1
|
Teterina AA, Willis JH, Baer CF, Phillips PC. Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600681. [PMID: 38979286 PMCID: PMC11230420 DOI: 10.1101/2024.06.25.600681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
With within-species genetic diversity estimates that span the gambit of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri, currently known as one of the most genetically diverse nematodes within its genus and metazoan phyla. Here, we present a high-quality gapless genome assembly and annotation for C. brenneri, revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat rich peripheral parts. Comparison of C. brenneri with other nematodes from the 'Elegans' group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation iof orthogroup sizes, indicative of high rates of gene turnover. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. Comparison of gene structures revealed strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri, facilitating research into various aspects of nematode biology and evolutionary processes.
Collapse
Affiliation(s)
- Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| |
Collapse
|
2
|
Lee WK, Chan BKK, Kim JY, Ju SJ, Kim SJ. Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents. Mol Ecol Resour 2024; 24:e13895. [PMID: 37955198 DOI: 10.1111/1755-0998.13895] [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: 11/06/2022] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.
Collapse
Affiliation(s)
- Won-Kyung Lee
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Division of EcoScience, Ewha Womans University, Seoul, Korea
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jae-Yoon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Jong Ju
- Marine Resources & Environment Research Division, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Se-Joo Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| |
Collapse
|
3
|
Johannesson K, Leder EH, André C, Dupont S, Eriksson SP, Harding K, Havenhand JN, Jahnke M, Jonsson PR, Kvarnemo C, Pavia H, Rafajlović M, Rödström EM, Thorndyke M, Blomberg A. Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative. Evol Appl 2023; 16:530-541. [PMID: 36793681 PMCID: PMC9923476 DOI: 10.1111/eva.13389] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 03/08/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
The Centre for Marine Evolutionary Biology (CeMEB) at the University of Gothenburg, Sweden, was established in 2008 through a 10-year research grant of 8.7 m€ to a team of senior researchers. Today, CeMEB members have contributed >500 scientific publications, 30 PhD theses and have organised 75 meetings and courses, including 18 three-day meetings and four conferences. What are the footprints of CeMEB, and how will the centre continue to play a national and international role as an important node of marine evolutionary research? In this perspective article, we first look back over the 10 years of CeMEB activities and briefly survey some of the many achievements of CeMEB. We furthermore compare the initial goals, as formulated in the grant application, with what has been achieved, and discuss challenges and milestones along the way. Finally, we bring forward some general lessons that can be learnt from a research funding of this type, and we also look ahead, discussing how CeMEB's achievements and lessons can be used as a springboard to the future of marine evolutionary biology.
Collapse
Affiliation(s)
- Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Erica H. Leder
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
- Natural History MuseumUniversity of OsloOsloNorway
| | - Carl André
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Sam Dupont
- Department of Biology and Environmental ScienceUniversity of Gothenburg, Kristineberg Marine Research StationFiskebäckskilSweden
- International Atomic Energy AgencyPrincipality of MonacoMonaco
| | - Susanne P. Eriksson
- Department of Biology and Environmental ScienceUniversity of Gothenburg, Kristineberg Marine Research StationFiskebäckskilSweden
| | - Karin Harding
- Department of Biology and Environmental ScienceUniversity of GothenburgGothenburgSweden
| | - Jonathan N. Havenhand
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Marlene Jahnke
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Per R. Jonsson
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Charlotta Kvarnemo
- Department of Biology and Environmental ScienceUniversity of GothenburgGothenburgSweden
| | - Henrik Pavia
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Marina Rafajlović
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Eva Marie Rödström
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - Michael Thorndyke
- Department of Biology and Environmental ScienceUniversity of Gothenburg, Kristineberg Marine Research StationFiskebäckskilSweden
- Department of Genomics Research in Ecology & Evolution in Nature (GREEN)Groningen Institute for Evolutionary Life Sciences (GELIFES)De Rijksuniversiteit GroningenGroningenThe Netherlands
| | - Anders Blomberg
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| |
Collapse
|
4
|
Guo C, Zhang X, Li Y, Xie J, Gao P, Hao P, Han L, Zhang J, Wang W, Liu P, Ding J, Chang Y. Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus. BMC Genomics 2023; 24:25. [PMID: 36647018 PMCID: PMC9843871 DOI: 10.1186/s12864-023-09113-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown. RESULT In this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses. CONCLUSIONS This study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.
Collapse
Affiliation(s)
- Chao Guo
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Jiahui Xie
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Pingping Gao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
- Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
| | - Jinyuan Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Peng Liu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, People's Republic of China.
| |
Collapse
|
5
|
Yamashiro T, Shiraishi A, Nakayama K, Satake H. Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants. Int J Mol Sci 2022; 23:7039. [PMID: 35806039 PMCID: PMC9267051 DOI: 10.3390/ijms23137039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
The plant Tanacetum coccineum (painted daisy) is closely related to Tanacetum cinerariifolium (pyrethrum daisy). However, T. cinerariifolium produces large amounts of pyrethrins, a class of natural insecticides, whereas T. coccineum produces much smaller amounts of these compounds. Thus, comparative genomic analysis is expected to contribute a great deal to investigating the differences in biological defense systems, including pyrethrin biosynthesis. Here, we elucidated the 9.4 Gb draft genome of T. coccineum, consisting of 2,836,647 scaffolds and 103,680 genes. Comparative analyses of the draft genome of T. coccineum and that of T. cinerariifolium, generated in our previous study, revealed distinct features of T. coccineum genes. While the T. coccineum genome contains more numerous ribosome-inactivating protein (RIP)-encoding genes, the number of higher-toxicity type-II RIP-encoding genes is larger in T. cinerariifolium. Furthermore, the number of histidine kinases encoded by the T. coccineum genome is smaller than that of T. cinerariifolium, suggesting a biological correlation with pyrethrin biosynthesis. Moreover, the flanking regions of pyrethrin biosynthesis-related genes are also distinct between these two plants. These results provide clues to the elucidation of species-specific biodefense systems, including the regulatory mechanisms underlying pyrethrin production.
Collapse
Affiliation(s)
- Takanori Yamashiro
- Dainihon Jochugiku Co., Ltd., 1-1-11 Daikoku-cho, Toyonaka, Osaka 561-0827, Japan; (T.Y.); (K.N.)
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Souraku, Kyoto 619-0284, Japan;
| | - Koji Nakayama
- Dainihon Jochugiku Co., Ltd., 1-1-11 Daikoku-cho, Toyonaka, Osaka 561-0827, Japan; (T.Y.); (K.N.)
| | - Honoo Satake
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Souraku, Kyoto 619-0284, Japan;
| |
Collapse
|
6
|
Cleverley R, Webb D, Middlemiss S, Duke P, Clare A, Okano K, Harwood C, Aldred N. In Vitro Oxidative Crosslinking of Recombinant Barnacle Cyprid Cement Gland Proteins. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:928-942. [PMID: 34714445 PMCID: PMC8639568 DOI: 10.1007/s10126-021-10076-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Barnacle adhesion is a focus for fouling-control technologies as well as the development of bioinspired adhesives, although the mechanisms remain very poorly understood. The barnacle cypris larva is responsible for surface colonisation. Cyprids release cement from paired glands that contain proteins, carbohydrates and lipids, although further compositional details are scant. Several genes coding for cement gland-specific proteins were identified, but only one of these showed database homology. This was a lysyl oxidase-like protein (lcp_LOX). LOX-like enzymes have been previously identified in the proteome of adult barnacle cement secretory tissue. We attempted to produce recombinant LOX in E. coli, in order to identify its role in cyprid cement polymerisation. We also produced two other cement gland proteins (lcp3_36k_3B8 and lcp2_57k_2F5). lcp2_57k_2F5 contained 56 lysine residues and constituted a plausible substrate for LOX. While significant quantities of soluble lcp3_36k_3B8 and lcp2_57k_2F5 were produced in E. coli, production of stably soluble lcp_LOX failed. A commercially sourced human LOX catalysed the crosslinking of lcp2_57k_2F5 into putative dimers and trimers, and this reaction was inhibited by lcp3_36k_3B8. Inhibition of the lcp_LOX:lcp2_57k_2F5 reaction by lcp3_36k_3B8 appeared to be substrate specific, with no inhibitory effect on the oxidation of cadaverine by LOX. The results demonstrate a possible curing mechanism for barnacle cyprid cement and, thus, provide a basis for a more complete understanding of larval adhesion for targeted control of marine biofouling and adhesives for niche applications.
Collapse
Affiliation(s)
- Robert Cleverley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - David Webb
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Stuart Middlemiss
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Phillip Duke
- Defence Science and Technology Laboratory, Dstl Porton Down, Salisbury, SP4 0JQ, UK
| | - Anthony Clare
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Keiju Okano
- Department of Biotechnology, Akita Prefectural University, Akita, Japan
| | - Colin Harwood
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Nick Aldred
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| |
Collapse
|