Diepeningen, A.D., van

Hoog, S., de

Lee, T.A.J., van der

Waalwijk, C.

Name not available

Fusarium oxysporum mitochondria in the next generation sequencing era

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15GEWASBESCHERMING | JAARGANG 46 | NUMMER 1 | MAART 2015
[ VERENIGINGSNIEUWS
In recent years more and more WGS (whole ge-
nome sequencing) projects are becoming publicly 
available. Despite this fact, the number of pub-
lished mitochondrial genomes is lagging behind. 
There are only six mitochondrial genomes ready 
for Fusarium spp., but there are more than twenty 
WGS projects available.
Our group has developed a program, GRAbB 
(Genomic Region Assembly by Baiting), which 
can selectively assemble regions of the genome 
from next generation sequencing reads. Using this 
program and the publicly available WGS reads 
we have assembled and annotated twenty-seven 
mitochondrial genomes of Fusarium oxysporum 
strains. We also re-sequenced the first F. oxyspo-
rum strain (F11) that had its mitochondrion se-
quenced and a F. proliferatum strain to be used as 
an outgroup. Besides the mitochondrial genomes 
we also extracted seven nuclear marker sequences 
that have been used for phylogenetic study of the 
FOSC.
Previous studies have identified a highly variable 
region in the mitogenome of Fusarium spp, which 
is found between MT-RNR2 and MT-ND2 genes. 
This variable region encodes a large (~6kb) ORF. 
In our dataset we found that within the FOSC 
there are two more variants of this region. All three 
variants contain the same tRNA genes, except for 
one of the variants, which contains an additional 
tRNA gene. Only one of the variants contains the 
typical large ORF, which was described in other 
Fusarium spp. The variants are not clade specific 
and the trees inferred from the variable regions are 
similar to the trees inferred using an eight-marker 
dataset. These findings make it likely that there is 
mitochondrial recombination going on within the 
species.
Balázs Brankovics1, 
Anne D. van 
Diepeningen1, Theo van 
der Lee2, Cees Waalwijk2 
& G. Sybren de Hoog1,2
1 CBS-KNAW Fungal 
Biodiversity Centre, Utrecht, 
the Netherlands
2 Plant Research 
International, Wageningen 
University and Research 
Centre, Wageningen, the 
Netherlands
3 Institute of Biodiversity 
and Ecosystem Dynamics, 
University of Amsterdam, 
Amsterdam, the Netherlands
e-mail: 
b.brankovics@cbs.knaw.nl
Chunzhao Zhao1, Cees 
Waalwijk2, Pierre JGM 
de Wit3, Dingzhong 
Tang1 & Theo AJ van 
der Lee2
1 State Key Laboratory of 
Plant Cell and Chromosome 
Engineering, Institute of 
Genetics and Developmental 
Biology, Chinese Academy of 
Sciences, Beijing, China
2Wageningen UR, Plant 
Research International, 
Department Bio-interactions 
and Plant Health,
Droevendaalsesteeg 1, 6708 
PB, Wageningen
3 Laboratory of 
Phytopathology, 
Wageningen University, 
Wageningen, The 
Netherlands
e-mail: 
theo.vanderlee@wur.nl
Fusarium oxysporum mitochondria in the Next Generation 
Sequencing era
Relocation and co-regulated gene expression patterns 
in Fusarium graminearum
Genome comparisons between closely related 
species often show non-conserved regions across
chromosomes. Some of them are located in spe-
cific regions of chromosomes and some are even 
confined to one or more entire chromosomes. The 
origin and biological relevance of these non-con-
served regions are still largely unknown. The 
genome of Fusarium graminearum genome was 
studied to elucidate the significance of non-con-
served regions. In the genome of F. graminearum 
harbours thirteen non-conserved regions dis-
persed over all of the four chromosomes. Using 
RNA-Seq data from the mycelium of F. gramin-
earum, 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 the developmental 
stage. In addition, genes involved in the produc-
tion of secondary metabolites and secreted pro-
teins are enriched in non-conserved regions, sug-
gesting that these regions could also be important 
for adaptations to new environments, including 
adaptation to new hosts. Finally, we found evi-
dence 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 bio-
logical functions, which was clearly exemplified 
by the PKS2 gene cluster. 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. 
Reference:
Relocation of genes generates non-conserved chromosomal 
segments in Fusarium graminearum that show distinct and 
co-regulated gene expression patterns. C Zhao, C Waalwijk, 
PJGM de Wit, D Tang, T van der Lee. BMC genomics 15 (1), 191


Fusarium oxysporum mitochondria in the next generation sequencing era

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