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Raw and high quality (HQ) sequences, percent successful sequencing, and HQ sequencing as well as singletons, contigs, and unigenes found in and across the high and low P root expressed sequence tag (EST) libraries.

 
EST numbers High P Low P Total
Plates sequenced† 15 23 38
Raw sequences 1440 2208 3648
Successful sequences 1338 2008 3344
Percent success 99.6 99.6 91.7%
HQ sequences 1137 1684 2821
Percent HQ 84.5 83.9 84.4
Average length 704 nt‡ 659 nt 677.1 nt
Singletons 850 1292 2142
Contigs§ 98 132 230
Unigenes§ (total) 948 1424 2372
Average length 734 nt 685 nt 704.6 nt
Gene annotation¶ 638 953 1591
Hit but no annotation 139 176 315
No hit§ 171 294 465
Assumes 96-well plates sequenced on ABI3700 automated sequencer (Applied Biosystems, Foster City, CA).
nt, nucleotides.
§According to CAP3 assembly (Huang and Madan, 1999) and default parameters.
According to Blast2GO annotation (Conesa and Götz, 2008) and Blastx searches.



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Differences in categorization of the unigenes from the high P (HP) and low P (LP) root expressed sequence tag (EST) libraries according to biological processes, molecular function, and cellular compartmentalization.

 
Gene Ontology No. HP† No. LP Total No. Percent HP Percent LP
Biological process‡
Biological regulation 83 121 204 6.5 6.5
Carbon utilization 1 2 3 0.1 0.1
Cell proliferation 0 4 4 0.0 0.2
Cellular component organization 45 74 119 3.5 4.0
Cellular processes 365 555 920 28.7 29.9
Cellular component biogenesis 36 44 80 2.8 2.4
Developmental process 55 81 136 4.3 4.4
Death 3 4 7 0.2 0.2
Immune system process 5 6 11 0.4 0.3
Localization 95 117 212 7.5 6.3
Metabolic process 351 520 871 27.6 28.0
Multiorganism process 23 31 54 1.8 1.7
Multicellular organismal process 45 70 115 3.5 3.8
Nitrogen utilization 2 2 4 0.2 0.1
Pigmentation 0 1 1 0.0 0.1
Rhythmic processes 1 1 2 0.1 0.1
Reproduction 29 43 72 2.3 2.3
Response to stimulus 129 181 310 10.2 9.7
Sulfur utilization 2 2 4 0.2 0.1
Molecular function‡
Antioxidant activity 16 12 28 1.9 1.0
Binding 337 504 841 40.1 40.6
Catalytic activity 278 426 704 33.1 34.3
Electron carrier activity 27 34 61 3.2 2.7
Enzyme regulator activity 10 11 21 1.2 0.9
Metallochaperone activity 0 1 1 0.0 0.1
Molecular transducer activity 7 8 15 0.8 0.6
Nutrient reservoir activity 2 3 5 0.2 0.2
Structural molecular activity 80 113 193 9.5 9.1
Translation regulator activity 12 28 40 1.4 2.3
Transporter activity 47 66 113 5.6 5.3
Transcription regulator activity 24 36 60 2.9 2.9
Cellular component§
Apoplast 22 36 58 1.9 2.0
Cell part 490 710 1200 41.5 40.4
Extracellular region 1 1 2 0.1 0.1
Organelle part 148 216 364 12.5 12.3
Organelle – membrane bounded 309 470 779 26.2 26.8
Organelle – non-membrane bound 108 157 265 9.2 8.9
Protein complex 54 80 134 4.6 4.6
Protein–DNA complex 10 13 23 0.8 0.7
Vesicle 38 74 112 3.2 4.2
Refers to number of unigenes in each case for HP or LP root libraries.
Performed at level 2 for greater details of biological process and molecular function.
§Performed at level 3 for greater details of cellular component placement.



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Comparison of high P (HP) and low P (LP) root derived expressed sequence tags (ESTs) with the EST libraries of Ramírez et al. (2005).

 
No. of ESTs No. of Unigenes HP library LP library
Library used for the comparison with HP and LP libraries ESTs with unique hit Percent ESTs with hit Percent ESTs with unique hit Percent ESTs with hit Percent
ALV (Andean leaf library) 2555 1684 96 10 117 12 164 12 212 15
LVS (Mesoamerican leaf library) 2704 1418 153 16 171 18 205 14 254 18
NOD (Mesoamerican nodule library) 3901 2247 162 17 188 20 277 19 330 23
POD (Mesoamerican bean pod library) 2985 1945 213 22 260 27 284 20 366 26
RTS (Mesoamerican root library) 3188 2302 227 24 286 30 319 22 409 29



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Unigenes with the most different gene expression between the high P (HP) and low P (LP) root libraries.

 
Query identification Description EST† no. Subject identification Description EST no. Δ Percent identity
LP_Contig36 Elongation factor 1- 7 HP_Contig51 Elongation factor 1- 2 5 85.7
LP_Contig6 tonoplast intrinsic protein 8 HP_Contig15 Tonoplast intrinsic protein 3 5 97.2
LP3b09 Elongation factor 1- 1 HP_Contig61 Elongation factor 1- 6 5 98.3
LP5c08 Elongation factor 1-alpha 1 HP_Contig61 Elongation factor 1- 6 5 84.7
LP6f10 14 kDa proline-rich protein 1 HP_Contig72 Extensin-like protein 6 5 85.6
PV_DEd0001b_.b1_D07 Elongation factor 1- 1 HP_Contig81 Elongation factor 1- 6 5 98.9
PV_DEd0001b_.b1_H04 Elongation factor 1- 1 HP_Contig81 Elongation factor 1- 6 5 98.9
PV_DEd0001b_.b1_H04 Elongation factor 1- 1 HP_Contig61 Elongation factor 1- 6 5 87.9
PV_DEd0002c_.b1_A01 Elongation factor-1 alpha 1 HP_Contig81 Elongation factor 1- 6 5 98.2
PV_DEd0002d_.b1_C08 Elongation factor-1 alpha 1 HP_Contig81 Elongation factor 1- 6 5 79.1
PV_DEd0002d_.b1_F10. Elongation factor 1- 1 HP_Contig81 Elongation factor 1- 6 5 99.3
PV_DEd0002d_.b1_F10 Elongation factor 1- 1 HP_Contig61 Elongation factor 1- 6 5 86.9
LP_Contig36 Elongation factor 1- 7 HP1e06 No hits 1 6 97.8
LP_Contig2 No hits 10 HP_Contig29 No hits 3 7 99.4
LP_Contig51 No hits 4 HP_Contig98 No hits 11 7 93.9
LP_Contig6 Tonoplast intrinsic protein 8 HP3f07 Tonoplast intrinsic protein 1 7 93.9
LP_Contig6 Tonoplast intrinsic protein 8 HP1b03 Tonoplast intrinsic protein 1 7 86.5
LP_Contig76 No hits 8 HP1f04 No hits 1 7 93.9
LP_Contig132 Cyclophilin 10 HP2b07 cyclophilin 1 9 96.0
LP_Contig39 No hits 2 HP_Contig98 No hits 11 9 100.0
LP1c01 No hits 1 HP_Contig32 No hits 11 10 97.9
LP7b02. No hits 1 HP_Contig32 No hits 11 10 99.7
LP4e01 14 kDa proline-rich protein 1 HP_Contig58 14 kDa proline-rich protein 12 11 92.1
LP6g05 14 kDa proline-rich protein 1 HP_Contig58 14 kDa proline-rich protein 12 11 94.5
PV_DEd0001a_F0 14 kDa proline-rich protein 1 HP_Contig58 14 kDa proline-rich protein 12 11 97.6
PV_DEd0001c_C10 Proline-rich protein 1 HP_Contig58 14 kDa proline-rich protein 12 11 97.4
LP_Contig81 Pathogenesis-related protein 13 HP4g08 Pathogenesis-related protein 1 12 98.2
LP_Contig81 Pathogenesis-related protein 13 HP2d01 Pathogenesis-related protein 1 12 91.0
LP_Contig85 14 kDa proline-rich protein 24 HP_Contig58 14 kDa proline-rich protein 12 12 99.7
LP4b12.g1.ab1 Pathogenesis related protein 1 HP_Contig24 Pathogenesis-related protein 15 14 99.0
PV_DEd0002c_F11 Pathogenesis-related protein 1 HP_Contig24 Pathogenesis-related protein 15 14 80.4
PV_DEd0003b_B12 Pathogenesis related protein 1 HP_Contig24 Pathogenesis-related protein 15 14 88.2
LP_Contig85 14 kDa proline-rich protein 24 HP1b11 14 kDa proline-rich protein 1 23 97.1
LP_Contig85 14 kDa proline-rich protein 24 HP2e01 14 kDa proline-rich protein 1 23 92.6
EST, expressed sequence tag.