First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
PubMed
32069939
PubMed Central
PMC7157233
DOI
10.3390/tropicalmed5010025
PII: tropicalmed5010025
Knihovny.cz E-zdroje
- Klíčová slova
- Trypanosomatidae, genome assembly, insect trypanosomatids, monoxenous trypanosomatids, whole genome,
- Publikační typ
- časopisecké články MeSH
Here, we present first draft genome sequence of the trypanosomatid Herpetomonas muscarum ingenoplastis. This parasite was isolated repeatedly in the black blowfly, Phormia regina, and it forms a phylogenetically distinct clade in the Trypanosomatidae family.
e Duve Institute University of Louvain B 1200 Brussels Belgium
Life Science Research Centre Faculty of Science University of Ostrava 71000 Ostrava Czech Republic
Martsinovsky Institute of Medical Parasitology Sechenov University 119435 Moscow Russia
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Lukeš J., Butenko A., Hashimi H., Maslov D.A., Votýpka J., Yurchenko V. Trypanosomatids are much more than just trypanosomes: Clues from the expanded family tree. Trends Parasitol. 2019;34:466–480. doi: 10.1016/j.pt.2018.03.002. PubMed DOI
Nussbaum K., Honek J., Cadmus C.M., Efferth T. Trypanosomatid parasites causing neglected diseases. Curr. Med. Chem. 2010;17:1594–1617. doi: 10.2174/092986710790979953. PubMed DOI
Sangenito L.S., da Silva Santos V., d’Avila-Levy C.M., Branquinha M.H., Santos A.L.S., Oliveira S.S.C. Leishmaniasis and Chagas Disease—Neglected Tropical Diseases: Treatment Updates. Curr. Top. Med. Chem. 2019;19:174–177. doi: 10.2174/156802661903190328155136. PubMed DOI
Podlipaev S.A. Insect trypanosomatids: The need to know more. Mem. Inst. Oswaldo Cruz. 2000;95:517–522. doi: 10.1590/S0074-02762000000400013. PubMed DOI
Maslov D.A., Votýpka J., Yurchenko V., Lukeš J. Diversity and phylogeny of insect trypanosomatids: All that is hidden shall be revealed. Trends Parasitol. 2013;29:43–52. doi: 10.1016/j.pt.2012.11.001. PubMed DOI
d’Avila-Levy C.M., Boucinha C., Kostygov A., Santos H.L., Morelli K.A., Grybchuk-Ieremenko A., Duval L., Votýpka J., Yurchenko V., Grellier P., et al. Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era. Mem. Inst. Oswaldo Cruz. 2015;110:956–965. doi: 10.1590/0074-02760150253. PubMed DOI PMC
Rogers W.E., Wallace F.G. Two new subspecies of Herpetomonus muscurum (Leidy, 1856) Kent, 1880. J. Protozool. 1971;18:645–649. doi: 10.1111/j.1550-7408.1971.tb03390.x. PubMed DOI
Putnam R.J. The role of carrion-frequenting arthropods in the decay process. Ecol. Entomol. 1978;3:133–139. doi: 10.1111/j.1365-2311.1978.tb00911.x. DOI
Votýpka J., Klepetková H., Jirků M., Kment P., Lukeš J. Phylogenetic relationships of trypanosomatids parasitising true bugs (Insecta: Heteroptera) in sub-Saharan Africa. Int. J. Parasitol. 2012;42:489–500. doi: 10.1016/j.ijpara.2012.03.007. PubMed DOI
Týč J., Votýpka J., Klepetková H., Suláková H., Jirků M., Lukeš J. Growing diversity of trypanosomatid parasites of flies (Diptera: Brachycera): Frequent cosmopolitism and moderate host specificity. Mol. Phylogenet. Evol. 2013;69:255–264. doi: 10.1016/j.ympev.2013.05.024. PubMed DOI
Ishemgulova A., Butenko A., Kortišová L., Boucinha C., Grybchuk-Ieremenko A., Morelli K.A., Tesařová M., Kraeva N., Grybchuk D., Pánek T., et al. Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila. PLoS ONE. 2017;12:e0174165. doi: 10.1371/journal.pone.0174165. PubMed DOI PMC
Brunoro G.V.F., Menna-Barreto R.F.S., Garcia-Gomes A.S., Boucinha C., Lima D.B., Carvalho P.C., Teixeira-Ferreira A., Trugilho M.R.O., Perales J., Schwämmle V., et al. Quantitative Proteomic Map of the Trypanosomatid Strigomonas culicis: The Biological Contribution of its Endosymbiotic Bacterium. Protist. 2019;170:125698. doi: 10.1016/j.protis.2019.125698. PubMed DOI
Camargo E.P. Phytomonas and other trypanosomatid parasites of plants and fruit. Adv. Parasitol. 1999;42:29–112. PubMed
d’Avila-Levy C.M., Yurchenko V., Votýpka J., Grellier P. Protist Collections: Essential for Future Research. Trends Parasitol. 2016;32:840–842. doi: 10.1016/j.pt.2016.08.001. PubMed DOI
Koren S., Walenz B.P., Berlin K., Miller J.R., Bergman N.H., Phillippy A.M. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722–736. doi: 10.1101/gr.215087.116. PubMed DOI PMC
Walker B.J., Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo C.A., Zeng Q., Wortman J., Young S.K., et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9:e112963. doi: 10.1371/journal.pone.0112963. PubMed DOI PMC
Gurevich A., Saveliev V., Vyahhi N., Tesler G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–1075. doi: 10.1093/bioinformatics/btt086. PubMed DOI PMC
Mikheenko A., Valin G., Prjibelski A., Saveliev V., Gurevich A. Icarus: Visualizer for de novo assembly evaluation. Bioinformatics. 2016;32:3321–3323. doi: 10.1093/bioinformatics/btw379. PubMed DOI
Steinbiss S., Silva-Franco F., Brunk B., Foth B., Hertz-Fowler C., Berriman M., Otto T.D. Companion: A web server for annotation and analysis of parasite genomes. Nucleic Acids Res. 2016;44:W29–W34. doi: 10.1093/nar/gkw292. PubMed DOI PMC
Hall T.A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999;41:95–98.
Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: Advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst. Biol. 2004;53:793–808. doi: 10.1080/10635150490522304. PubMed DOI
Helaers R., Milinkovitch M.C. MetaPIGA v2.0: Maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. BMC Bioinform. 2010;11:379. doi: 10.1186/1471-2105-11-379. PubMed DOI PMC
Huelsenbeck J.P., Ronquist F., Nielsen R., Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 2001;294:2310–2314. doi: 10.1126/science.1065889. PubMed DOI
Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Hohna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012;61:539–542. doi: 10.1093/sysbio/sys029. PubMed DOI PMC
The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions