNA-seq datasets to decipher the secret of eLRs. Extensive validations and analyses were performed to ensure the involvement of identified eLRs in early embryo development. Process analysis identified that eLRs could be divided into six temporal windows corresponding to sequential events in the early embryo development process. With the interpolation strategy, TimeTalk is powerful in revealing paracrine settings and studying cell-cell communication during early embryo development. Furthermore, by using TimeTalk in the blastocyst and blastoid models, we found that the blastoid models share the core communication pathways with the epiblast and primitive endoderm lineages in the blastocysts. This result suggests that TimeTalk has transferability to other bio-dynamic processes. We also curated eLRs recognized by TimeTalk, which may provide valuable clues for understanding early embryo development and relevant disorders.
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Affiliation(s)
- Longteng Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, 100871, China
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Shulin Mao
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Yuanpei College, Peking University, Beijing, 100871, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xiaochen Bo
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
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15
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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16
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Barkdull M, Moreau CS. Worker Reproduction and Caste Polymorphism Impact Genome Evolution and Social Genes Across the Ants. Genome Biol Evol 2023; 15:evad095. [PMID: 37243539 PMCID: PMC10287540 DOI: 10.1093/gbe/evad095] [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: 08/01/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Eusocial insects are characterized by several traits, including reproductive division of labor and caste polymorphisms, which likely modulate genome evolution. Concomitantly, evolution may act on specific genes and pathways underlying these novel, sociality-associated phenotypes. Reproductive division of labor should increase the magnitude of genetic drift and reduce the efficacy of selection by reducing effective population size. Caste polymorphism has been associated with relaxed selection and may facilitate directional selection on caste-specific genes. Here, we use comparative analyses of 22 ant genomes to test how reproductive division of labor and worker polymorphism influence positive selection and selection intensity across the genome. Our results demonstrate that worker reproductive capacity is associated with a reduction in the degree of relaxed selection but is not associated with any significant change to positive selection. We find decreases in positive selection in species with polymorphic workers, but no increase in the degree of relaxed selection. Finally, we explore evolutionary patterns in specific candidate genes associated with our focal traits in eusocial insects. Two oocyte patterning genes previously implicated in worker sterility evolve under intensified selection in species with reproductive workers. Behavioral caste genes generally experience relaxed selection associated with worker polymorphism, whereas vestigial and spalt, both associated with soldier development in Pheidole ants, experience intensified selection in worker polymorphic species. These findings expand our understanding of the genetic mechanisms underlying elaborations of sociality. The impacts of reproductive division of labor and caste polymorphisms on specific genes illuminate those genes' roles in generating complex eusocial phenotypes.
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Affiliation(s)
- Megan Barkdull
- Department of Ecology & Evolutionary Biology, Cornell University
| | - Corrie S Moreau
- Department of Ecology & Evolutionary Biology, Cornell University
- Department of Entomology, Cornell University
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17
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Pan B, Ye F, Li T, Wei F, Warren A, Wang Y, Gao S. Potential role of N 6-adenine DNA methylation in alternative splicing and endosymbiosis in Paramecium bursaria. iScience 2023; 26:106676. [PMID: 37182097 PMCID: PMC10173741 DOI: 10.1016/j.isci.2023.106676] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 12/02/2022] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
N6-adenine DNA methylation (6mA), a rediscovered epigenetic mark in eukaryotic organisms, diversifies in abundance, distribution, and function across species, necessitating its study in more taxa. Paramecium bursaria is a typical model organism with endosymbiotic algae of the species Chlorella variabilis. This consortium therefore serves as a valuable system to investigate the functional role of 6mA in endosymbiosis, as well as the evolutionary importance of 6mA among eukaryotes. In this study, we report the first genome-wide, base pair-resolution map of 6mA in P. bursaria and identify its methyltransferase PbAMT1. Functionally, 6mA exhibits a bimodal distribution at the 5' end of RNA polymerase II-transcribed genes and possibly participates in transcription by facilitating alternative splicing. Evolutionarily, 6mA co-evolves with gene age and likely serves as a reverse mark of endosymbiosis-related genes. Our results offer new insights for the functional diversification of 6mA in eukaryotes as an important epigenetic mark.
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Affiliation(s)
- Bo Pan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fei Ye
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Tao Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Fan Wei
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Yuanyuan Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- Corresponding author
| | - Shan Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
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18
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Jones BM, Rubin BER, Dudchenko O, Kingwell CJ, Traniello IM, Wang ZY, Kapheim KM, Wyman ES, Adastra PA, Liu W, Parsons LR, Jackson SR, Goodwin K, Davidson SM, McBride MJ, Webb AE, Omufwoko KS, Van Dorp N, Otárola MF, Pham M, Omer AD, Weisz D, Schraiber J, Villanea F, Wcislo WT, Paxton RJ, Hunt BG, Aiden EL, Kocher SD. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. Nat Ecol Evol 2023; 7:557-569. [PMID: 36941345 DOI: 10.1038/s41559-023-02001-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2023]
Abstract
Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two pleiotropic proteins that bind and transport juvenile hormone (JH)-a key regulator of insect development and reproduction. We find that one of these proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behaviour and suggest that eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral developmental hormone may have been co-opted during one of life's major transitions. More broadly, our results highlight how evolutionary trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.
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Affiliation(s)
- Beryl M Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Benjamin E R Rubin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Callum J Kingwell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Ian M Traniello
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Z Yan Wang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Karen M Kapheim
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biology, Utah State University, Logan, UT, USA
| | - Eli S Wyman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Per A Adastra
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Liu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - S RaElle Jackson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Shawn M Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Matthew J McBride
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Andrew E Webb
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kennedy S Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Nikki Van Dorp
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mauricio Fernández Otárola
- Biodiversity and Tropical Ecology Research Center (CIBET) and School of Biology, University of Costa Rica, San José, Costa Rica
| | - Melanie Pham
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joshua Schraiber
- Department of Biology, Temple University, Philadelphia, PA, USA
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Fernando Villanea
- Department of Biology, Temple University, Philadelphia, PA, USA
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Robert J Paxton
- Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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19
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Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biol 2023; 24:7. [PMID: 36639687 PMCID: PMC9837924 DOI: 10.1186/s13059-022-02844-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. RESULTS Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal-distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. CONCLUSIONS Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.
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Affiliation(s)
- Long Zhao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jinchao Chen
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongzhe Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaomin Bie
- Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiafu Jiang
- Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiaoqi Feng
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhuo Du
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Goemann CL, Wilkinson R, Henriques W, Bui H, Goemann HM, Carlson RP, Viamajala S, Gerlach R, Wiedenheft B. Genome sequence, phylogenetic analysis, and structure-based annotation reveal metabolic potential of Chlorella sp. SLA-04. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Minelli A. Two-way exchanges between animal and plant biology, with focus on evo-devo. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1057355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
By definition, biology is the science of all living beings. However, horizons restricted to either plants or animals have characterized the development of life sciences well beyond the emergence of unified perspectives applying to all forms of life, such as the cell theory or the theory of evolution. Separation between botanical and zoological traditions is not destined to go extinct easily, or shortly. Disciplinary isolation is emphasized by institutional contexts such as scientific societies and their congresses, specialist journals, disciplines recognized as teaching subjects and legitimate and fundable research fields. By shaping the personal agendas of individual scientists, this has a strong impact on the development of biology. In some fields, botanical and zoological contributions have long being effectively intertwined, but in many others plant and animal biology have failed to progress beyond a marginal dialogue. Characteristically, the so-called “general biology” and the philosophy of biology are still zoocentric (and often vertebrato- or even anthropocentric). In this article, I discuss legitimacy and fruitfulness of some old lexical and conceptual exchanges between the two traditions (cell, tissue, and embryo). Finally, moving to recent developments, I compare the contributions of plant vs. animal biology to the establishment of evolutionary developmental biology. We cannot expect that stronger integration between the different strands of life sciences will soon emerge by self-organization, but highlighting this persisting imbalance between plant and animal biology will arguably foster progress.
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22
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Islam MT, Kudla-Williams C, Kar S, Londo JP, Centinari M, Rosa C. Deciphering genome-wide transcriptomic changes in grapevines heavily infested by spotted lanternflies. FRONTIERS IN INSECT SCIENCE 2022; 2:971221. [PMID: 38468776 PMCID: PMC10926465 DOI: 10.3389/finsc.2022.971221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/09/2022] [Indexed: 03/13/2024]
Abstract
The spotted lanternfly, a newly invasive insect in the U.S. that is a great concern for the grapevine industry, produces damage on its host plants through aggressive feeding, using a piercing and sucking method to feed on the phloem of plants. In the eastern US, adult SLF can invade vineyards through fruit ripening until the end of the growing season; however, it is still unclear how prolonged late-season SLF feeding can affect the health of grapevines, as well as the host responses to this extensive damage. Thus, we have performed a comprehensive genome-wide transcriptome analysis in grapevines heavily infested by the spotted lanternfly, as it occurs in Pennsylvania vineyards, and compared it to other relevant transcriptomes in grapes with different degrees to susceptibility to similar pests. Among a variety of plant responses, we highlight here a subset of relevant biological pathways that distinguish or are common to the spotted lanternfly and other phloem feeders in grapevine. The molecular interaction between spotted lanternfly and the vine begins with activation of signal transduction cascades mediated mainly by protein kinase genes. It also induces the expression of transcription factors in the nucleus, of other signaling molecules like phytohormones and secondary metabolites, and their downstream target genes responsible for defense and physiological functions, such as detoxification and photosynthesis. Grapevine responses furthermore include the activation of genes for cell wall strengthening via biosynthesis of major structural components. With this study, we hope to provide the regulatory network to explain effects that the invasive spotted lanternfly has on grapevine health with the goal to improve its susceptibility.
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Affiliation(s)
- Md Tariqul Islam
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States
| | - Crosley Kudla-Williams
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States
| | - Suraj Kar
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Jason P. Londo
- School of Integrative Plant Science Horticulture Section, Cornell AgriTech, Cornell University, Geneva, NY, United States
| | - Michela Centinari
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States
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23
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Richardson MK, Keuck G. The revolutionary developmental biology of Wilhelm His, Sr. Biol Rev Camb Philos Soc 2022; 97:1131-1160. [PMID: 35106889 PMCID: PMC9304566 DOI: 10.1111/brv.12834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
Abstract
Swiss-born embryologist Wilhelm His, Sr. (1831-1904) was the first scientist to study embryos using paraffin histology, serial sectioning and three-dimensional modelling. With these techniques, His made many important discoveries in vertebrate embryology and developmental neurobiology, earning him two Nobel Prize nominations. He also developed several theories of mechanical and evolutionary developmental biology. His argued that adult form is determined by the differential growth of developmental primordia. Furthermore, he suggested that changes in the growth parameters of those primordia are responsible for generating new phenotypes during evolution. His developed these theories in his book 'Our Bodily Form' (Unsere Körperform). Here, we review His's work with special emphasis on its potential importance to the disciplines of evolutionary developmental biology (evo-devo) and mechanobiology.
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Affiliation(s)
- Michael K. Richardson
- Institute of Biology, University of Leiden, Sylvius LaboratorySylviusweg 72Leiden2333 BEThe Netherlands
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24
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Crow M, Suresh H, Lee J, Gillis J. Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Res 2022; 50:4302-4314. [PMID: 35451481 PMCID: PMC9071420 DOI: 10.1093/nar/gkac276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
What makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. We find that ancient genes are expressed in multiple cell types and have well conserved coexpression patterns, however they are expressed at different levels across cell types. Thus, differential regulation of ancient gene programs contributes to transcriptional cell identity. We propose that this differential regulation may play a role in cell diversification in both the animal and plant kingdoms.
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Affiliation(s)
- Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - Hamsini Suresh
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - John Lee
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
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25
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Thompson AW, Wojtas H, Davoll M, Braasch I. Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments. G3 (BETHESDA, MD.) 2022; 12:6533448. [PMID: 35188191 PMCID: PMC8982402 DOI: 10.1093/g3journal/jkac045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 12/13/2022]
Abstract
The Rio Pearlfish, Nematolebias whitei, is a bi-annual killifish species inhabiting seasonal pools in the Rio de Janeiro region of Brazil that dry twice per year. Embryos enter dormant diapause stages in the soil, waiting for the inundation of the habitat which triggers hatching and commencement of a new life cycle. Rio Pearlfish represents a convergent, independent origin of annualism from other emerging killifish model species. While some transcriptomic datasets are available for Rio Pearlfish, thus far, a sequenced genome has been unavailable. Here, we present a high quality, 1.2 Gb chromosome-level genome assembly, genome annotations, and a comparative genomic investigation of the Rio Pearlfish as representative of a vertebrate clade that evolved environmentally cued hatching. We show conservation of 3D genome structure across teleost fish evolution, developmental stages, tissues, and cell types. Our analysis of mobile DNA shows that Rio Pearlfish, like other annual killifishes, possesses an expanded transposable element profile with implications for rapid aging and adaptation to harsh conditions. We use the Rio Pearlfish genome to identify its hatching enzyme gene repertoire and the location of the hatching gland, a key first step in understanding the developmental genetic control of hatching. The Rio Pearlfish genome expands the comparative genomic toolkit available to study convergent origins of seasonal life histories, diapause, and rapid aging phenotypes. We present the first set of genomic resources for this emerging model organism, critical for future functional genetic, and multiomic explorations of “Eco-Evo-Devo” phenotypes of resilience and adaptation to extreme environments.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
| | - Harrison Wojtas
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Myles Davoll
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution & Behavior (EEB) Program, Michigan State University, East Lansing, MI 48824, USA
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26
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27
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Richardson MK. Theories, laws, and models in evo-devo. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:36-61. [PMID: 34570438 PMCID: PMC9292786 DOI: 10.1002/jez.b.23096] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary developmental biology (evo-devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo-devo, past and present. Nineteenth-century evo-devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the "inverted invertebrate" theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old "primordial leaf," "inverted invertebrate," and "segmented head" theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal-zygotic transition. There are many supposed "laws" of evo-devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the "body plan" is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo-devo will be to develop new theories and models to accommodate the wealth of new data from high-throughput sequencing, including single-cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the "transcriptomic hourglass" models.
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28
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Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle. mSystems 2021; 6:e0094421. [PMID: 34609172 PMCID: PMC8547437 DOI: 10.1128/msystems.00944-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism, and biogeography within the SAR116 clade. This increased genomic diversity has led to the discovery of two subclades that, despite coexisting in the same environment, display different properties in their genomic makeup. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlined features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp), and strong purifying selection (low ratio of nonsynonymous to synonymous polymorphisms [dN/dS]). Besides, they were more abundant in metagenomic databases recruiting at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in metagenome-assembled genomes (MAGs), included the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way both clades can metabolize dimethylsulfoniopropionate (DMSP). IMPORTANCE The SAR116 clade of Alphaproteobacteria is a ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study these kinds of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genomic makeup of the two subclades that could serve to illustrate how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.
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29
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López-Pérez M, Jayakumar JM, Grant TA, Zaragoza-Solas A, Cabello-Yeves PJ, Almagro-Moreno S. Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations. Proc Natl Acad Sci U S A 2021; 118:e2103470118. [PMID: 34593634 PMCID: PMC8501797 DOI: 10.1073/pnas.2103470118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.
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Affiliation(s)
- Mario López-Pérez
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Jane M Jayakumar
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
| | - Trudy-Ann Grant
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
| | - Asier Zaragoza-Solas
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Pedro J Cabello-Yeves
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816;
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL 32816
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30
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Raas MWD, Zijlmans DW, Vermeulen M, Marks H. There is another: H3K27me3-mediated genomic imprinting. Trends Genet 2021; 38:82-96. [PMID: 34304914 DOI: 10.1016/j.tig.2021.06.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022]
Abstract
DNA methylation has long been considered the primary epigenetic mediator of genomic imprinting in mammals. Recent epigenetic profiling during early mouse development revealed the presence of domains of trimethylation of lysine 27 on histone H3 (H3K27me3) and chromatin compaction specifically at the maternally derived allele, independent of DNA methylation. Within these domains, genes are exclusively expressed from the paternally derived allele. This novel mechanism of noncanonical imprinting plays a key role in the development of mouse extraembryonic tissues and in the regulation of imprinted X-chromosome inactivation, highlighting the importance of parentally inherited epigenetic histone modifications. Here, we discuss the mechanisms underlying H3K27me3-mediated noncanonical imprinting in perspective of the dynamic chromatin landscape during early mouse development and explore evolutionary origins of noncanonical imprinting.
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Affiliation(s)
- Maximilian W D Raas
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525GA Nijmegen, The Netherlands.
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31
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Innovation, conservation, and repurposing of gene function in root cell type development. Cell 2021; 184:3333-3348.e19. [PMID: 34010619 DOI: 10.1016/j.cell.2021.04.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/19/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022]
Abstract
Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.
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32
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Wei FJ, Ueno S, Ujino-Ihara T, Saito M, Tsumura Y, Higuchi Y, Hirayama S, Iwai J, Hakamata T, Moriguchi Y. Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1). PLoS One 2021; 16:e0247180. [PMID: 33630910 PMCID: PMC7935350 DOI: 10.1371/journal.pone.0247180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 02/02/2021] [Indexed: 11/18/2022] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated proteins. According to the benchmark set by BUSCO, 87.01% of cDNAs identified were complete genes, and 78.47% were complete and single-copy genes. Compared to other full-length cDNA resources collected by Sanger and PacBio sequencers, the extent of the coverage in our dataset was the highest, indicating that these data can be safely used for further studies. When two tissue-specific libraries were compared, there were significant expression differences between male strobili and leaf and bark sets. Moreover, subtle expression difference between male-fertile and sterile libraries were detected. Orthologous genes from other model plants and conifer species were identified. We demonstrated that our transcriptome assembly output (CJ3006NRE) can serve as a reference transcriptome for future functional genomics and evolutionary biology studies.
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Affiliation(s)
- Fu-Jin Wei
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
- * E-mail:
| | - Tokuko Ujino-Ihara
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Maki Saito
- Forest Research Institute, Toyama Prefectural Agricultural Forestry and Fisheries Research Center, Toyama, Japan
| | - Yoshihiko Tsumura
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yuumi Higuchi
- Niigata Prefectural Forest Research Institute, Niigata, Japan
| | | | - Junji Iwai
- Niigata Prefectural Forest Research Institute, Niigata, Japan
| | - Tetsuji Hakamata
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Shizuoka, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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Uesaka M, Kuratani S, Irie N. The developmental hourglass model and recapitulation: An attempt to integrate the two models. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:76-86. [PMID: 33503326 PMCID: PMC9292893 DOI: 10.1002/jez.b.23027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome‐based studies, on the other hand, have reported that mid‐embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid‐embryonic period. In accordance with this, recapitulation‐like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility‐based study provided molecular evidence for recapitulation in the mid‐to‐late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular‐based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass‐like evolutionary conservation in vertebrate embryogenesis. Recapitulation pattern has been reported for chromatin accessibility during the mid‐to‐late embryogenesis. The observed recapitulation pattern and the developmental hourglass model may coexist. The possible evolutionary mechanisms underlying tendencies of embryonic evolution were discussed.
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Affiliation(s)
- Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory for Evolutionary Morphology, RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Naoki Irie
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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35
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Mycoavidus sp. Strain B2-EB: Comparative Genomics Reveals Minimal Genomic Features Required by a Cultivable Burkholderiaceae-Related Endofungal Bacterium. Appl Environ Microbiol 2020; 86:AEM.01018-20. [PMID: 32651207 DOI: 10.1128/aem.01018-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
Obligate bacterial endosymbionts are critical to the existence of many eukaryotes. Such endobacteria are usually characterized by reduced genomes and metabolic dependence on the host, which may cause difficulty in isolating them in pure cultures. Family Burkholderiaceae-related endofungal bacteria affiliated with the Mycoavidus-Glomeribacter clade can be associated with the fungal subphyla Mortierellomycotina and Glomeromycotina. In this study, a cultivable endosymbiotic bacterium, Mycoavidus sp. strain B2-EB, present in the fungal host Mortierella parvispora was obtained successfully. The B2-EB genome (1.88 Mb) represents the smallest genome among the endofungal bacterium Mycoavidus cysteinexigens (2.64-2.80 Mb) of Mortierella elongata and the uncultured endosymbiont "Candidatus Glomeribacter gigasporarum" (1.37 to 2.36 Mb) of arbuscular mycorrhizal fungi. Despite a reduction in genome size, strain B2-EB displays a high genome completeness, suggesting a nondegenerative reduction in the B2-EB genome. Compared with a large proportion of transposable elements (TEs) in other known Mycoavidus genomes (7.2 to 11.5% of the total genome length), TEs accounted for only 2.4% of the B2-EB genome. This pattern, together with a high proportion of single-copy genes in the B2-EB genome, suggests that the B2-EB genome reached a state of relative evolutionary stability. These results represent the most streamlined structure among the cultivable endofungal bacteria and suggest the minimal genome features required by both an endofungal lifestyle and artificial culture. This study allows us to understand the genome evolution of Burkholderiaceae-related endosymbionts and to elucidate microbiological interactions.IMPORTANCE This study attempted the isolation of a novel endobacterium, Mycoavidus sp. B2-EB (JCM 33615), harbored in the fungal host Mortierella parvispora E1425 (JCM 39028). We report the complete genome sequence of this strain, which possesses a reduced genome size with relatively high genome completeness and a streamlined genome structure. The information indicates the minimal genomic features required by both the endofungal lifestyle and artificial cultivation, which furthers our understanding of genome reduction in fungal endosymbionts and extends the culture resources for biotechnological development on engineering synthetic microbiomes.
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36
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Xie Y, Chang J, Kwan HS. Carbon metabolism and transcriptome in developmental paths differentiation of a homokaryotic Coprinopsis cinerea strain. Fungal Genet Biol 2020; 143:103432. [PMID: 32681999 DOI: 10.1016/j.fgb.2020.103432] [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] [Received: 03/23/2020] [Revised: 06/01/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
The balance and interplay between sexual and asexual reproduction is one of the most intriguing mysteries in the study of fungi. The choice of developmental strategy reflects the ability of fungi to adapt to the changing environment. However, the evolution of developmental paths and the metabolic regulation during differentiation and morphogenesis are poorly understood. Here, an analysis was performed of carbohydrate metabolism and gene expression regulation during the early differentiation process from the vegetative mycelium, to the differentiated structures, fruiting body, oidia and sclerotia, of a homokaryotic fruiting Coprinopsis cinerea strain A43mutB43mut pab1-1 #326. Changes during morphogenesis and the evolution of developmental strategies were followed. Conversion between glucose and glycogen and between glucose and beta-glucan were the main carbon flows in the differentiation processes. Genes related to carbohydrate transport and metabolism were significantly differentially expressed among paths. Sclerotia displayed a set of specifically up-regulated genes that were enriched in the carbon metabolism and energy production and conversion processes. Evolutionary transcriptomic analysis of four developmental paths showed that all transcriptomes were under the purifying selection, and the more stressful the environment, the younger the transcriptome age. Oidiation has the lowest value of transcriptome age index (TAI) and transcriptome divergence index (TDI), while the fruiting process has the highest of both indexes. These findings provide new insights into the regulations of carbon metabolism and gene expressions during the early stages of fungal developmental paths differentiation, and improve our understanding of the evolutionary process of life history and reproductive strategy in fungi.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Jinhui Chang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region.
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37
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Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES. phylostratr: a framework for phylostratigraphy. Bioinformatics 2020; 35:3617-3627. [PMID: 30873536 DOI: 10.1093/bioinformatics/btz171] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. This is done by searching for homologs within increasingly broad clades. The deepest clade that contains a homolog of the protein(s) encoded by a gene is that gene's phylostratum. RESULTS We have created a general R-based framework, phylostratr, to estimate the phylostratum of every gene in a species. The program fully automates analysis: selecting species for balanced representation, retrieving sequences, building databases, inferring phylostrata and returning diagnostics. Key diagnostics include: detection of genes with inferred homologs in old clades, but not intermediate ones; proteome quality assessments; false-positive diagnostics, and checks for missing organellar genomes. phylostratr allows extensive customization and systematic comparisons of the influence of analysis parameters or genomes on phylostrata inference. A user may: modify the automatically generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae. AVAILABILITY AND IMPLEMENTATION Source code available at https://github.com/arendsee/phylostratr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zebulun Arendsee
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
| | - Jing Li
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Arun Seetharam
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Department of Statistics, Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
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38
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McGowan J, O’Hanlon R, Owens RA, Fitzpatrick DA. Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae. Microorganisms 2020; 8:E653. [PMID: 32365808 PMCID: PMC7285336 DOI: 10.3390/microorganisms8050653] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species-Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.
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Affiliation(s)
- Jamie McGowan
- Department of Biology, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland; (R.A.O.); (D.A.F.)
- Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland
| | | | - Rebecca A. Owens
- Department of Biology, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland; (R.A.O.); (D.A.F.)
- Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland
| | - David A. Fitzpatrick
- Department of Biology, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland; (R.A.O.); (D.A.F.)
- Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland
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39
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Wang J, Zhang L, Lian S, Qin Z, Zhu X, Dai X, Huang Z, Ke C, Zhou Z, Wei J, Liu P, Hu N, Zeng Q, Dong B, Dong Y, Kong D, Zhang Z, Liu S, Xia Y, Li Y, Zhao L, Xing Q, Huang X, Hu X, Bao Z, Wang S. Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae. Nat Ecol Evol 2020; 4:725-736. [PMID: 32203475 DOI: 10.1038/s41559-020-1138-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 02/06/2020] [Indexed: 12/16/2022]
Abstract
The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The 'larva-first' hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added biphasic life cycle; the 'adult-first' hypothesis suggests that the first metazoans were adult forms, with the biphasic life cycle arising later via larval intercalation. Here, we investigate the evolutionary origin of primary larvae by conducting ontogenetic transcriptome profiling for Mollusca-the largest marine phylum characterized by a trochophore larval stage and highly variable adult forms. We reveal that trochophore larvae exhibit rapid transcriptome evolution with extraordinary incorporation of novel genes (potentially contributing to adult shell evolution), and that cell signalling/communication genes (for example, caveolin and innexin) are probably crucial for larval evolution. Transcriptome age analysis of eight metazoan species reveals the wide presence of young larval transcriptomes in both trochozoans and other major metazoan lineages, therefore arguing against the prevailing larva-first hypothesis. Our findings support an adult-first evolutionary scenario with a single metazoan larval intercalation, and suggest that the first appearance of proto-larva probably occurred after the divergence of direct-developing Ctenophora from a metazoan ancestor.
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Affiliation(s)
- Jing Wang
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shanshan Lian
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenkui Qin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuan Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Jiankai Wei
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Naina Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bo Dong
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Dexu Kong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Sinuo Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Xia
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Liang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoli Hu
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- 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, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,The Sars-Fang Centre, Ocean University of China, Qingdao, China.
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40
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Friedman DA, York RA, Hilliard AT, Gordon DM. Gene expression variation in the brains of harvester ant foragers is associated with collective behavior. Commun Biol 2020; 3:100. [PMID: 32139795 PMCID: PMC7057964 DOI: 10.1038/s42003-020-0813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/10/2020] [Indexed: 01/10/2023] Open
Abstract
Natural selection on collective behavior acts on variation among colonies in behavior that is associated with reproductive success. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success. We used RNA-seq to examine gene expression in the brains of foragers in a natural setting. We find that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with two colony traits: sensitivity of foraging activity to humidity, and forager brain dopamine to serotonin ratio. Loci that were correlated with colony behavioral differences were enriched in neurotransmitter receptor signaling & metabolic functions, tended to be more central to coexpression networks, and are evolving under higher protein-coding sequence constraint. Natural selection may shape colony foraging behavior through variation in gene expression.
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Affiliation(s)
| | | | | | - Deborah M Gordon
- Stanford University, Department of Biology, Stanford, CA, 94305, USA.
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41
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Xiang D, Quilichini TD, Liu Z, Gao P, Pan Y, Li Q, Nilsen KT, Venglat P, Esteban E, Pasha A, Wang Y, Wen R, Zhang Z, Hao Z, Wang E, Wei Y, Cuthbert R, Kochian LV, Sharpe A, Provart N, Weijers D, Gillmor CS, Pozniak C, Datla R. The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development. THE PLANT CELL 2019; 31:2888-2911. [PMID: 31628162 PMCID: PMC6925018 DOI: 10.1105/tpc.19.00397] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 05/17/2023]
Abstract
Modern wheat production comes from two polyploid species, Triticum aestivum and Triticum turgidum (var durum), which putatively arose from diploid ancestors Triticum urartu, Aegilops speltoides, and Aegilops tauschii How gene expression during embryogenesis and grain development in wheats has been shaped by the differing contributions of diploid genomes through hybridization, polyploidization, and breeding selection is not well understood. This study describes the global landscape of gene activities during wheat embryogenesis and grain development. Using comprehensive transcriptomic analyses of two wheat cultivars and three diploid grasses, we investigated gene expression at seven stages of embryo development, two endosperm stages, and one pericarp stage. We identified transcriptional signatures and developmental similarities and differences among the five species, revealing the evolutionary divergence of gene expression programs and the contributions of A, B, and D subgenomes to grain development in polyploid wheats. The characterization of embryonic transcriptional programming in hexaploid wheat, tetraploid wheat, and diploid grass species provides insight into the landscape of gene expression in modern wheat and its ancestral species. This study presents a framework for understanding the evolution of domesticated wheat and the selective pressures placed on grain production, with important implications for future performance and yield improvements.plantcell;31/12/2888/FX1F1fx1.
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Affiliation(s)
- Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ziying Liu
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Peng Gao
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Kirby T Nilsen
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Prakash Venglat
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University, Shenzhen 518060, China
| | - Rui Wen
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Zhongjuan Zhang
- Laboratory of Biochemistry, Wageningen University, 6703HA Wageningen, The Netherlands
| | - Zhaodong Hao
- Laboratory of Biochemistry, Wageningen University, 6703HA Wageningen, The Netherlands
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Yangdou Wei
- College of Art and Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A5, Canada
| | - Richard Cuthbert
- Agriculture and Agri-Food Canada, Swift Current, Saskatchewan S9H 3X2, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada
| | - Andrew Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703HA Wageningen, The Netherlands
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 36824, México
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
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42
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Mustafin ZS, Zamyatin VI, Konstantinov DK, Doroshkov AV, Lashin SA, Afonnikov DA. Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana. Genes (Basel) 2019; 10:genes10120963. [PMID: 31766757 PMCID: PMC6947294 DOI: 10.3390/genes10120963] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/27/2022] Open
Abstract
Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution. The study of the network structure and evolution may highlight mechanisms of plants adaptation to adverse conditions, as well as their response to stresses and help in discovery and functional characterization of the stress-related genes. We performed an analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) at the network level using a phylostratigraphic approach. Our results show that a substantial fraction of genes associated with various types of abiotic stress is of ancient origin and evolves under strong purifying selection. The interaction networks of genes associated with stress response have a modular structure with a regulatory component being one of the largest for five of seven stress types. We demonstrated a positive relationship between the number of interactions of gene in the stress gene network and its age. Moreover, genes of the same age tend to be connected in stress gene networks. We also demonstrated that old stress-related genes usually participate in the response for various types of stress and are involved in numerous biological processes unrelated to stress. Our results demonstrate that the stress response genes represent the ancient and one of the fundamental molecular systems in plants.
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Affiliation(s)
- Zakhar S. Mustafin
- The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (IC & G SB RAS), 630090 Novosibirsk, Russia; (Z.S.M.); (V.I.Z.); (D.K.K.); (A.V.D.)
- Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | - Vladimir I. Zamyatin
- The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (IC & G SB RAS), 630090 Novosibirsk, Russia; (Z.S.M.); (V.I.Z.); (D.K.K.); (A.V.D.)
- Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University (NSU), 630090 Novosibirsk, Russia
| | - Dmitrii K. Konstantinov
- The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (IC & G SB RAS), 630090 Novosibirsk, Russia; (Z.S.M.); (V.I.Z.); (D.K.K.); (A.V.D.)
- Faculty of Natural Sciences, Novosibirsk State University (NSU), 630090 Novosibirsk, Russia
| | - Aleksej V. Doroshkov
- The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (IC & G SB RAS), 630090 Novosibirsk, Russia; (Z.S.M.); (V.I.Z.); (D.K.K.); (A.V.D.)
- Faculty of Natural Sciences, Novosibirsk State University (NSU), 630090 Novosibirsk, Russia
| | - Sergey A. Lashin
- The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (IC & G SB RAS), 630090 Novosibirsk, Russia; (Z.S.M.); (V.I.Z.); (D.K.K.); (A.V.D.)
- Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University (NSU), 630090 Novosibirsk, Russia
- Correspondence: (S.A.L.); (D.A.A.); Tel.: +7-383-363-49-63 (D.A.A.)
| | - Dmitry A. Afonnikov
- The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (IC & G SB RAS), 630090 Novosibirsk, Russia; (Z.S.M.); (V.I.Z.); (D.K.K.); (A.V.D.)
- Kurchatov Genomics Center, Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University (NSU), 630090 Novosibirsk, Russia
- Correspondence: (S.A.L.); (D.A.A.); Tel.: +7-383-363-49-63 (D.A.A.)
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43
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Dudin O, Ondracka A, Grau-Bové X, Haraldsen AA, Toyoda A, Suga H, Bråte J, Ruiz-Trillo I. A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife 2019; 8:49801. [PMID: 31647412 PMCID: PMC6855841 DOI: 10.7554/elife.49801] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/23/2019] [Indexed: 12/30/2022] Open
Abstract
In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly regulated transcriptional activation of genes involved in cell adhesion. Hereby we demonstrate the presence of a self-organized, clonally-generated, polarized layer of cells in a unicellular relative of animals.
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Affiliation(s)
- Omaya Dudin
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Andrej Ondracka
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Arthur Ab Haraldsen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Jon Bråte
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
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44
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Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications. mBio 2019; 10:mBio.02367-19. [PMID: 31615963 PMCID: PMC6794485 DOI: 10.1128/mbio.02367-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing techniques have considerably increased the number of completely sequenced eukaryotic genomes. These genomes are mostly automatically annotated, and ab initio gene prediction is commonly combined with homology-based search approaches and often supported by transcriptomic data. The latter in particular improve the prediction of intron splice sites and untranslated regions. However, correct prediction of translation initiation sites (TIS), alternative splice junctions, and protein-coding potential remains challenging. Here, we present an advanced proteogenomics approach, namely, the combination of proteogenomics and de novo peptide sequencing analysis, in conjunction with Blast2GO and phylostratigraphy. Using the model fungus Sordaria macrospora as an example, we provide a comprehensive view of the proteome that not only increases the functional understanding of this multicellular organism at different developmental stages but also immensely enhances the genome annotation quality. Proteogenomics combines proteomics, genomics, and transcriptomics and has considerably improved genome annotation in poorly investigated phylogenetic groups for which homology information is lacking. Furthermore, it can be advantageous when reinvestigating well-annotated genomes. Here, we applied an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in the detection of 104 so-far hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single-amino-acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Coexpression and phylostratigraphic analysis of the refined proteome suggest that new functions in evolutionarily young genes correlate with distinct developmental stages. In conclusion, our advanced proteogenomics approach supports and promotes functional studies of fungal model systems.
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45
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Leiboff S, Hake S. Reconstructing the Transcriptional Ontogeny of Maize and Sorghum Supports an Inverse Hourglass Model of Inflorescence Development. Curr Biol 2019; 29:3410-3419.e3. [PMID: 31587998 DOI: 10.1016/j.cub.2019.08.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/29/2019] [Accepted: 08/19/2019] [Indexed: 12/31/2022]
Abstract
Assembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely related species with architecturally distinct inflorescences, we collected RNA-seq profiles encompassing inflorescence body-plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BTx623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence development, we used random forest machine learning to determine stage by RNA-seq. We used two descriptions of transcriptional conservation to identify hourglass-like stages during inflorescence development. Despite a relatively short 12 million years since their last common ancestor, we found maize and sorghum inflorescences are most different during their hourglass-like stages of development, following an inverse-hourglass model of development. We discuss whether agricultural selection may account for the rapid divergence signatures in these species and the observed separation of evolutionary pressure and developmental reprogramming.
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Affiliation(s)
- Samuel Leiboff
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California, Berkeley, Albany, CA 94710, USA.
| | - Sarah Hake
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California, Berkeley, Albany, CA 94710, USA
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46
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Coronado-Zamora M, Salvador-Martínez I, Castellano D, Barbadilla A, Salazar-Ciudad I. Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle. Genome Biol Evol 2019; 11:1463-1482. [PMID: 31028390 PMCID: PMC6535812 DOI: 10.1093/gbe/evz086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2019] [Indexed: 01/09/2023] Open
Abstract
Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and divergence data between D. melanogaster and Drosophila yakuba. For the set of genes expressed at different life-cycle stages of D. melanogaster, as reported in modENCODE, we estimate the ratio of substitutions relative to polymorphism between nonsynonymous and synonymous sites (α) and then α is discomposed into the ratio of adaptive (ωa) and nonadaptive (ωna) substitutions to synonymous substitutions. We find that the genes expressed in mid- and late-embryonic development are the most conserved, whereas those expressed in early development and postembryonic stages are the least conserved. Importantly, we found that low conservation in early development is due to high rates of nonadaptive substitutions (high ωna), whereas in postembryonic stages it is due, instead, to high rates of adaptive substitutions (high ωa). By using estimates of different genomic features (codon bias, average intron length, exon number, recombination rate, among others), we also find that genes expressed in mid- and late-embryonic development show the most complex architecture: they are larger, have more exons, more transcripts, and longer introns. In addition, these genes are broadly expressed among all stages. We suggest that all these genomic features are related to the conservation of mid- and late-embryonic development. Globally, our study supports the hourglass pattern of conservation and adaptation over the life-cycle.
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Affiliation(s)
- Marta Coronado-Zamora
- Genomics, Bioinformatics and Evolution, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Irepan Salvador-Martínez
- Evo-Devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland.,Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | | | - Antonio Barbadilla
- Genomics, Bioinformatics and Evolution, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Isaac Salazar-Ciudad
- Genomics, Bioinformatics and Evolution, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Evo-Devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland.,Centre de Recerca Matemàtica, Cerdanyola del Vallès, Spain
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47
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Cutter AD, Garrett RH, Mark S, Wang W, Sun L. Molecular evolution across developmental time reveals rapid divergence in early embryogenesis. Evol Lett 2019; 3:359-373. [PMID: 31388446 PMCID: PMC6675142 DOI: 10.1002/evl3.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
Ontogenetic development hinges on the changes in gene expression in time and space within an organism, suggesting that the demands of ontogenetic growth can impose or reveal predictable pattern in the molecular evolution of genes expressed dynamically across development. Here, we characterize coexpression modules of the Caenorhabditis elegans transcriptome, using a time series of 30 points from early embryo to adult. By capturing the functional form of expression profiles with quantitative metrics, we find fastest evolution in the distinctive set of genes with transcript abundance that declines through development from a peak in young embryos. These genes are highly enriched for oogenic function and transient early zygotic expression, are nonrandomly distributed in the genome, and correspond to a life stage especially prone to inviability in interspecies hybrids. These observations conflict with the "early conservation model" for the evolution of development, although expression-weighted sequence divergence analysis provides some support for the "hourglass model." Genes in coexpression modules that peak toward adulthood also evolve fast, being hyper-enriched for roles in spermatogenesis, implicating a history of sexual selection and relaxation of selection on sperm as key factors driving rapid change to ontogenetically distinguishable coexpression modules of genes. We propose that these predictable trends of molecular evolution for dynamically expressed genes across ontogeny predispose particular life stages, early embryogenesis in particular, to hybrid dysfunction in the speciation process.
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Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Rose H. Garrett
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
- Division of Biostatistics, Dalla Lana School of Public HealthUniversity of TorontoTorontoONM6G1W3Canada
- Department of Statistical SciencesUniversity of TorontoTorontoONM6G1W3Canada
| | - Stephanie Mark
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Wei Wang
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public HealthUniversity of TorontoTorontoONM6G1W3Canada
- Department of Statistical SciencesUniversity of TorontoTorontoONM6G1W3Canada
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48
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Liu J, Robinson-Rechavi M. Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo. Mol Biol Evol 2019; 35:2862-2872. [PMID: 30184095 PMCID: PMC6278863 DOI: 10.1093/molbev/msy175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A driving hypothesis of evolutionary developmental biology is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here, we have tested Darwin’s “selection opportunity” hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a “developmental constraint” hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and postembryonically. To distinguish between adaptation and relaxation hypotheses, we investigated the evidence of positive selection on protein-coding genes in relation to their expression over development, in fly Drosophila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. First, we found that genes specifically expressed in late development have stronger signals of positive selection. Second, over the full transcriptome, genes with evidence for positive selection trend to be expressed in late development. Finally, genes involved in pathways with cumulative evidence of positive selection have higher expression in late development. Overall, there is a consistent signal that positive selection mainly affects genes and pathways expressed in late embryonic development and in adult. Our results imply that the evolution of embryogenesis is mostly conservative, with most adaptive evolution affecting some stages of postembryonic gene expression, and thus postembryonic phenotypes. This is consistent with the diversity of environmental challenges to which juveniles and adults are exposed.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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49
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Warner MR, Qiu L, Holmes MJ, Mikheyev AS, Linksvayer TA. Convergent eusocial evolution is based on a shared reproductive groundplan plus lineage-specific plastic genes. Nat Commun 2019; 10:2651. [PMID: 31201311 PMCID: PMC6570765 DOI: 10.1038/s41467-019-10546-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Eusociality has convergently evolved multiple times, but the genomic basis of caste-based division of labor and degree to which independent origins of eusociality have utilized common genes remain largely unknown. Here we characterize caste-specific transcriptomic profiles across development and adult body segments from pharaoh ants (Monomorium pharaonis) and honey bees (Apis mellifera), representing two independent origins of eusociality. We identify a substantial shared core of genes upregulated in the abdomens of queen ants and honey bees that also tends to be upregulated in mated female flies, suggesting that these genes are part of a conserved insect reproductive groundplan. Outside of this shared groundplan, few genes are differentially expressed in common. Instead, the majority of the thousands of caste-associated genes are plastically expressed, rapidly evolving, and relatively evolutionarily young. These results emphasize that the recruitment of both highly conserved and lineage-specific genes underlie the convergent evolution of novel traits such as eusociality. Eusocial caste systems have evolved independently multiple times. Here, Warner et al. investigate the amount of shared vs. lineage-specific genes involved in the evolution of caste in pharaoh ants and honey bees by comparing transcriptomes across tissues, developmental stages, and castes.
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Affiliation(s)
| | - Lijun Qiu
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Michael J Holmes
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,School of Life and Environmental Science, University of Sydney, Sydney, 2006, Australia
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,Research School of Biology, Australian National University, Canberra, 0200, Australia
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50
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 DOI: 10.1101/514356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 05/20/2023] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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