Biology Reference
In-Depth Information
Table 1
Large-scale plant genome sequencing projects [
5
] and representative proteome databases
Order
Organism
Proteome database
Dicot
Malpighiales California poplar,
Cassava(P)
Fabales
Soybean, Medicago,
Lotus(P)
Proteomics of Oilseeds, Soybean
Proteome Databes, SoyKB,
ProMEX
Brassicales
Arabidopsis,
Papaya(P)
PPDB, AtProteome, ProMEX,
SUBA, PhosPhAt, AT_
CHLORO, AtPID, plprot, TAIR
Rhamnales Wine grape
Solanales
Tomato(P), Potato(P) plprot
Monocot
Poales
Rice, Sorghum,
Corn, Purple
false brome(P)
PPDB, Rice Proteome Database,
OryzaPG-DB, plprot, DIPOS,
PRIN
The phylogenetic tree among the orders is based on the Angiosperm Phylogeny Group classifi cation [
6
]. The letter “P”
attached to an organism name means that large-scale sequencing analysis of the genome is still in progress [
5
]
These proteomic data also need to be integrated and organized in
databases that enable us to retrieve, leverage, and share public data
through up-to-date computational technology such as the latest data
management systems and Web-interface techniques.
This overview of the large-scale genome sequencing studies
and the status of proteomic data repositories will provide a guide
for datasets currently available and also those that should be
prepared in future studies. We positioned large-scale sequencing
projects [
5
] and major proteomic databases on a phylogenetic tree
of fl owering plants that was based on the biological classifi cation
by the Angiosperm Phylogeny Group [
6
] (Table
1
). In the dicot
plants, large-scale genome sequences have been analyzed across
various orders of the biological classifi cation. In the monocot
plants large-scale genome sequences are localized in the order
Poales, which includes the major cereal grain species. Many pro-
teomic databases have been developed for the model dicot plant
Arabidopsis thaliana
such as AtProteome [
7
], ProMEX [
8
], and
SUBA [
9
]. For monocot plants, rice databases such as the Rice
Proteome Database [
10
] and OryzaPG-DB [
11
] have been devel-
oped. The PPDB [
12
,
13
] covers two major species in dicots and
monocots,
A
.
thaliana
and maize (
Zea mays
). The Proteomics of
Oilseeds [
14
] and Soybean Proteome Database [
15
] store pro-
teomic data primarily based on 2-DE in legumes. The plprot [
16
]
database specializes in plant plastids and covers
A
.
thaliana
,
tobacco, and rice. AtPID [
17
] contains large-scale protein-protein
interaction data. Such molecular interaction databases have been
