Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies Page: 9
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Jung et al. BMC Genomics 2012, 13:129
both the ancestors of Rosaceae and Malus have genomes
consisting of nine chromosomes.
To show how the genomes of the three taxa have
evolved since they diverged from this common ancestral
karyotypes, the nine ancestral chromosomes, Al through
A9, along with genomes of three species, colored by the
ancestral chromosomal origin, were constructed (Addi-
tional file 4: Figure S3). In this figure, the 24 CARs in Fig-
ure 4 were reassigned with colors based on which of the
nine ancestral chromosomes they reside in. The ortholo-
gous relationships amongst the three Rosaceae genomes
are shown in the Rosaceae concentric circle with the puta-
tive nine chromosomes of Rosaceae ancestral genome as
the innermost circle (Figure 5). This allows the identifica-
tion of orthologous regions between the three genomes
that have a common ancestral origin.
The availability of whole genome sequence data has per-
mitted for the first time a detailed evaluation of the con-
servation of macro- and micro-synteny in the Rosaceae
which has demonstrated that the genomes of Fragaria,
Malus and Prunus have undergone different modes of
evolution since they diverged from a common ancestor.
This study has revealed that a greater number of small
scale rearrangements have occurred in Fragaria than in
either Malus or Prunus and has indicated that Malus
went through more translocations potentially as a conse-
quence of the WGD event in the lineage of the genus.
The results of this investigation suggest that Prunus has
the most conserved karyotype at both the macro- and
micro-syntenic level in relation to the ancestral genome
configuration for the Rosaceae, which in concordance
with other studies is hypothesised to have had nine chro-
mosomes. The resolution obtained in this comparison of
genome structure demonstrates the utility of whole gen-
ome sequencing data to the elucidation of mechanisms
driving genome evolution between related organisms at a
level of resolution that would not have been possible
through conventional comparative mapping endeavours.
Materials and methods
Detection of orthologous regions
To detect orthologous regions between the peach and
grape genomes, the whole genome sequence and annota-
tion data of grape were downloaded from Genoscope .
Whole genome sequence of Prunus persica v1.0, primary
assembly of Malus domestica and Fragaria vesca beta ver-
sion FvH4 pseudochromosomes were downloaded from
GDR, Genome Database for Rosaceae [37,38]. The annota-
tion data that includes the prediction of exons and genes
were also downloaded from the databases above. All the
sequence and annotation files that have been used in this
study are available from GDR http://www.rosaceae.org/
BMC_rosaceae_Genome_paper. The whole genome
sequences of peach and grape were masked for repeats
using RepeatMasker , as well as the nmerge, WU-
BLAST distribution, and faSoftMask distribution utilities
of Mercator . Mercator identifies orthologous regions
with one to one ortholgy relationships, rather than produ-
cing any syntenic regions in which one region can have
many syntenic regions. Mercator employs BLAT-similar
anchor pairs to identify orthologous segments in a modi-
fied k-way reciprocal best hit algorithm . Translated
sequences of exons, provided by the annotation data, have
been used as anchors in these analyses. Two exons from
each genome were determined to be similar if the BLAT
 score of the pair was below le -10. BLAT scores were
computed in protein space. To select the optimal criteria
to assess conservation of synteny between Rosaceous gen-
omes, Mercator parameters were varied from between a
minimum of 30 exons and a maximum distance of 300
kbp between exons, to a minimum of two exons and a
maximum distance of 3 Mbp between exons. As the para-
meters become less stringent, we observed a sudden
increase of the number of orthologous regions without the
accompanying increase of the percent geonome coverage.
Parameters selected for further analysis were a minimum
of ten exons and a maximum distance of 300 kbp between
exons as these parameters gave high percentage coverage
within the genomes but reduced small-size syntenic
regions that are potentially artefactual. With the exception
of the analysis shown in Figure 1, the Malus genome was
split into two arbitrary 'sub-genomes' based on the data of
Velasco et al ; sub-genome 1 consisted of chromo-
somes 1, 2, 3, 4, 5, 8, 9, 13 and 14, whilst sub-genome 2
was composed of chromosomes 6, 7, 10, 11, 12, 15, 16 and
17 to use as an input for the Mercator program. This was
done to detect orthologous regions in each of the homeo-
logous Malus chromosomes. The anchored position of
RosCOS markers in the peach genome were downloaded
from GDR [37,38]. RosCOS markers were anchored to
orthologous regions when their anchored positions in
peach belong to the corresponding positions of ORs.
Reconstruction of hypothetical ancestral genome
We used the Multiple Genome Rearrangements and
Ancestors (MGRA) algorithm  to predict Contigu-
ous Ancestral Regions (CARs) that existed in a common
ancestor. The orthology map of Prunus, Fragaria and
Vitis genomes, produced by Mercator, was used as an
input for the MGRA program. The Vitis genome was
included in the analysis as anoutgroup. The hypothetical
ancestral genome was manually constructed using CARs
generated from MGRA, as written in the Result and dis-
cussion section above.
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Jung, Sook; Cestaro, Alessandro; Troggio, Michela; Main, Dorrie; Zheng, Ping; Cho, Ilhyung et al. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies, article, April 4, 2012; [London, United Kingdom]. (digital.library.unt.edu/ark:/67531/metadc122145/m1/9/: accessed July 28, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT College of Arts and Sciences.