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Gornik SG, Flores V, Reinhardt F, Erber L, Salas-Leiva DE, Douvropoulou O, Lassadi I, Einarsson E, Mörl M, Git A, Stadler PF, Pain A, Waller RF. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes. Mol Biol Evol 2022; 39:6701636. [PMID: 36108082 PMCID: PMC9550989 DOI: 10.1093/molbev/msac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.
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Affiliation(s)
| | - Victor Flores
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Franziska Reinhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Dayana E Salas-Leiva
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Olga Douvropoulou
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany,Discrete Biomathematics, Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany,Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währinger Str. 17, Alsergrund, Vienna 1090, Austria,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Arnab Pain
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,International Institute for Zoonosis Control, Hokkaido University, 001-0020 North 20, West 10 Kita-ku, Sapporo 001-0020, Japan
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Mourier T, Shuaib M, Hala S, Mfarrej S, Alofi F, Naeem R, Alsomali A, Jorgensen D, Subudhi AK, Ben Rached F, Guan Q, Salunke RP, Ooi A, Esau L, Douvropoulou O, Nugmanova R, Perumal S, Zhang H, Rajan I, Al-Omari A, Salih S, Shamsan A, Al Mutair A, Taha J, Alahmadi A, Khotani N, Alhamss A, Mahmoud A, Alquthami K, Dageeg A, Khogeer A, Hashem AM, Moraga P, Volz E, Almontashiri N, Pain A. SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Nat Commun 2022; 13:601. [PMID: 35105893 PMCID: PMC8807822 DOI: 10.1038/s41467-022-28287-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive mutations (R203K/G204R) in the nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, the host cell transcriptome analysis suggests that the mutant N protein produces dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein to modulations of host-virus interactions and underline the potential of the nucleocapsid protein as a drug target during infection.
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Affiliation(s)
- Tobias Mourier
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Muhammad Shuaib
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Sharif Hala
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Sara Mfarrej
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Fadwa Alofi
- Infectious Diseases Department, King Fahad Hospital, Madinah, MOH, Saudi Arabia
| | - Raeece Naeem
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Afrah Alsomali
- Infectious Diseases Department, King Abdullah Medical Complex, Jeddah, MOH, Saudi Arabia
| | - David Jorgensen
- School of Public Health, Faculty of Medicine, Imperial College, Norfolk Place, St Mary's Campus, London, United Kingdom
| | - Amit Kumar Subudhi
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Fathia Ben Rached
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Qingtian Guan
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Rahul P Salunke
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Amanda Ooi
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Luke Esau
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Olga Douvropoulou
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Raushan Nugmanova
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Sadhasivam Perumal
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Huoming Zhang
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Issaac Rajan
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Awad Al-Omari
- Dr. Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | - Samer Salih
- Dr. Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | - Abbas Shamsan
- Dr. Suliman Al-Habib Medical Group, Riyadh, Saudi Arabia
| | | | - Jumana Taha
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdulaziz Alahmadi
- Department of Preventive Medicine, Ministry of National Guard - Health Affairs, Riyadh, Saudi Arabia
| | - Nashwa Khotani
- Infectious Diseases Medical Department, Al Noor Specialist Hospital Makkah, Makkah, MOH, Saudi Arabia
| | - Abdelrahman Alhamss
- Gastroenterology Department, King Abdul Aziz Hospital Makkah, Makkah, MOH, Saudi Arabia
| | - Ahmed Mahmoud
- College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Khaled Alquthami
- Infectious Diseases Medical Department, Al Noor Specialist Hospital Makkah, Makkah, MOH, Saudi Arabia
| | - Abdullah Dageeg
- Department of Medicine, King Abdulaziz University Jeddah, Jeddah, Saudi Arabia
| | - Asim Khogeer
- Plan and Research Department, General Directorate of Health Affairs Makkah Region, Makkah, MOH, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Paula Moraga
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Science and Engineering Division (CEMSE), Thuwal-Jeddah, 23955-6900, Saudi Arabia
| | - Eric Volz
- School of Public Health, Faculty of Medicine, Imperial College, Norfolk Place, St Mary's Campus, London, United Kingdom
| | - Naif Almontashiri
- College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
- Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Arnab Pain
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah, 23955-6900, Saudi Arabia.
- Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020, Japan.
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Mourier T, de Alvarenga DAM, Kaushik A, de Pina-Costa A, Douvropoulou O, Guan Q, Guzmán-Vega FJ, Forrester S, de Abreu FVS, Júnior CB, de Souza Junior JC, Moreira SB, Hirano ZMB, Pissinatti A, Ferreira-da-Cruz MDF, de Oliveira RL, Arold ST, Jeffares DC, Brasil P, de Brito CFA, Culleton R, Daniel-Ribeiro CT, Pain A. The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching. BMC Biol 2021; 19:219. [PMID: 34592986 PMCID: PMC8485552 DOI: 10.1186/s12915-021-01139-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/03/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history and to identify any genetic adaptions that may underlie the ability of this parasite to switch between host species. RESULTS Phylogenetic analyses based on whole genome sequences of P. simium from humans and NHPs reveals that P. simium is monophyletic within the broader diversity of South American Plasmodium vivax, suggesting P. simium first infected NHPs as a result of a host switch of P. vivax from humans. The P. simium isolates show the closest relationship to Mexican P. vivax isolates. Analysis of erythrocyte invasion genes reveals differences between P. vivax and P. simium, including large deletions in the Duffy-binding protein 1 (DBP1) and reticulocyte-binding protein 2a genes of P. simium. Analysis of P. simium isolated from NHPs and humans revealed a deletion of 38 amino acids in DBP1 present in all human-derived isolates, whereas NHP isolates were multi-allelic. CONCLUSIONS Analysis of the P. simium genome confirmed a close phylogenetic relationship between P. simium and P. vivax, and suggests a very recent American origin for P. simium. The presence of the DBP1 deletion in all human-derived isolates tested suggests that this deletion, in combination with other genetic changes in P. simium, may facilitate the invasion of human red blood cells and may explain, at least in part, the basis of the recent zoonotic infections.
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Affiliation(s)
- Tobias Mourier
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Denise Anete Madureira de Alvarenga
- Grupo de Pesquisa em Biologia Molecular e Imunologia da Malária, Instituto René Rachou, Fundação Oswaldo Cruz (Fiocruz), Belo Horizonte, MG, 30190-009, Brazil
| | - Abhinav Kaushik
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anielle de Pina-Costa
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Centro Universitário Serra dos Órgãos (UNIFESO), Teresópolis, RJ, 25964-004, Brazil
| | - Olga Douvropoulou
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Qingtian Guan
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francisco J Guzmán-Vega
- Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sarah Forrester
- Department of Biology and York Biomedical Research Institute, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Filipe Vieira Santos de Abreu
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz (IOC), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Cesare Bianco Júnior
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Laboratório de Pesquisa em Malária, IOC, Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Julio Cesar de Souza Junior
- Universidade Regional de Blumenau (FURB), Centro de Pesquisas Biológicas de Indaial (CEPESBI)/ Projeto bugio, Blumenau, Indaial, SC, Brazil
| | | | - Zelinda Maria Braga Hirano
- Universidade Regional de Blumenau (FURB), Centro de Pesquisas Biológicas de Indaial (CEPESBI)/ Projeto bugio, Blumenau, Indaial, SC, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro (CPRJ/Inea), Guapimirim, RJ, 25940-000, Brazil
| | - Maria de Fátima Ferreira-da-Cruz
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Laboratório de Pesquisa em Malária, IOC, Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Ricardo Lourenço de Oliveira
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz (IOC), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Stefan T Arold
- Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, 34090, Montpellier, France
| | - Daniel C Jeffares
- Department of Biology and York Biomedical Research Institute, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Patrícia Brasil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Cristiana Ferreira Alves de Brito
- Grupo de Pesquisa em Biologia Molecular e Imunologia da Malária, Instituto René Rachou, Fundação Oswaldo Cruz (Fiocruz), Belo Horizonte, MG, 30190-009, Brazil
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Ehime, 791-0295, Japan
| | - Cláudio Tadeu Daniel-Ribeiro
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil.
- Laboratório de Pesquisa em Malária, IOC, Fiocruz, Rio de Janeiro, RJ, 21040-360, Brazil.
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, Japan.
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Ramaprasad A, Klaus S, Douvropoulou O, Culleton R, Pain A. Plasmodium vinckei genomes provide insights into the pan-genome and evolution of rodent malaria parasites. BMC Biol 2021; 19:69. [PMID: 33888092 PMCID: PMC8063448 DOI: 10.1186/s12915-021-00995-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 01/27/2023] Open
Abstract
Background Rodent malaria parasites (RMPs) serve as tractable tools to study malaria parasite biology and host-parasite-vector interactions. Among the four RMPs originally collected from wild thicket rats in sub-Saharan Central Africa and adapted to laboratory mice, Plasmodium vinckei is the most geographically widespread with isolates collected from five separate locations. However, there is a lack of extensive phenotype and genotype data associated with this species, thus hindering its use in experimental studies. Results We have generated a comprehensive genetic resource for P. vinckei comprising of five reference-quality genomes, one for each of its subspecies, blood-stage RNA sequencing data for five P. vinckei isolates, and genotypes and growth phenotypes for ten isolates. Additionally, we sequenced seven isolates of the RMP species Plasmodium chabaudi and Plasmodium yoelii, thus extending genotypic information for four additional subspecies enabling a re-evaluation of the genotypic diversity and evolutionary history of RMPs. The five subspecies of P. vinckei have diverged widely from their common ancestor and have undergone large-scale genome rearrangements. Comparing P. vinckei genotypes reveals region-specific selection pressures particularly on genes involved in mosquito transmission. Using phylogenetic analyses, we show that RMP multigene families have evolved differently across the vinckei and berghei groups of RMPs and that family-specific expansions in P. chabaudi and P. vinckei occurred in the common vinckei group ancestor prior to speciation. The erythrocyte membrane antigen 1 and fam-c families in particular show considerable expansions among the lowland forest-dwelling P. vinckei parasites. The subspecies from the highland forests of Katanga, P. v. vinckei, has a uniquely smaller genome, a reduced multigene family repertoire and is also amenable to transfection making it an ideal parasite for reverse genetics. We also show that P. vinckei parasites are amenable to genetic crosses. Conclusions Plasmodium vinckei isolates display a large degree of phenotypic and genotypic diversity and could serve as a resource to study parasite virulence and immunogenicity. Inclusion of P. vinckei genomes provide new insights into the evolution of RMPs and their multigene families. Amenability to genetic crossing and transfection make them also suitable for classical and functional genetics to study Plasmodium biology. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00995-5.
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Affiliation(s)
- Abhinay Ramaprasad
- Pathogen Genomics Group, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.,Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Present address: Malaria Biochemistry Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | - Severina Klaus
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Biomedical Sciences, University of Heidelberg, Heidelberg, Germany
| | - Olga Douvropoulou
- Pathogen Genomics Group, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Richard Culleton
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. .,Division of Molecular Parasitology, Proteo-Science Center, Ehime University, 454 Shitsukawa, Toon, Ehime, 791-0295, Japan. .,Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Arnab Pain
- Pathogen Genomics Group, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia. .,Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, 001-0020, Japan.
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