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Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses.
Sci Rep. 2020 04 03; 10(1):5928.SR

Abstract

Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. It is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. The genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. The expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms.

Authors+Show Affiliations

Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France. Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France. Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France. Amoéba, 38 avenue des Frères Montgolfier, 69680, Chassieu, France.Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France. Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France. Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France. bernard.la-scola@univ-amu.fr. Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France. bernard.la-scola@univ-amu.fr.Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEPHI); Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 27 boulevard Jean Moulin, 13005, Marseille, France. philippe.colson@univ-amu.fr. Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France. philippe.colson@univ-amu.fr.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32246084

Citation

Chelkha, Nisrine, et al. "Vermamoeba Vermiformis CDC-19 Draft Genome Sequence Reveals Considerable Gene Trafficking Including With Candidate Phyla Radiation and Giant Viruses." Scientific Reports, vol. 10, no. 1, 2020, p. 5928.
Chelkha N, Hasni I, Louazani AC, et al. Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses. Sci Rep. 2020;10(1):5928.
Chelkha, N., Hasni, I., Louazani, A. C., Levasseur, A., La Scola, B., & Colson, P. (2020). Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses. Scientific Reports, 10(1), 5928. https://doi.org/10.1038/s41598-020-62836-9
Chelkha N, et al. Vermamoeba Vermiformis CDC-19 Draft Genome Sequence Reveals Considerable Gene Trafficking Including With Candidate Phyla Radiation and Giant Viruses. Sci Rep. 2020 04 3;10(1):5928. PubMed PMID: 32246084.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses. AU - Chelkha,Nisrine, AU - Hasni,Issam, AU - Louazani,Amina Cherif, AU - Levasseur,Anthony, AU - La Scola,Bernard, AU - Colson,Philippe, Y1 - 2020/04/03/ PY - 2019/02/07/received PY - 2020/03/08/accepted PY - 2020/4/5/entrez PY - 2020/4/5/pubmed PY - 2020/12/15/medline SP - 5928 EP - 5928 JF - Scientific reports JO - Sci Rep VL - 10 IS - 1 N2 - Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. It is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. The genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. The expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/32246084/Vermamoeba_vermiformis_CDC_19_draft_genome_sequence_reveals_considerable_gene_trafficking_including_with_candidate_phyla_radiation_and_giant_viruses_ L2 - https://doi.org/10.1038/s41598-020-62836-9 DB - PRIME DP - Unbound Medicine ER -