دورية أكاديمية
أعرض في EDS

Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.

التفاصيل البيبلوغرافية
العنوان: Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.
المؤلفون: Valach M; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada. matus.a.valach@gmail.com., Moreira S; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada., Petitjean C; School of Biological Sciences, University of Bristol, Bristol, UK., Benz C; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic., Butenko A; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.; Faculty of Science, University of Ostrava, Ostrava, Czech Republic., Flegontova O; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.; Faculty of Science, University of Ostrava, Ostrava, Czech Republic., Nenarokova A; School of Biological Sciences, University of Bristol, Bristol, UK.; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic., Prokopchuk G; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic., Batstone T; School of Biological Sciences, University of Bristol, Bristol, UK.; Present address: High Performance Computing Centre, Bristol, UK., Lapébie P; Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France., Lemogo L; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada.; Present address: Environment Climate Change Canada, Dorval, QC, Canada., Sarrasin M; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada., Stretenowich P; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada.; Present address: Canadian Centre for Computational Genomics; McGill Genome Centre, McGill University, Montreal, QC, Canada., Tripathi P; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic., Yazaki E; RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), Hirosawa, Wako, Saitama, Japan., Nara T; Laboratory of Molecular Parasitology, Graduate School of Life Science and Technology, Iryo Sosei University, Iwaki City, Fukushima, Japan., Henrissat B; Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, Marseille, France.; Present address: DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark.; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia., Lang BF; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada., Gray MW; Department of Biochemistry and Molecular Biology, Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada., Williams TA; School of Biological Sciences, University of Bristol, Bristol, UK., Lukeš J; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.; Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic., Burger G; Department of Biochemistry, Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, QC, Canada. gertraud.burger@umontreal.ca.
المصدر: BMC biology [BMC Biol] 2023 May 04; Vol. 21 (1), pp. 99. Date of Electronic Publication: 2023 May 04.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101190720 Publication Model: Electronic Cited Medium: Internet ISSN: 1741-7007 (Electronic) Linking ISSN: 17417007 NLM ISO Abbreviation: BMC Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : BioMed Central, c2003-
مواضيع طبية MeSH: Eukaryota*/genetics , Kinetoplastida*/genetics, Humans ; Meiotic Prophase I ; Euglenozoa/genetics ; Multigene Family ; Phylogeny
مستخلص: Background: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.
Results: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.
Conclusions: Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.
(© 2023. The Author(s).)
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معلومات مُعتمدة: BB/R016437/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council
فهرسة مساهمة: Keywords: CAZymes; Ecological distribution; Feeding strategy; Gene-family evolution; Genome; Geographical distribution; Lateral gene transfer; Paradiplonema papillatum; Proteome; Protists; Transcriptome
تواريخ الأحداث: Date Created: 20230504 Date Completed: 20230508 Latest Revision: 20230515
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC10161547
DOI: 10.1186/s12915-023-01563-9
PMID: 37143068
قاعدة البيانات: MEDLINE
الوصف
تدمد:1741-7007
DOI:10.1186/s12915-023-01563-9