Comparative Genomics Uncovers the Genetic Diversity and Synthetic Biology of Secondary Metabolite Production of Trametes

Abstract

The carbohydrate-active enzyme (CAZyme) genes of Trametes contribute to polysaccharide degradation. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters (BGCs) of Trametes remain unclear. Here, we conducted comparative analysis, detected the CAZyme genes, and predicted the BGCs for nine Trametes strains. Among the 82,053 homologous clusters obtained for Trametes, we identified 8518 core genes, 60,441 accessory genes, and 13,094 specific genes. A large proportion of CAZyme genes were cataloged into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes were divided into six strategies, and the nine Trametes strains harbored 47.78 BGCs on average. Our study revealed that Trametes exhibits an open pan-genome structure. These findings provide insights into the genetic diversity and explored the synthetic biology of secondary metabolite production for Trametes.

Keywords:

• Trametes
• pan-genome
• CAZymes
• biosynthetic gene clusters

Authors’ contributions

This study was designed by YZ and ZDX. YZ collected and downloaded the data. YZ and YJC analyzed the data. YZ, JJW, and ZDX wrote the initial draft of the manuscript. All authors revised the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was partially supported by Natural Science Foundation of the Anhui Higher Education Institutions of China Grant [KJ2018A0494], Youth Elite Support Plan in Universities of Anhui Province Grant [gxyq2018056], National Science Foundation of China Grant [31800049], Natural Science Foundation of the Anhui Grant [1608085MC64], “Six Outstanding, One Top” Outstanding Talent training Innovation Project of Anhui Province [2018zygc068].