Table 2 |
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|
Summary of unigene sequences of asterids, basal eudicots, non-grass monocots, and basal angiosperms included in phylogenetic study |
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|
Species |
Lineage |
Source |
Number of reads/ESTs |
Size of data |
Assembly method(s) |
Number of unigenes |
|
|
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|
Panax quinquefolius |
Asterid |
NCBI-SRA |
209,745 |
89.7 Mb |
MIRA |
22,881 |
|
Lindenbergia phillipensis |
Asterid |
PPGP |
69,545,362 |
5.9 Gb |
CLC |
104,904 |
|
Helianthus annuus |
Asterid |
TIGR PTA |
93,279 |
NA |
Megablast-CAP3 |
44,662 |
|
Solanum tuberosum |
Asterid |
TIGR PTA |
219,485 |
NA |
Megablast-CAP3 |
81,072 |
|
Mimulus gutatus |
Asterid |
PlantGDB |
231,012 |
NA |
Vmatch-PaCE-CAP3 |
39,577 |
|
Papaver somniferum |
Basal eudicot |
1KP + SRA |
140,604,904 + 3,709,876 |
10.3 Gb + 1.3 Gb |
MIRA-SOAPDenovo-CAP3 |
252,894 |
|
Papaver setigerum |
Basal eudicot |
1KP |
134,478,938 |
9.8 Gb |
SOAPDenovo-CAP3 |
406,167 |
|
Papaver rhoeas |
Basal eudicot |
1KP |
157,506,374 |
11.5 Gb |
SOAPDenovo-CAP3 |
383,426 |
|
Papaver bracteatum |
Basal eudicot |
1KP |
89,663,900 |
6.5 Gb |
SOAPDenovo-CAP3 |
201,564 |
|
Eschscholzia californica |
Basal eudicot |
NCBI + SRA + 1KP |
14,381 + 559,470 + 133,422,402 |
6.8 Mb + 55 Mb + 9.7 Gb |
MIRA-SOAPDenovo-CAP3 |
165,260 |
|
Argemone mexicana |
Basal eudicot |
1KP + NCBI |
144,520,360 + 1,692 |
10.5 Gb + 1 Mb |
SOAPDenovo- CAP3 |
148,533 |
|
Akebia trifoliata |
Basal eudicot |
1KP |
29,156,514 |
2.1 Gb |
CLC-CAP3 |
46,024 |
|
Podophyllum pelatum |
Basal eudicot |
1KP |
20,139,210 |
1.5 Gb |
CLC-CAP3 |
31,472 |
|
Platanus occidentalis |
Basal eudicot |
1KP |
25,508,642 |
1.9 Gb |
CLC-CAP3 |
42,373 |
|
Aquilegia formosa x Aquilegia pubescens |
Basal eudicot |
PlantGDB |
85,040 |
NA |
Vmatch-PaCE-CAP3 |
19,615 |
|
Mesembryanthemum crystallinum |
Caryophillid |
PlantGDB |
27,553 |
NA |
Vmatch-PaCE-CAP3 |
11,317 |
|
Beta vulgaris |
Caryophillid |
PlantGDB |
25,883 |
NA |
Vmatch-PaCE-CAP3 |
18,009 |
|
Acorus americanus |
Monocot |
MonATOL + 1KP |
149,320 + 15,427,316 |
44.9 Mb + 1.1 Gb |
MIRA-SOAPDenovo-CAP3 |
59,453 |
|
Chamaedorea seifrizii |
Monocot |
MonATOL |
33,100,948 |
2.5 Gb |
CLC |
68,489 |
|
Chlorophytum rhizopendulum |
Monocot |
MonATOL |
59,505,714 |
4.5 Gb |
CLC |
58,766 |
|
Neoregelia sp. |
Monocot |
MonATOL |
49,121,506 |
3.7 Gb |
CLC |
63,269 |
|
Typha angustifolia |
Monocot |
MonATOL |
70,733,124 |
5.7 Gb |
CLC |
57,980 |
|
Persea americana (avocado) |
Magnoliid |
AAGP |
2,336,819 |
683 Mb |
MIRA |
132,532 |
|
Aristolochia fimbriata (Dutchman's pipe) |
Magnoliid |
AAGP |
3,930,505 |
880 Mb |
MIRA |
155,371 |
|
Liriodendron tulipifera (yellow-poplar) |
Magnoliid |
AAGP |
2,327,654 |
543 Mb |
MIRA |
137,923 |
|
Nuphar advena (yellow pond lily) |
Basal angiosperm |
AAGP |
3,889,719 |
1.1 Gb |
MIRA |
289,773 |
|
Amborella trichopoda |
Basal angiosperm |
AAGP |
2,943,273 |
776 Mb |
MIRA |
208394 |
|
|
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|
1KP, 1000 Green Plant Transcriptome Project; AAGP, Ancestral Angiosperm Genome Project [44]; MonATOL, Monocot Tree of Life Project [42]; NA, not available; NCBI, National Center for Biotechnology Information; PPGP, Parasitic Plant Genome Project [65]; SRA, Sequence Read Archive; TIGR PTA, The Institute for Genomic Research Plant Transcript Assemblies [66]. |
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|
Jiao et al. Genome Biology 2012 13:R3 doi:10.1186/gb-2012-13-1-r3 |
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