Phylogenomics shows that novel tapeworm-like traits of haplozoan parasites evolved from within the Peridiniales (Dinoflagellata)
Tài liệu tham khảo
Andrews, S., 2010. FastQC: a quality control tool for high throughput sequence data [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/].
Angel, 2021, Insights into the morphology of Haplozoan parasites (Dinoflagellata) using confocal laser scanning microscopy, J. Eukaryot. Microbiol., 68, 10.1111/jeu.12855
Bolger, A.M., Lohse, M., Usadel, B., 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170.
Burki, 2016, Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista, Proc. R. Soc. B Biol. Sci., 283, 20152802, 10.1098/rspb.2015.2802
Bushmanova, 2019, RnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data, Gigascience, 8, 10.1093/gigascience/giz100
Cachon, 1987, Parasitic dinoflagellates, 571
Calkins, 1915, Microtaeniella clymenellae, a new genus and new species of colonial gregarines, Biol. Bull., 29, 46, 10.2307/1536259
Capella-Gutiérrez, S., Silla-Martínez, J.M., Gabaldón, T., 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973. 10.1093/bioinformatics/btp348.
Chatton, 1920, Les Péridiniens parasites: morphologie, reproduction, ethologie, Arch. Zool. Exp. Gén, 59, 1
Coats, 1999, Parasitic life styles of marine dinoflagellates, Journal of Eukaryotic Microbiology., 46, 402, 10.1111/j.1550-7408.1999.tb04620.x
Cooney, E.C., Okamoto, N., Cho, A., Hehenberger, E., Richards, T.A., Santoro, A.E., Worden, A.Z., Leander, B.S., Keeling, P.J., 2020. Single-cell transcriptomics of Abedinium reveals a new early-branching dinoflagellate lineage. Genome Biol. Evol. 12, 2417–2428. 10.1093/GBE/EVAA196.
Cooney, E.C., S., L.B., Keeling, P.J., 2022. Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral. PNAS Nexus 1, 1–11.
De Assis, 2011, Phylogenetic relationships within maldanidae (Capitellida, annelida) based on morphological characters, Syst. Biodivers., 9, 233, 10.1080/14772000.2011.604358
Dogiel, 1906, Haplozoon armatum n. gen. nova sp., der Vertreter einer neuen Mesozoa-Gruppe, Zool. Anz., 30, 895
Dogiel, 1907, Haplozoon lineare und Haplozoon armiatum, neue Mesozoa-form, Trav. Soc. Imp. Nat. St., 28
Fensome, 1999, Dinoflagellate phylogeny revisited: reconciling morphological and molecular based phylogenies, Grana, 38, 66, 10.1080/00173139908559216
Folmer, 1994, DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol. Mar. Biol. Biotechnol., 3, 294
Gómez, 2012, A checklist and classification of living dinoflagellates (Dinoflagellata, Alveolata), CICIMAR Oceánides, 27, 65, 10.37543/oceanides.v27i1.111
Gómez, F., 2020. Diversity and classification of dinoflagellates, in: Dinoflagellates: classification, evolution, physiology and ecological significance. pp. 1–38.
Haas, 2013, De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat. Protoc., 8, 1494, 10.1038/nprot.2013.084
Hackett, 2004, Dinoflagellates: a remarkable evolutionary experiment, Am. J. Bot., 91, 1523, 10.3732/ajb.91.10.1523
Janouskovec, 2017, Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics, Proc. Natl. Acad. Sci. U. S. A., 114, E171, 10.1073/pnas.1614842114
Katoh, 2013, MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010
Landers, 2000, Light and electron microscopic examination of the parasitic dinoflagellate Haplozoon, Microsc. Microanal., 6, 884, 10.1017/S1431927600036916
Landsberg, J., Steldlnger, K., Blakesley, B., Zondervan, R., 1994. Scanning electron microscope study of dinospores of Amyloodinium cf. ocellatum , a pathogenic dinoflagellate parasite of marine fish, and comments on its relationship to the Peridiniales. Dis. Aquat. Organ. 20. 10.3354/dao020023.
Leander, 2008, A hierarchical view of convergent evolution in microbial eukaryotes, J. Eukaryotic Microbiol., 59, 10.1111/j.1550-7408.2008.00308.x
Leander, 2002, Surface morphology of the marine parasite Haplozoon axiothellae Siebert (Dinoflagellata), Eur. J. Protistol., 38, 287, 10.1078/0932-4739-00882
Lin, 2011, Genomic understanding of dinoflagellates, Res. Microbiol., 162, 551, 10.1016/j.resmic.2011.04.006
Neresheimer, 1908, Die Mesozoen. Zool. Zent., 15, 257
Nguyen, 2015, IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol. Biol. Evol., 32, 268, 10.1093/molbev/msu300
Not, 2012, Diversity and ecology of eukaryotic marine phytoplankton, Advances in Botanical Research., 1
Orr, 2012, When naked became armored: an eight-gene phylogeny reveals monophyletic origin of theca in dinoflagellates, PLoS One, 7, e50004, 10.1371/journal.pone.0050004
Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006
Poche, 1913, Das System der Protozoa. Arch. Protistenkd., 30, 125
Poux, S., Arighi, C.N., Magrane, M., Bateman, A., Wei, C.H., Lu, Z., Boutet, E., Bye-A-Jee, H., Famiglietti, M.L., Roechert, B., UniProt Consortium, T., 2017. On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinformatics 33, 3454–3460. 10.1093/bioinformatics/btx439.
Roure, 2007, SCaFoS: A tool for selection, concatenation and fusion of sequences for phylogenomics, in, BMC Evolutionary Biology., 7
Rueckert, 2008, Morphology and molecular phylogeny of Haplozoon praxillellae n. sp. (Dinoflagellata): A novel intestinal parasite of the maldanid polychaete Praxillella pacifica Berkeley, Eur. J. Protistol., 44, 299, 10.1016/j.ejop.2008.04.004
Saldarriaga, 2001, Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements, J. Mol. Evol., 53, 204, 10.1007/s002390010210
Saldarriaga, 2004, Molecular data and the evolutionary history of dinoflagellates, Eur. J. Protistol., 40, 85, 10.1016/j.ejop.2003.11.003
Sarai, 2020, Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis, Proc. Natl. Acad. Sci. U. S. A., 117, 5364, 10.1073/pnas.1911884117
Seemann, 2013, barrnap 0.9: rapid ribosomal RNA prediction, Github. Com.
Shumway, 1924, The genus Haplozoon, Dogiel. Observations on the life history and systematic position, J. Parasitol., 11, 59, 10.2307/3270863
Siebert, 1973, A description of Haplozoon axiothellae n.sp., an endosymbiont of the polychaete Axiothella rubrocincta, J. Phycol., 9, 185, 10.1111/j.1529-8817.1973.tb04077.x
Siebert, 1974, The fine structure of the parasitic dinoflagellate Haplozoon axiothellae, Protoplasma, 81, 17, 10.1007/BF02055771
Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E. V., Zdobnov, E.M., 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212. 10.1093/bioinformatics/btv351.
Skovgaard, 2007, Parasitic species of the genus Blastodinium (Blastodiniphyceae) are peridinioid dinoflagellates, J. Phycol., 43, 553, 10.1111/j.1529-8817.2007.00338.x
Song, 2015, Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads, Gigascience, 4, 10.1186/s13742-015-0089-y
Taylor, F.J.R., 2004. Illumination or confusion? Dinoflagellate molecular phylogenetic data viewed from a primarily morphological standpoint, in: Phycological Research. pp. 308–324. 10.1111/j.1440-1835.2004.tb00341.x.
Taylor, 2008, Dinoflagellate diversity and distribution, Biodivers. Conserv., 17, 407, 10.1007/s10531-007-9258-3
Wakeman, 2018, Molecular phylogeny and morphology of Haplozoon ezoense n. sp. (Dinophyceae): a parasitic dinoflagellate with ultrastructural evidence of remnant non-photosynthetic plastids, Protist, 169, 333, 10.1016/j.protis.2018.04.008
Yamamoto, M., Wakeman, K.C., Tomioka, S., Horiguchi, T., 2020. Molecular phylogeny and ultrastructure of two novel parasitic dinoflagellates, Haplozoon gracile sp. nov. and H. pugnus sp. nov. Phycologia 59, 305–319. 10.1080/00318884.2020.1753427.
