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Table 1 Top 70 up-regulated contigs in initiating storage roots compared to fibrous roots

From: Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation

Contig Length ISR reads FR reads Fold change Annotation
S_PBL_c2971 936 3135.5 2.1 1466.5 ABB97549.1 Sporamin A precursor [Ipomoea batatas]
S_PBL_c9555 931 1843.7 2.1 862.3 AAA33391.1 Sporamin A precursor
S_PBL_c21625 450 672.6 1.1 629.1 BAA00828.1 Beta-amylase [Ipomoea batatas]
S_PBL_c2075 958 502.3 1.1 469.9 not annotated
S_PBL_c1053 954 455.5 1* 455.6 AAA33390.1 Sporamin B
S_PBL_c54 918 2525.6 6.4 393.8 P10917.1 Sporamin A; Flags: Precursor
S_PBL_c17697 844 753.0 2.1 352.2 AAB52547.1 Sporamin precursor
S_PBL_c18468 263 311.5 1* 311.5 not annotated
S_PBL_c15531 438 2823.1 11.8 240.1 AAA33391.1 Sporamin A precursor
S_PBL_c8154 557 238.5 1* 238.5 not annotated
S_PBL_c3494 967 252.6 1.1 236.3 AAL55800.1 Sporamin [Ipomoea batatas]
S_PBL_c3628 759 195.5 1* 195.5 ABB90968.1 Sporamin B precursor [Ipomoea batatas]
S_PBL_c12997 481 190.8 1* 190.8 not annotated
S_PBL_c2027 1665 186.1 1.1 174.1 BAA02286.1 Beta-amylase [Ipomoea batatas]
S_PBL_lrc44407 487 158.1 1* 158.1 not annotated
S_PBL_c25030 652 150.6 1* 150.6 XP_001677106.1 Hypothetical protein CBG16734 [Caenorhabditis briggsae AF16]
S_PBL_c12797 567 134.7 1* 134.7 not annotated
S_PBL_c21769 669 131.0 1* 131.0 not annotated
S_PBL_lrc53020 508 386.3 3.2 120.5 not annotated
S_PBL_lrc25060 898 128.2 1.1 119.9 CAO23244.1 unnamed protein product [Vitis vinifera]
S_PBL_c34561 465 117.9 1* 117.9 XP_002298721.1 predicted protein [Populus trichocarpa]
S_PBL_c9857 630 581.8 5.3 108.9 not annotated
S_PBL_c3428 1350 577.2 5.3 108.0 not annotated
S_PBL_c18337 561 1035.5 9.6 107.6 AAX27911.1 unknown [Schistosoma japonicum]
S_PBL_c3870 696 104.8 1.1 98.0 ABB83474.1 Beta-expansin precursor [Solanum lycopersicum]
S_PBL_c45358 560 96.3 1* 96.3 CAO47717.1 unnamed protein product [Vitis vinifera]
S_PBL_c4363 735 199.2 2.1 93.2 not annotated
S_PBL_c20072 900 91.7 1* 91.7 P10965.1 Sporamin B; Flags: Precursor
S_PBL_c3830 725 291.8 3.2 91.0 EEF50674.1 conserved hypothetical protein [Ricinus communis]
S_PBL_c7863 397 90.7 1* 90.7 not annotated
S_PBL_lrc52376 494 189.9 2.1 88.8 not annotated
S_PBL_c2723 895 93.5 1.1 87.5 CAO43166.1 unnamed protein product [Vitis vinifera]
S_PBL_c1850 702 182.4 2.1 85.3 not annotated
S_PBL_c15391 502 89.8 1.1 84.0 not annotated
S_PBL_c26497 974 83.3 1* 83.3 XP_002327563.1 predicted protein [Populus trichocarpa]
S_PBL_c48117 388 262.9 3.2 82.0 P10933.1 Ferredoxin-NADP reductase, leaf isozyme, chloroplastic
S_PBL_c20358 683 85.1 1.1 79.6 CAO22863.1 unnamed protein product [Vitis vinifera]
S_PBL_c3576 454 169.3 2.1 79.2 not annotated
S_PBL_c8690 813 75.8 1* 75.8 AAU93595.1 HVA22-like protein c, putative [Solanum demissum]
S_PBL_c7526 860 79.5 1.1 74.4 not annotated
S_PBL_lrc53818 757 4080.3 58.8 69.4 BAF47746.1 ADP-glucose pyrophosphorylase beta subunit IbAGPb1A [Ipomoea batatas]
S_PBL_lrc52525 509 73.0 1.1 68.3 XP_002274272.1 PREDICTED: hypothetical protein [Vitis vinifera]
S_PBL_lrc30491 523 145.9 2.1 68.3 P27598.1 Starch phosphorylase L
S_PBL_c41294 520 68.3 1.1 63.9 not annotated
S_PBL_c32227 418 63.6 1* 63.6 not annotated
S_PBL_c54084 609 135.6 2.1 63.4 not annotated
S_PBL_c31475 869 66.4 1.1 62.1 not annotated
S_PBL_lrc52682 527 66.4 1.1 62.1 XP_002306992.1 predicted protein [Populus trichocarpa]
S_PBL_c10411 496 64.5 1.1 60.4 BAA31699.1 PKn2 [Ipomoea nil]
S_PBL_lrc27049 954 255.4 4.3 59.7 not annotated
S_PBL_c14744 705 63.6 1.1 59.5 EEF31509.1 Ubiquitin-protein ligase bre-1, putative [Ricinus communis]
S_PBL_c18129 413 1393.8 23.5 59.3 BAF47744.2 ADP-glucose pyrophosphorylase alpha subunit IbAGPa1 [Ipomoea batatas]
S_PBL_c7810 531 123.5 2.1 57.8 not annotated
S_PBL_c14132 307 57.1 1* 57.1 not annotated
S_PBL_c1234 886 2045.8 36.3 56.3 BAF47746.1 ADP-glucose pyrophosphorylase beta subunit IbAGPb1A [Ipomoea batatas]
S_PBL_c695 596 721.2 12.8 56.2 P27598.1 Starch phosphorylase L
S_PBL_c30129 726 56.1 1* 56.1 AAP41026.1 NTA15 protein [Nicotiana tabacum]
S_PBL_c12308 666 115.1 2.1 53.8 P93262.1 Phosphoglucomutase, cytoplasmic
S_PBL_c28076 644 53.3 1* 53.3 CAO21883.1 unnamed protein product [Vitis vinifera]
S_PBL_c16839 282 55.2 1.1 51.6 not annotated
S_PBL_c47419 537 55.2 1.1 51.6 EEF50087.1 Serine-threonine protein kinase, plant-type, putative [Ricinus communis]
S_PBL_c51126 492 661.3 12.8 51.6 BAF47744.2 ADP-glucose pyrophosphorylase alpha subunit IbAGPa1 [Ipomoea batatas]
S_PBL_c19033 878 51.4 1* 51.4 not annotated
S_PBL_lrc28526 555 51.4 1* 51.4 not annotated
S_PBL_c7145 689 161.8 3.2 50.5 not annotated
S_PBL_c12588 493 49.6 1* 49.6 not annotated
S_PBL_lrc53425 456 211.4 4.3 49.4 BAF47746.1 ADP-glucose pyrophosphorylase beta subunit IbAGPb1A [Ipomoea batatas]
S_PBL_c21020 403 103.8 2.1 48.6 not annotated
S_PBL_c1397 989 408.8 8.6 47.8 BAF47744.2 ADP-glucose pyrophosphorylase alpha subunit IbAGPa1 [Ipomoea batatas]
S_PBL_c19766 429 984.1 21.4 46.0 P27598.1 Starch phosphorylase L
  1. Expression values are expressed as normalized read number. ‘Fold change’ is calculated as ISR reads/FR reads. One annotation is given for each contig. Annotations of the two best hits for each contig (E value ≤ 1.0E-3) are available in Additional file 1. ISR, Initiating storage root, FR fibrous root. * - Read counts were changed from zero to one to enable ‘Fold change’ calculation (avoid dividing by zero).