Genome-wide macrosynteny among Fusarium species in the Gibberella fujikuroi complex revealed by amplified fragment length polymorphisms

PLoS One. 2014 Dec 8;9(12):e114682. doi: 10.1371/journal.pone.0114682. eCollection 2014.

Abstract

The Gibberella fujikuroi complex includes many Fusarium species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including Fusarium circinatum, Fusarium fujikuroi and Fusarium verticillioides, each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between Fusarium temperatum and F. circinatum, together with genomic sequence data, was utilized to consider the level of synteny between the three Fusarium genomes. Regions that are homologous amongst the Fusarium genomes examined were identified using in silico and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to F. fujikuroi and F. verticillioides. This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in F. verticillioides and F. fujikuroi, as well as to assign two previously unmapped supercontigs of F. verticillioides to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of F. circinatum and F. temperatum. Overall, a remarkable level of macrosynteny was observed among the three Fusarium genomes, when comparing AFLP fragments. This study not only demonstrates how in silico AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amplified Fragment Length Polymorphism Analysis / methods*
  • Computational Biology / methods*
  • DNA, Fungal / genetics*
  • Fusarium / classification*
  • Fusarium / genetics*
  • Genome, Fungal*
  • Molecular Sequence Data
  • Phylogeny
  • Sequence Analysis, DNA
  • Synteny / genetics*

Substances

  • DNA, Fungal

Associated data

  • GENBANK/AYJV00000000

Grant support

The authors thank the University of Pretoria, members of the Tree Protection Cooperative Program (TPCP), the Mellon Foundation, the National Research Foundation (NRF)/Department of Science and Technology (DST), Centre of Excellence in Tree Health Biotechnology (CTHB) and the THRIP initiative of the Department of Trade and Industry (DTI) in South Africa for financial assistance. This work was based on the research supported in part by a number of grants from the National Research Foundation of South Africa (includes Grant specific unique reference number (UID) 83924). The Grant holders acknowledge that opinions, findings and conclusions or recommendations expressed in any publication generated by the NRF supported research are that of the author(s), and that the NRF accepts no liability whatsoever in this regard. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.