Agriculture Reference
In-Depth Information
(a)
Eudicots
(
Arabidopsis
,
Carica
,
Glycine
,
Populus
,
Vitis
)
(b)
Algae, mosses
(
Chlamydomonas
,
Physcomitrella
)
Solanum
tuberosum
group Phureja
8
Monocots
(
Brachypodium
,
Oryza
,
Sorghum
,
Zea
)
Speciation event
Potato-grape
6
373
(1112)
104
(852)
177
(2321)
2
(17)
4
1
(4)
1291
(8035)
2653
(
12,805)
Potato-potato
Recent duplication
Ancient duplication
Grape-grape
406
(5853)
19
(223)
2
3181
(
59,681)
500
(4802)
1
(11)
2107
(
34,243)
49
(347)
0
0 (0)
0.0
0.5
1. 0
1.5
2.0
4DTv
(c)
Chr3
Chr5
Chr1
Chr4
Chr2
Arabidopsis
Potato
Chr1
Chr2
Chr3
Chr4
Chr5
Chr6
Chr7
Chr8
Chr9
Chr10
Chr11
Chr12
Grape
Chr13
Chr16
Chr3
Chr14
Chr17
Chr18
Chr1
Chr9
Chr15
Chr6
Chr2
Chr12
Chr4
Chr19
Chr8
Chr7
Chr11
Chr10
Chr5
Fig.
17.
2.
Comparative analyses and evolution of the potato genome. (a) Clusters of orthologous and
paralogous gene families in
12
plant species as identified by OrthoMCL33. Gene family number is
listed in each of the components; the number of genes within the families for all of the species within the
component is noted in parentheses. (b) Genome duplication in dicot genomes as revealed through 4DTv
analyses. (c) Syntenic blocks between
Arabidopsis thaliana
, potato, and
Vitis vinifera
(grape), demonstrating a
high degree of conserved gene order between these taxa (Potato Genome Sequencing Consortium, 2011).
assist crop improvement, explore genome organ-
ization, and study the evolution of gene families.
In fact, detailed analyses of repetitive sequences,
transposable elements (TEs), and comparative
genomics of genes including intergenic regions
shed new light on the mechanisms of genome
evolution, speciation, and domestication (Bara-
baschi
et al
., 2012).
Crop genomes show tremendous diversity
in both size and structure, much of which has
likely been created by whole-genome duplication
(WGD) events. In the past
10
years, the availabil-
ity of complete or draft genome sequences has
allowed the reconstruction of a more detailed
picture of plant genome evolution from the early
angiosperm ancestor, to the origin of present
plants characterized by segment and genome
duplications, fragment rearrangements, and
genome size reductions (Hancock, 2012).
Potato is the first sequenced genome of an
asterid, a clade within eudicots that encom-
passes nearly
70,000
species characterized by
unique morphological, developmental, and
compositional features. The sequencing effort
identified 2642 high-confidence asterid-specific
genes and 3372 potato lineage-specific genes.
Genes encoding transcription factors, self-
incompatibility, and defense-related proteins
were evident, and presumably contributed to the
unique characteristics of asterids (Potato Gen-
ome Sequencing Consortium, 2011). Based on
genomics 4DTv results analysis, the authors
suggest two WGD events
(Fig. 17.2b
). The same
events were identified in three rosid genomes
(
V. vinifera
,
A. thaliana
, and
Populus trichocarpa
).
The ancient WGD corresponds to the ancestral
hexaploidization event in grape, consistent with
a previous report based on EST analysis that the
