1
|
Sandin MM, Renaudie J, Suzuki N, Not F. Extant diversity, biogeography, and evolutionary history of Radiolaria. Curr Biol 2025:S0960-9822(25)00495-6. [PMID: 40334664 DOI: 10.1016/j.cub.2025.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 03/12/2025] [Accepted: 04/14/2025] [Indexed: 05/09/2025]
Abstract
Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons left an extensive fossil record extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography, and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B, and Rad-C. We suggest that most of this undescribed diversity comprises skeleton-less life forms or endosymbionts, explaining their elusive, yet abundant, nature. Phylogenetic analyses highlight the need for a major revision of high-level Radiolaria taxonomy, including placement of Collodaria within the order Nassellaria. Global metabarcoding surveys show that Radiolaria contributes more than 12% to the total eukaryotic community, displaying distinct biogeographic patterns with the skeleton-less lineages at depth and photosymbiont-bearing lineages in the surface. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria ∼760 million years ago (mya), the development of the skeleton in the early Paleozoic (∼500 mya), and the onset of photosymbiotic relationships during the mid to late Mesozoic (∼140 mya), related to geological periods of oligotrophy and anoxia. The results presented here provide a robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.
Collapse
Affiliation(s)
- Miguel M Sandin
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France; Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain.
| | - Johan Renaudie
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Noritoshi Suzuki
- Department of Earth Science, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Fabrice Not
- Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| |
Collapse
|
2
|
Jia X, Li Y, Chen L, Xiao Y, Yang N, Luo H, Guan J, Xu D. Identification and comparative genomic analysis of endophytic fungi in Bletilla striata and its potential for promoting militarine bioaccumulation. Fitoterapia 2025; 181:106356. [PMID: 39716505 DOI: 10.1016/j.fitote.2024.106356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 12/15/2024] [Accepted: 12/18/2024] [Indexed: 12/25/2024]
Abstract
Bletilla striata (Thunb.) Reichb.f is renowned for its traditional medicinal applications and a spectrum of pharmacological activities, which is intricately linked to militarine. Addressing sustainable production of B. striata and militarine necessitates innovative strategies. Endophytic fungi, residing within plant tissues and establishing symbiotic relationships, act as secondary genomes of plants, co-regulating plant growth and secondary metabolite synthesis. Despite their potential, the genetic and metabolic diversity, functional activity, and regulatory interactions of endophytic fungi with B. striata remain unexplored. This study aims to bridge this gap by investigating endophytic fungi that could enhance B. striata growth and militarine biosynthesis. The study revealed that endophytic fungi from pseudobulbs, roots, and stems were co-cultured with callus tissue of B. striata, and it was discovered that Serendipita indica from the Serendipita genus can enhance militarine accumulation. Subsequently, key genes, core enzymes, and regulatory factors related to militarine biosynthesis in the S. indica genome were analyzed. By employing advanced biotechnological and comparative genomic approaches, we elucidated the composition and distribution of regulatory factors across different endophytic fungal genomes associated with B. striata. This research not only advances our understanding of the symbiotic relationship between B. striata and its endophytic fungi but also provides a foundational blueprint for the sustainable exploitation and enhancement of militarine production.
Collapse
Affiliation(s)
- Xueyan Jia
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou 563099, China; Department of Cell Biology, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Yang Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Lang Chen
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Yexin Xiao
- Department of Cell Biology, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Ning Yang
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Hongyuan Luo
- Department of Cell Biology, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Jing Guan
- Department of Cell Biology, Zunyi Medical University, Zunyi, Guizhou 563099, China
| | - Delin Xu
- Department of Medical Instrumental Analysis, Zunyi Medical University, Zunyi, Guizhou 563099, China.
| |
Collapse
|
3
|
Kirsch R, Okamura Y, García-Lozano M, Weiss B, Keller J, Vogel H, Fukumori K, Fukatsu T, Konstantinov AS, Montagna M, Moseyko AG, Riley EG, Slipinski A, Vencl FV, Windsor DM, Salem H, Kaltenpoth M, Pauchet Y. Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles. Curr Biol 2025; 35:640-654.e7. [PMID: 39826554 DOI: 10.1016/j.cub.2024.12.028] [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: 04/12/2024] [Revised: 11/01/2024] [Accepted: 12/10/2024] [Indexed: 01/22/2025]
Abstract
Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one-quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall-degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macroevolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle HGT and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles' digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.
Collapse
Affiliation(s)
- Roy Kirsch
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Yu Okamura
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Marleny García-Lozano
- Mutualisms Research Group, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Benjamin Weiss
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Jean Keller
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Heiko Vogel
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Kayoko Fukumori
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Alexander S Konstantinov
- Systematic Entomology Laboratory, USDA, ARS, c/o Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue, Washington, DC 20560, USA
| | - Matteo Montagna
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (Naples), Italy; Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, Via Università 100, 80055 Portici (Naples), Italy
| | - Alexey G Moseyko
- Zoological Institute, Russian Academy of Sciences, Universitetskaya embankment 1, 199034 St. Petersburg, Russia
| | - Edward G Riley
- Department of Entomology, Texas A&M University, 400 Bizzell Street, College Station, TX 77843, USA
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Black Mountain Laboratories, Clunies Ross Street, GPO Box 1700, Canberra, ACT, Australia
| | - Fredric V Vencl
- Ecology and Evolution, Stony Brook University, Stony Brook, NY 11790, USA; Entomology, National Museum of Natural History, Smithsonian Institution, 10th Street & Constitution Avenue, Washington, DC 20560, USA
| | - Donald M Windsor
- Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper Ancon, Panama City, Republic of Panama
| | - Hassan Salem
- Mutualisms Research Group, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany.
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany.
| |
Collapse
|
4
|
Chen BZ, Yang ZJ, Yang L, Zhu YF, Li XZ, Wang L, Zhou YP, Zhang GH, Li DW, Dong Y, Duan SC. Chromosome-scale genome assembly of Codonopsis pilosula and comparative genomic analyses shed light on its genome evolution. FRONTIERS IN PLANT SCIENCE 2024; 15:1469375. [PMID: 39559763 PMCID: PMC11570261 DOI: 10.3389/fpls.2024.1469375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 10/14/2024] [Indexed: 11/20/2024]
Abstract
Introduction Codonopsis pilosula is a significant plant in traditional Chinese medicine, valued for its edible and medicinal properties. However, the lack of available genomic resources has hindered further research. Methods This study presents the first chromosome-scale genome assembly of C. pilosula using PacBio CLR reads and Hi-C scaffolding technology. Additionally, Ks analysis and syntenic depth analysis were performed to elucidate its evolutionary history. Results The final assembly yielded a high-quality genome of 679.20 Mb, which was anchored to 8 pseudo-chromosomes with an anchoring rate of 96.5% and a scaffold N50 of 80.50 Mb. The genome assembly showed a high completeness of 97.6% based on Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis. Repetitive elements constituted approximately 76.8% of the genome, with long terminal repeat retrotransposons (LTRs) accounting for about 39.17%. Ks and syntenic depth analyses revealed that the polyploidization history of three platycodonoid clade species involved only the γ-WGT event. Karyotype evolutionary analysis identified an ancestral karyotype with 9 protochromosomes for the three platycodonoid clade species. Moreover, non-WGD genes, particularly those arising from tandem duplications, were found to contribute significantly to gene family expansion. Discussion These findings provide essential insights into the genetic diversity and evolutionary biology of C. pilosula, aiding its conservation and sustainable use.
Collapse
Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Zi-Jiang Yang
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Ling Yang
- Institute of Agro-Products of Processing and Design, Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Yi-Fan Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Zhen Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lei Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ye-Peng Zhou
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Guang-Hui Zhang
- National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Wei Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sheng-Chang Duan
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| |
Collapse
|
5
|
Boyd BM, House N, Carduck CW, Reed DL. Genomic Diversity in the Endosymbiotic Bacteria of Human Head Lice. Mol Biol Evol 2024; 41:msae064. [PMID: 38513084 PMCID: PMC10986857 DOI: 10.1093/molbev/msae064] [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: 10/25/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont's genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting that natural selection slows genetic drift and maintains functional consistency between symbiont populations. By sampling in multiple countries, we examine genomic diversity within a symbiont species, a heritable symbiotic bacterium found only in human head lice. We find that human head louse symbionts contain genetic diversity that appears to have arisen contemporaneously with the appearance of anatomically modern humans within Africa and/or during the colonization of Eurasia by humans. We predict that the observed genetic diversity underlies functional differences in extant symbiont lineages, through the inactivation of genes involved in symbiont membrane construction. Furthermore, we find evidence of additional gene losses prior to the appearance of modern humans, also impacting the symbiont membrane. From this, we conclude that symbiont genome degeneration is proceeding, via gene inactivation and subsequent loss, in human head louse symbionts, while genomic diversity is maintained. Collectively, our results provide a look into the genomic diversity within a single symbiont species and highlight the shared evolutionary history of humans, lice, and bacteria.
Collapse
Affiliation(s)
- Bret M Boyd
- Center for Biological Data Science, Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Niyomi House
- Department of Biology, University of Nevada Reno, Reno, NV, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Christopher W Carduck
- Center for Biological Data Science, Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - David L Reed
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| |
Collapse
|
6
|
Liu H, Hou Z, Xu L, Ma Q, Wei M, Tembrock LR, Zhang S, Wu Z. Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives. FRONTIERS IN PLANT SCIENCE 2023; 14:1228551. [PMID: 37662149 PMCID: PMC10471889 DOI: 10.3389/fpls.2023.1228551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.
Collapse
Affiliation(s)
- Huihui Liu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lei Xu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Qing Ma
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Min Wei
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen, China
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| |
Collapse
|