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Open Access Research article

Relocation of genes generates non-conserved chromosomal segments in Fusarium graminearum that show distinct and co-regulated gene expression patterns

Chunzhao Zhao1234, Cees Waalwijk12, Pierre JGM de Wit25, Dingzhong Tang3 and Theo van der Lee12*

Author Affiliations

1 Plant Research International, Wageningen, The Netherlands

2 Graduate School Experimental Plant Sciences, Wageningen University, Wageningen, The Netherlands

3 State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

4 Graduate University of Chinese Academy of Sciences, Beijing, China

5 Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands

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BMC Genomics 2014, 15:191  doi:10.1186/1471-2164-15-191

Published: 13 March 2014

Abstract

Background

Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions.

Results

The genome of F. graminearum harbours thirteen non-conserved regions dispersed over all of the four chromosomes. Using RNA-Seq data from the mycelium of F. graminearum, we found weakly expressed regions on all of the four chromosomes that exactly matched with non-conserved regions. Comparison of gene expression between two different developmental stages (conidia and mycelium) showed that the expression of genes in conserved regions is stable, while gene expression in non-conserved regions is much more influenced by developmental stage. In addition, genes involved in the production of secondary metabolites and secreted proteins are enriched in non-conserved regions, suggesting that these regions could also be important for adaptations to new environments, including adaptation to new hosts. Finally, we found evidence that non-conserved regions are generated by sequestration of genes from multiple locations. Gene relocations may lead to clustering of genes with similar expression patterns or similar biological functions, which was clearly exemplified by the PKS2 gene cluster.

Conclusions

Our results showed that chromosomes can be functionally divided into conserved and non-conserved regions, and both could have specific and distinct roles in genome evolution and regulation of gene expression.

Keywords:
Gene expression; Non-conserved region; Gene relocation; Secondary metabolite gene cluster; Fusarium graminearum