African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12294

Full Length Research Paper

Whole-genome optical mapping: Improving assembly of Macrophomina phaseolina MS6 through spanning of twelve blunt end chromosomes by obviating all errors and misassembles

Quazi Md. Mosaddeque Hossen
  • Quazi Md. Mosaddeque Hossen
  • Basic and Applied Research on Jute (BARJ) Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
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Md. Shahidul Islam
  • Md. Shahidul Islam
  • Basic and Applied Research on Jute (BARJ) Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
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Emdadul Mannan Emdad
  • Emdadul Mannan Emdad
  • Basic and Applied Research on Jute (BARJ) Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
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Md. Samiul Haque
  • Md. Samiul Haque
  • Basic and Applied Research on Jute (BARJ) Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
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Md. Monjurul Alam
  • Md. Monjurul Alam
  • Basic and Applied Research on Jute (BARJ) Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
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Maqsudul Alam
  • Maqsudul Alam
  • Basic and Applied Research on Jute (BARJ) Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
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  •  Received: 07 October 2019
  •  Accepted: 08 November 2019
  •  Published: 30 November 2019

Abstract

Deciphering genetic information through next-generation sequencing (NGS) is considered as the basic platform to unveil in details of an organism. However, as it produces short reads that lead to difficulties in assembly, we generated long scaffold-based optical mapping (OM) data of previously sequenced devastating fungus, Macrophomina phaseolina MS6. In the process, KpnI identified as the most effective restriction endonuclease among tested 13, used to digest high molecular weight (HMW) DNA that generated 270,343 genomic DNA molecules size in more than 250 kb. The molecules were assembled and constructed 12 super-scaffolds (terminated with telomeric blunt-ends and denoted as chromosomes) that were aligned with NGS generated 17 (out of 88 reduced from 94) reference scaffolds. The state-of-the-art technology revealed concordances and different discordances viz., inversions, low-quality assembly, gaps, overlaps followed to correct the NGS misassembles. Based on the results, OM generated improved and validated assembly advance our understanding of the chromosome evolution of fungi. This furnished data might be considered as valuable resources to accelerate the precise planning for the protection of M. phaseolina MS6 infected sequenced crops through developing the cross-talk phenomenon between the host and pathogen.
 
Key words: Macrophomina phaseolina MS-6, optical mapping, assembly improvement, assembly validation.