OpenLB
Open Library of Bioscience
Advanced Search
Life (Basel, Switzerland)
Feb 28, 2023;13 (3):

De Novo Hybrid Assembled Draft Genome of (Arnott) Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis.

Rudra Prasad Banerjee, Gopal Ji Tiwari, Babita Joshi, Satya Narayan Jena, Om Prakash Sidhu, Baleshwar Meena, Tikam S Rana, Saroj K Barik
Author Information
  1. Rudra Prasad Banerjee: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India. ORCID
  2. Gopal Ji Tiwari: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
  3. Babita Joshi: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
  4. Satya Narayan Jena: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
  5. Om Prakash Sidhu: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
  6. Baleshwar Meena: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
  7. Tikam S Rana: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
  8. Saroj K Barik: CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India. ORCID
PMID: 36983818 DOI: 10.3390/life13030662

Abstract

Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine-cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in .

Keywords

draft genome flow cytometry-based genome size estimation guggulsterone phytosterol biosynthesis pathway

References

  1. BMC Genomics. 2012 Sep 09;13:464 [PMID: 22958331]
  2. Annu Rev Nutr. 2003;23:303-13 [PMID: 12626688]
  3. J Biol Chem. 2016 Apr 8;291(15):8189-98 [PMID: 26872973]
  4. Prog Lipid Res. 2003 May;42(3):163-75 [PMID: 12689617]
  5. Nat Genet. 2014 Aug;46(8):919-25 [PMID: 24952747]
  6. Science. 2012 Nov 9;338(6108):758-67 [PMID: 23145453]
  7. Obesity (Silver Spring). 2008 Jan;16(1):16-22 [PMID: 18223606]
  8. Physiol Mol Biol Plants. 2015 Jan;21(1):71-81 [PMID: 25648764]
  9. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):3160-5 [PMID: 14973198]
  10. Nature. 2007 Jun 7;447(7145):714-9 [PMID: 17554307]
  11. Genome Biol. 2018 Sep 11;19(1):131 [PMID: 30205843]
  12. Sci Data. 2018 May 22;5:180069 [PMID: 29786699]
  13. J Biol Chem. 2014 Jun 13;289(24):17249-67 [PMID: 24770414]
  14. Arch Biochem Biophys. 2003 Jun 15;414(2):232-43 [PMID: 12781775]
  15. Plant Mol Biol. 2019 Jul;100(4-5):543-560 [PMID: 31090025]
  16. Bioinformatics. 2013 Nov 1;29(21):2669-77 [PMID: 23990416]
  17. Nat Plants. 2016 Dec 22;3:16205 [PMID: 28005066]
  18. Plant Cell Physiol. 2016 May;57(5):961-75 [PMID: 27084593]
  19. Atherosclerosis. 2004 Feb;172(2):239-46 [PMID: 15019533]
  20. Plant Physiol. 1999 Mar;119(3):897-907 [PMID: 10069828]
  21. Int J Plant Genomics. 2008;2008:820274 [PMID: 18317508]
  22. Trends Endocrinol Metab. 2002 Sep;13(7):275-6 [PMID: 12163224]
  23. Plant J. 2015 Aug;83(4):582-99 [PMID: 26072661]
  24. Elife. 2016 Jun 14;5: [PMID: 27296645]
  25. Cardiovasc Drug Rev. 2007 Winter;25(4):375-90 [PMID: 18078436]
  26. Biochem Pharmacol. 2007 Jun 30;74(1):118-30 [PMID: 17475222]
  27. Nat Biotechnol. 2010 Sep;28(9):951-6 [PMID: 20729833]
  28. GigaByte. 2020 Aug 01;2020:gigabyte4 [PMID: 36824597]
  29. Mol Ecol. 2017 Oct;26(20):5369-5406 [PMID: 28746784]
  30. Science. 2018 Oct 19;362(6412):343-347 [PMID: 30166436]
  31. Nat Commun. 2013;4:2445 [PMID: 24048436]
  32. PeerJ. 2019 Sep 20;7:e7649 [PMID: 31579586]
  33. Nat Biotechnol. 2011 Nov 06;30(1):83-9 [PMID: 22057054]
  34. Plant Cell. 2014 Sep;26(9):3763-74 [PMID: 25217510]
  35. Sci Rep. 2019 Nov 11;9(1):16511 [PMID: 31712633]
  36. PLoS One. 2015 Dec 02;10(12):e0144108 [PMID: 26630570]
  37. PLoS One. 2013 May 29;8(5):e64799 [PMID: 23734219]
  38. J Biol Chem. 1996 Apr 19;271(16):9384-9 [PMID: 8621604]
  39. Nature. 2012 May 30;485(7400):635-41 [PMID: 22660326]
  40. Bioorg Med Chem Lett. 2008 Jan 1;18(1):232-5 [PMID: 17998159]
  41. Bioinformatics. 2013 Apr 15;29(8):1072-5 [PMID: 23422339]
  42. Proc Natl Acad Sci U S A. 2018 May 1;115(18):E4151-E4158 [PMID: 29678829]
  43. Nat Rev Genet. 2005 Sep;6(9):699-708 [PMID: 16151375]
  44. Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):E8096-E8103 [PMID: 30082386]
  45. BMC Genomics. 2012 Jul 24;13:341 [PMID: 22827831]
  46. Scientifica (Cairo). 2015;2015:138039 [PMID: 26587309]
  47. Nat Genet. 2013 Jan;45(1):59-66 [PMID: 23179022]
  48. Plant J. 2001 Mar;25(6):605-15 [PMID: 11319028]
  49. Curr Opin Biotechnol. 2014 Apr;26:174-82 [PMID: 24556196]
  50. Nature. 2013 Aug 15;500(7462):335-9 [PMID: 23883927]
  51. New Phytol. 2017 Aug;215(3):1115-1131 [PMID: 28649699]
  52. Nat Genet. 2012 Oct;44(10):1098-103 [PMID: 22922876]
  53. Science. 2003 Nov 21;302(5649):1401-4 [PMID: 14631042]
  54. Genome Biol. 2011 Oct 20;12(10):R102 [PMID: 22014239]
  55. BMC Biol. 2017 Sep 19;15(1):86 [PMID: 28927400]
  56. Nat Rev Genet. 2015 Jun;16(6):344-58 [PMID: 25948246]
  57. BMC Genomics. 2017 Jan 11;18(1):69 [PMID: 28077077]
  58. Nat Protoc. 2007;2(9):2233-44 [PMID: 17853881]
  59. Annu Rev Anim Biosci. 2013 Jan;1:261-81 [PMID: 25387020]
  60. Nat Genet. 2015 Dec;47(12):1435-42 [PMID: 26523774]

Grants

  1. Project No.-HCP0010/Council of Scientific and Industrial Research
Journal Article
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.0genomegenesbiosynthesisguggulsteronepredictedphytosterolassembleddraftGenomesequenceinvolvedsecondarymedicinalplantArnottBhandarikeypathwaysize35identificationspecifictargetedmetabolitetwoessentialrequirementsimprovementfamily:BurseraceaenativeWesternIndiaproducesusefultreatingatherosclerosisarthritishighcholesterolacneobesityenhancedyieldneedspeciespre-requisiteThereforefirst-everhybrid103Gb107221contigsusingIlluminaPacBioplatformsN50L50values~74Kb3486bprespectivelyguanine-cytosineGCcontent6%987%BenchmarkingUniversalSingleCopyOrthologBUSCOvalueindicatedgoodintegrityassemblyAnalysispresence31187342MbrepeatelementscomparativeanalysisrelevantorthogroupsassociatedmetabolismpathwayshelpfuturevarietydevelopmentprogramimprovedcontentsDeNovoHybridAssembledDraftRevealsKeyEnzymesInvolvedPhytosterolBiosynthesisflowcytometry-basedestimation

Similar Articles

Cited By