Table S2: Queried plant genomes.
Organism
Robusta coffee
(Coffea
canephora)
Canabis sativa
Manihot esculenta
Ricinus communis
Linum
usitatissimum
Populus
trichocarpa
Web site
http://www.coffeegenome.org/
http://solgenomics.net/organism/17/view
Source & reference
International Cofee Genome Network
http://genome.ccbr.utoronto.ca/
http://www.phytozome.net/cassava.php
http://www.phytozome.net/ricinus.php
http://www.phytozome.net/flax.php
Van Bakel et al. 2011, Assemblies Finola and Purple Kush
Assembly version 4, JGI annotation v4.1
TIGR release 0.1
BGI v1.0 on assembly v1.0
http://www.phytozome.net/dataUsagePolicy.php?org=Org_Ptrichocarpa
Medicago
truncatula
http://www.medicagohapmap.org/
Phaseolus
vulgaris
Glycine max
http://www.phytozome.net/commonbean.php
JGI assembly release v3.0, annotation v3.0
Science. 2006 Vol. 313 no. 5793 pp. 1596-1604. DOI:
10.1126/science.1128691
Mt3.5v4 on assembly MedtrA17_3.5 from the Medicago Genome
Sequence Consortium
Medicago Genome Sequence Consortium, Mt3.5 genome assembly;
Epstein B, Branca A, Mudge J, Bharti AK, Briskine R, Farmer A,
Sugawara M, Young ND, Sadowsky MJ, Tiffin P 2012 Population
genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti
and S. medicae. PLoS Genetics 8(8): e1002868
JGI annotation v1.0 on assembly v1.0 using published ESTs, and JGI
RNAseq
JGI Glyma1.1 annotation of the chromosome-based Glyma1 assembly
The Soybean (Glycine max) genome project was initiated through the
DOE-JGI Community Sequencing Program (CSP) by a consortium led
by Gary Stacey, Randy Shoemaker, Scott Jackson, Jeremy Schmutz, and
Dan Rokhsar.; Schmutz J, et al. (2010). "Genome sequence of the
palaeopolyploid soybean." Nature 463, 178-183 (14 January 2010) |
doi:10.1038/nature08670
Glycine
tomentella
Cucumis sativus
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=44015
http://www.phytozome.net/soybean
http://www.phytozome.net/cucumber.php
The cucumber genome project collaborators include Jason Affourtit,
Chinnappa Kodira, James R. Knight, Brian A. Desany, Mohammed
Mohiuddin, Gerald Irzyk, Cynthia Turcotte, and Pascal Bouffard (454);
Tim T Harkins (Roche); Jason Miller, Sergey Koren, Brian Walenz, and
Granger Sutton (JCVI); Therese Mitros and Dan Rokhsar (Berkeley and
DOE JGI), and Yiqun Weng and Jack Staub (USDA). A manuscript
describing the sequencing and analysis of the genome is in preparation.
Prunus persica
http://www.phytozome.org/dataUsagePolicy.php?org=Org_Ppersica
Malus x domestica http://www.rosaceae.org/species/malus/malus_x_domestica
Fragaria vesca
http://www.rosaceae.org/species/fragaria/fragaria_vesca
Arabidopsis
thaliana
http://solanaceae.plantbiology.msu.edu/
http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Arabidopsis lyrata http://www.arabidopsis.org/
Capsella rubella
http://www.phytozome.net/capsella.php
Brassica rapa
http://brassicadb.org/brad/
Thellungiella
halophila
Carica papaya
http://www.phytozome.net/thellungiella.php
Carica monoica
Gossypium
raimondii
Theobroma cacao
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=262687
http://www.phytozome.net/cotton.php
Citrus sinensis
Citrus clementina
Eucalyptus
grandis
http://www.citrusgenomedb.org/species/sinensis/genome1.0
http://www.citrusgenomedb.org/species/clementina/genome1.0
http://www.phytozome.net/eucalyptus.php
Vitis vinifera
http://www.genoscope.cns.fr/vitis
http://www.appliedgenomics.org/
http://tgrc.ucdavis.edu/
Solanum
lycopersicum
http://www.phytozome.net/papaya.php
http://www.phytozome.net/cacao.php
JGI release v1.0
The high-quality draft genome of peach (Prunus persica) identifies
unique patterns of genetic diversity, domestication and genome
evolution. Nature Genetics 45,487–494 (2013) doi:10.1038/ng.2586
GDR prediction v1.0 on Malus x domestica assembly v1.0
Nature Genetics 42, 833–839 (2010) doi:10.1038/ng.654
v1.1 assembly and v1.0 annotation from Shulaev et. al., hosted at GDR
Nature Genetics 43, 109–116 (2011) doi:10.1038/ng.740
TAIR release 10 acquired from TAIR
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M,
Foerster H, Li D, Meyer T, Muller R, Ploetz L, et al. 2008. The
Arabidopsis Information Resource (TAIR): gene structure and function
annotation. Nucleic Acids Research 36:D1009-D1014.
JGI release v1.0
The Arabidopsis Information Resource (TAIR)
JGI annotation v1.0 on assembly v1
Slotte T et al. The Capsella rubella genome and the genomic
consequences of rapid mating system evolution. Nat. Genet.. 2013 Jun 9;
45(7):831-5
Annotation v1.2 on assembly v1.1 from brassicadb.org
BMC Plant Biology 2011, 11:136 doi:10.1186/1471-2229-11-136
JGI annotation v1.0 on assembly v1
8X mapped Thellungiella halophila genome assembly
ASGPB release of 2007
Nature 452, 991-996 (24 April 2008) | doi:10.1038/nature06856
JGI annotation v2.1 on assembly v2.0
DOE Joint Genome Institute: Cotton D V2.0
D. Gilbert public gene set 8 Mar 2012 on assembly v1.1
The Cacao Genome Project (a MARS, Incorporated initiative in
partnership with USDA, IBM and other important institutions)
JGI v1.1 annotation on v1 assembly
JGI v1 assembly and v1.0 annotation
JGI assembly v1.0, annotation v1.1
BMC Proceedings 2011, 5(Suppl 7):I20 doi:10.1186/1753-6561-5-S7I20
March 2010 12X assembly and annotation from Genoscope
Nature. 2007 Sep 27; 449(7161):463-7
SGNTomato Genome Project ITAG2.3
Nature 485, 635–641 (31 May 2012) doi:10.1038/nature11119
Solanum
tuberosum
Solanum
pimpinellifolium
Petunia
integrifolia
Mimulus guttatus
Nicotiana
tabaccum
Aquilegia
coerulea
Sorghum bicolor
http://solgenomics.net/organism/Solanum_tuberosum/genome
Zea mays
http://www.maizegdb.org/
Oryza sativa
http://www.plantgdb.org/OsGDB/
Brachypodium
distachyon
http://www.brachypodium.org/
Jatropha curcas
http://www.kazusa.or.jp/jatropha/
Lotus japonicus
http://www.plantgdb.org/LjGDB/
Cucumis melo
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3656
http://solgenomics.net/genomes/Solanum_pimpinellifolium/index.pl
DM1-3 516R44 (CIP801092) Genome Annotation v3.4 mapped to
pseudomolecule sequence
D. Ware, W. R. McCombie, and Z. B. Lippman at Cold Spring Harbor
Laboratory
http://solgenomics.net/organism/32709/view
http://www.phytozome.net/
http://www.tobaccogenome.org/
JGI 7x assembly release v1.0 of strain IM62, annotation v1.1
Tobacco genome initiative
http://www.jgi.doe.gov/sequencing/why/51280.html
JGI 8X assembly v1.0, annotation v1.2a
http://www.plantgdb.org/SbGDB/
Sbi1.4 models from MIPS/PASA on v1.0 assembly
Nature 457, 551-556 (29 January 2009) | doi:10.1038/nature07723
5b.60 annotation (filtered set) of the maize "B73" genome v2 produced
by the Maize Genome Project
Science, 2009: Vol. 326 no. 5956 pp. 1112-1115. DOI:
10.1126/science.1178534; Science , 2009: Vol. 326 no. 5956 p. 1078.
DOI: 10.1126/science.1178437
MSU Release 7.0 of the Rice Genome Annotation
Oryza sativa (ssp. japonica) Genome
JGI 8x assembly release v1.0 of strain Bd21 with JGI/MIPS PASA
annotation v1.2
Nature. 2010;463(7282):763-8. DOI: 10.1038/nature08747
Release 4.5
Lotus japonicus genome assembly build 2.5
Genome Structure of the Legume, Lotus japonicus. Sato, S. et al. DNA
Research