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plants, it would be better to use the appropriate
code, the ICNCP.
these among
16
tuber-bearing
Solanum
species.
All species showed a distinct haplotype, sug-
gesting good resolution at the species level for
these four markers. Their results largely con-
firmed the relationships found in earlier studies
(e.g. Spooner and Castillo, 1997), with the
1
EBN diploid species from Central America dis-
playing higher divergence in comparison to the
other species and showing high similarity be-
tween
S. verrucosum
and the polyploid Mexican
species, confirming the accepted hypothesis on
the origin of these polyploids.
Visser
et al
. (2009) described the sequen-
cing effort of the Potato Genome Sequencing
Consortium (PGSC), a collaboration of
13
research
groups, which at that time had completed about
30% of the 840 Mb genome, announcing a draft
of the complete genome by the end of 2009.
A recent paper by the PGSC (2011) presented
that draft and discussed the insights in genome
evolution, tuber biology, and occurrence of dis-
ease resistance that could be derived from the
genome sequence. The availability of an ultra
high-density (UHD) genetic map was instru-
mental for assigning sequences to each of the
12
chromosomes. The authors expect that the
knowledge of the complete genome sequence
will be invaluable for the identification of genes
and novel alleles of genes for traits of interest for
potato breeders.
The recent special issue of the
American
Journal of Botany
(Volume 99(2), 2012) gives
an excellent overview of the applications of
next-generation sequencing (NGS) in plant biol-
ogy. Unfortunately, none of the contributions
deal with the potato or its wild relatives, even
though potato taxonomist David Spooner is one
of the organizers of this special issue. In their
introduction, Egan
et al
. (2012) point at the fu-
ture possibilities of NGS technologies. Summar-
izing the research presented in the issue, they
describe the possibilities for the development of
molecular markers, the detection of introgres-
sion, transcriptome investigations, phylogenetic
and ecological studies, polyploidy genetics, and
applications for gene bank collections. They note
that the application of NGS to large-scale popu-
lation and phylogenetic studies is hindered by
large genome sizes, variation in the proportion
of organellar DNA in total DNA, polyploidy, and
gene number/redundancy. An interesting appli-
cation is discussed by Kane
et al
. (2012), who
2.3 The Impact of Genomic Data
As outlined above (in the section on the remain-
ing problems in potato taxonomy), morphological
characters have proven to be problematic, due to
their plasticity and often insufficient variation,
and are unable to provide evidence for a clear-cut
classification of section
Petota
. As soon as mo-
lecular data became available, potato taxonom-
ists applied them to reconstruct the phylogeny
of the group. The markers used included restric-
tion fragment length polymorphism (RFLPs),
RAPDs, AFLPs, SSRs, various sequences and
single nucleotide polymorphism (SNPs). The
analyses of these molecular data sets, although
sometimes giving contradicting results, have
produced a rather robust phylogeny recon-
struction of section
Petota
as a whole, and many
detailed studies of subgroups (Van den Berg and
Jacobs, 2007), but the markers used could not
always provide sufficient resolution and details
of the phylogeny-based classification remain
debatable. Will this situation improve when
we turn to the recent developments in genome
sequencing?
With respect to chloroplast genomes, there
are a few papers reporting the application of
genome sequencing in species-level compari-
sons within section
Petota
. Daniell
et al
. (2006)
generated complete chloroplast genome se-
quences of
S. bulbocastanum
and
S. lycopersicum
,
and compared these with the genome organiza-
tion of two other representatives of the
Solanaceae
with completely sequenced chloroplast gen-
omes,
Nicotiana
and
Atropa
. They compared
these taxa for gene content and gene order, and
distribution and location of repeated sequences.
Not surprisingly, they found that sequence diver-
gence corresponded to the phylogenetic rela-
tionships, with the two most closely related spe-
cies, potato and tomato, having the lowest
divergence values for all classes of genes. Garga-
no
et al
. (2012) compared the plastome se-
quence of the cultivated potato (
S. tubersosum
subsp.
tuberosum
) with that of
S. bulbocastanum
,
to characterize the variability in different
genomic regions and to develop markers. They
selected four intergenic regions and compared
