Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don.
| Title: | Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don. |
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| Authors: | Quan ND; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Nguyen NL; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Giang TTH; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Ngan NTT; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Hien NT; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Tung NV; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Trang NHT; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Lien NTK; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Nguyen HH; Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam.; Department of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Str., Cau Giay, Hanoi 100000, Vietnam. |
| Source: | Journal of fungi (Basel, Switzerland) [J Fungi (Basel)] 2024 May 15; Vol. 10 (5). Date of Electronic Publication: 2024 May 15. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: MDPI AG Country of Publication: Switzerland NLM ID: 101671827 Publication Model: Electronic Cited Medium: Internet ISSN: 2309-608X (Electronic) Linking ISSN: 2309608X NLM ISO Abbreviation: J Fungi (Basel) Subsets: PubMed not MEDLINE |
| Imprint Name(s): | Original Publication: Basel, Switzerland : MDPI AG, [2015]- |
| Abstract: | Talaromyces sp. DC2 is an endophytic fungus that was isolated from the stem of Catharanthus roseus (L.) G. Don in Hanoi, Vietnam and is capable of producing vinca alkaloids. This study utilizes the PacBio Sequel technology to completely sequence the whole genome of Talaromyces sp. DC2The genome study revealed that DC2 contains a total of 34.58 Mb spanned by 156 contigs, with a GC content of 46.5%. The identification and prediction of functional protein-coding genes, tRNA, and rRNA were comprehensively predicted and highly annotated using various BLAST databases, including non-redundant (Nr) protein sequence, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Carbohydrate-Active Enzymes (CAZy) databases. The genome of DC2 has a total of 149, 227, 65, 153, 53, and 6 genes responsible for cellulose, hemicellulose, lignin, pectin, chitin, starch, and inulin degradation, respectively. The Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analyses revealed that strain DC2 possesses 20 biosynthetic gene clusters responsible for producing secondary metabolites. The strain DC2 has also been found to harbor the DDC gene encoding aromatic L-amino acid decarboxylase enzyme. Conclusively, this study has provided a comprehensive understanding of the processes involved in secondary metabolites and the ability of the Talaromyces sp. DC2 strain to degrade plant cell walls. |
| References: | Chem Commun (Camb). 2016 May 21;52(41):6777-80. (PMID: 27056201); BMC Bioinformatics. 2003 Sep 11;4:41. (PMID: 12969510); Chem Sci. 2018 Nov 15;10(4):1227-1231. (PMID: 30774923); J Appl Microbiol. 2021 Dec;131(6):2886-2898. (PMID: 34062037); Appl Microbiol Biotechnol. 2020 Jun;104(11):4811-4835. (PMID: 32303816); BMC Genomics. 2012 Jul 19;13:321. (PMID: 22812459); Front Microbiol. 2020 Dec 18;11:581309. (PMID: 33391201); J Agric Food Chem. 2015 Nov 4;63(43):9558-64. (PMID: 26466717); J Fungi (Basel). 2023 Jun 27;9(7):. (PMID: 37504693); Nucleic Acids Res. 1999 Jan 1;27(1):29-34. (PMID: 9847135); PLoS One. 2014 Dec 02;9(12):e114138. (PMID: 25461894); Bioresour Technol. 2021 Mar;324:124623. (PMID: 33434871); Nat Commun. 2021 Jun 23;12(1):3864. (PMID: 34162873); PLoS One. 2012;7(11):e49679. (PMID: 23166747); G3 (Bethesda). 2017 Jun 7;7(6):1791-1797. (PMID: 28381497); Cell Mol Life Sci. 2016 Jul;73(14):2781-807. (PMID: 27166931); J Fungi (Basel). 2023 Aug 18;9(8):. (PMID: 37623631); Proc Natl Acad Sci U S A. 1984 Dec;81(24):8014-8. (PMID: 6096873); Front Microbiol. 2021 Aug 04;12:665702. (PMID: 34421835); Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. (PMID: 25392425); Molecules. 2019 Jun 18;24(12):. (PMID: 31216742); Biotechnol Adv. 2023 Jul-Aug;65:108148. (PMID: 37030552); Org Lett. 2013 Feb 15;15(4):721-3. (PMID: 23360543); Microbiol Mol Biol Rev. 2001 Dec;65(4):497-522, table of contents. (PMID: 11729262); Anal Biochem. 2020 Mar 15;593:113530. (PMID: 31794703); J Biotechnol. 2013 Jan 10;163(1):38-44. (PMID: 23123260); PLoS One. 2013 Dec 19;8(12):e84102. (PMID: 24367630); FEMS Microbiol Rev. 1993 Apr;10(3-4):287-300. (PMID: 8318261); PLoS One. 2015 Dec 23;10(12):e0144476. (PMID: 26697875); Plant Mol Biol. 2001 Sep;47(1-2):9-27. (PMID: 11554482); J Fungi (Basel). 2021 Dec 01;7(12):. (PMID: 34947016); Metabolites. 2023 Feb 03;13(2):. (PMID: 36837841); Stud Mycol. 2014 Jun;78:175-341. (PMID: 25492983); PLoS One. 2018 Jul 12;13(7):e0200607. (PMID: 30001376); Int J Biol Macromol. 2020 Dec 1;164:3535-3545. (PMID: 32890562); Nat Biotechnol. 2007 Feb;25(2):221-31. (PMID: 17259976); MycoKeys. 2020 Jul 07;68:75-113. (PMID: 32733145); J Fungi (Basel). 2023 Sep 07;9(9):. (PMID: 37755017); Org Lett. 2020 Oct 16;22(20):7837-7841. (PMID: 33006285); Sci Rep. 2017 Mar 28;7(1):490. (PMID: 28352091); Sci Rep. 2014 Oct 22;4:6728. (PMID: 25335861); Plants (Basel). 2021 Mar 31;10(4):. (PMID: 33807415); Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. (PMID: 25428369); J Fungi (Basel). 2021 Mar 05;7(3):. (PMID: 33807546); ACS Chem Biol. 2020 Sep 18;15(9):2476-2484. (PMID: 32786262); J Fungi (Basel). 2021 Nov 30;7(12):. (PMID: 34947008); Nucleic Acids Res. 2023 Jul 5;51(W1):W46-W50. (PMID: 37140036); ACS Med Chem Lett. 2012 Sep 07;3(10):814-7. (PMID: 24900384); Chembiochem. 2016 Jan;17(2):132-6. (PMID: 26632772); Sci Rep. 2016 May 25;6:26583. (PMID: 27220774); 3 Biotech. 2017 Dec;7(6):368. (PMID: 29062678); Genome Announc. 2017 Mar 2;5(9):. (PMID: 28254987); PLoS One. 2013 Sep 16;8(9):e71805. (PMID: 24066024); Genome Announc. 2015 Feb 26;3(1):. (PMID: 25720677); Org Biomol Chem. 2019 Jan 2;17(2):248-251. (PMID: 30548032); Biotechnol Biofuels. 2017 Jul 3;10:170. (PMID: 28690679); Sci Rep. 2022 Oct 22;12(1):17791. (PMID: 36273028); Front Microbiol. 2022 Aug 19;13:984801. (PMID: 36060779); Front Pharmacol. 2023 Mar 23;14:1099380. (PMID: 37033617); Polymers (Basel). 2018 Dec 19;10(12):. (PMID: 30961332); Molecules. 2018 Jan 15;23(1):. (PMID: 29342967); Eng Life Sci. 2023 Jul 09;23(8):e2300003. (PMID: 37533727); Nat Prod Bioprospect. 2016 Feb;6(1):1-24. (PMID: 26746215); ACS Chem Biol. 2018 Dec 21;13(12):3343-3353. (PMID: 30484626); J Ethnopharmacol. 2022 Feb 10;284:114647. (PMID: 34562562); FEMS Microbiol Rev. 2008 May;32(3):501-21. (PMID: 18371173); Fungal Genet Biol. 2005 May;42(5):420-33. (PMID: 15809006); 3 Biotech. 2023 Nov;13(11):376. (PMID: 37881510) |
| Grant Information: | TĐCNSH.02/20-22 Vietnam Academy of Science and Technology |
| Contributed Indexing: | Keywords: Catharanthus roseus; DC2; DDC gene; Talaromyces; endophytic fungus; genome sequencing; plant cell wall degradation; secondary metabolites |
| Entry Date(s): | Date Created: 20240524 Latest Revision: 20240526 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC11122143 |
| DOI: | 10.3390/jof10050352 |
| PMID: | 38786707 |
| Database: | MEDLINE |
Journal Article