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Table 3 Top 70 up-regulated contigs in fibrous roots compared to initiating storage 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_c4848 510 0.9 546.3 607.0 not annotated
S_PBL_c22976 665 2.8 756.9 270.3 XP_002327317.1 Predicted protein [Populus trichocarpa]
S_PBL_lrc52198 626 0.9 228.8 254.2 AAK27968.1 Cysteine protease [Ipomoea batatas]
S_PBL_c1692 703 1* 251.2 251.2 not annotated
S_PBL_c14075 626 1* 232 232.0 XP_001837463.1 Tubulin alpha chain [Coprinopsis cinerea okayama7#130]
S_PBL_c36764 703 3.7 856.3 231.4 XP_002303479.1 predicted protein [Populus trichocarpa]
S_PBL_c1452 539 0.9 206.3 229.2 AAK27968.1 Cysteine protease [Ipomoea batatas]
S_PBL_c25084 735 1* 209.5 209.5 CAO14793.1 unnamed protein product [Vitis vinifera]
S_PBL_c2976 600 26.2 5316.4 202.9 Q40157.1 Metallothionein-like protein type 2 A
S_PBL_lrc52159 665 0.9 174.3 193.7 not annotated
S_PBL_c43111 446 0.9 168.9 187.7 not annotated
S_PBL_c39992 480 1* 187.1 187.1 XP_001874004.1 predicted protein [Laccaria bicolor]
S_PBL_c18994 719 20.6 3790.8 184.0 not annotated
S_PBL_c28403 834 0.9 164.6 182.9 XP_001884841.1 Delta 9-fatty acid desaturase protein [Laccaria bicolor]
S_PBL_c30965 742 0.9 153.9 171.0 CAO23367.1 unnamed protein product [Vitis vinifera]
S_PBL_c29652 772 0.9 151.8 168.7 XP_002304020.1 predicted protein [Populus trichocarpa]
S_PBL_c12455 525 34.6 5763.2 166.6 Q40157.1 Metallothionein-like protein type 2 A
S_PBL_c5087 783 2.8 465 166.1 not annotated
S_PBL_c18075 609 4.7 767.6 163.3 not annotated
S_PBL_c44512 388 0.9 145.4 161.6 XP_002279608.1 hypothetical protein [Vitis vinifera]
S_PBL_c19899 443 0.9 144.3 160.3 not annotated
S_PBL_c14724 532 1* 156.1 156.1 CAN80314.1 hypothetical protein [Vitis vinifera]
S_PBL_c30195 672 0.9 136.8 152.0 not annotated
S_PBL_c8847 687 1* 150.7 150.7 XP_002330606.1 predicted protein [Populus trichocarpa]
S_PBL_c6142 645 1.9 275.8 145.2 XP_002263033 Peroxidase 10-like [Vitis vinifera]
S_PBL_c11711 510 7.5 1082.9 144.4 XP_001880208.1 Fumarate reductase [Laccaria bicolor]
S_PBL_c35569 653 3.7 533.5 144.2 not annotated
S_PBL_c337 838 27.1 3771.6 139.2 AAL79832.2 Osmotin-like protein [Solanum nigrum]
S_PBL_c50215 567 1.9 261.9 137.8 not annotated
S_PBL_lrc32508 540 0.9 124 137.8 not annotated
S_PBL_c12800 554 1.9 260.8 137.3 XP_001881080.1 Histone 2A [Laccaria bicolor]
S_PBL_c13942 648 3.7 504.6 136.4 XP_001888404.1 Sphingolipid C9-methyltransferase [Laccaria bicolor]
S_PBL_c837 483 1.9 258.7 136.2 not annotated
S_PBL_c14357 689 3.7 488.6 132.1 EAY93058.1 hypothetical protein OsI_14861 [Oryza sativa Indica Group]
S_PBL_c44050 575 1.9 242.7 127.7 XP_001834214.1 hypothetical protein CC1G_09714 [Coprinopsis cinerea okayama7#130]
S_PBL_c47284 674 0.9 114.4 127.1 EEF39207.1 Rhicadhesin receptor precursor, putative [Ricinus communis]
S_PBL_c29183 616 0.9 113.3 125.9 not annotated
S_PBL_c15554 601 13.1 1644.2 125.5 Q40157.1 Metallothionein-like protein type 2 A
S_PBL_c28805 440 1* 122.9 122.9 CAO44491.1 unnamed protein product [Vitis vinifera]
S_PBL_c9181 557 1.9 230.9 121.5 AAY87888.1 Glutathione peroxidase [Taiwanofungus camphoratus]
S_PBL_lrc53720 379 52.4 6313.8 120.5 not annotated
S_PBL_c18857 626 1* 117.6 117.6 AAK27968.1 Cysteine protease [Ipomoea batatas]
S_PBL_c5350 526 1.9 221.3 116.5 not annotated
S_PBL_c41001 434 0.9 103.7 115.2 XP_572855.1 Polysaccharide synthase [Cryptococcus neoformans]
S_PBL_c17858 525 1* 113.3 113.3 not annotated
S_PBL_c30000 488 0.9 101.6 112.9 XP_001838960.1 hypothetical protein CC1G_05513 [Coprinopsis cinerea okayama7#130]
S_PBL_c25576 582 0.9 100.5 111.7 not annotated
S_PBL_c6293 718 12.2 1345.9 110.3 not annotated
S_PBL_c37132 470 0.9 95.1 105.7 not annotated
S_PBL_c3863 605 1.9 198.8 104.6 CAN80314.1 hypothetical protein [Vitis vinifera]
S_PBL_c12972 545 15.9 1651.7 103.9 AAL16409.1 Pathogenesis-related protein PR10a [Nicotiana tabacum]
S_PBL_c2399 892 2.8 290.8 103.9 CAO22665.1 unnamed protein product [Vitis vinifera]
S_PBL_c7735 565 1.9 196.7 103.5 NP_200248.1 Late embryogenesis abundant protein-related [Arabidopsis thaliana]
S_PBL_c28770 429 1.9 195.6 102.9 not annotated
S_PBL_c33041 444 1.9 194.6 102.4 not annotated
S_PBL_c27326 782 6.5 664.9 102.3 XP_001890326.1 GPA1 heterotrimeric G-protein alpha subunit [Laccaria bicolor]
S_PBL_c18989 540 1.9 193.5 101.8 AAK27968.1 Cysteine protease [Ipomoea batatas]
S_PBL_c6361 637 8.4 855.2 101.8 XP_001880208.1 Fumarate reductase [Laccaria bicolor]
S_PBL_c15414 674 1* 100.5 100.5 AAL14199.1 Cysteine proteinase precursor [Ipomoea batatas]
S_PBL_c15414 674 1* 100.5 100.5 AAL14199.1 Cysteine proteinase precursor [Ipomoea batatas]
S_PBL_c18957 652 1.9 190.3 100.2 not annotated
S_PBL_c12342 570 1* 98.4 98.4 not annotated
S_PBL_c10766 501 1* 94.1 94.1 not annotated
S_PBL_c40440 403 1* 94.1 94.1 not annotated
S_PBL_c11884 622 1* 93 93 XP_002273655.1 PREDICTED: hypothetical protein [Vitis vinifera]
S_PBL_lrc28732 494 1* 87.7 87.7 not annotated
S_PBL_c24730 463 1* 86.6 86.6 not annotated
S_PBL_c32483 699 1* 86.6 86.6 not annotated
S_PBL_c14615 660 1* 84.5 84.5 EEF31626.1 Kiwellin, putative [Ricinus communis]
S_PBL_c28823 729 1* 83.4 83.4 XP_001831241.1 hypothetical protein CC1G_00788 [Coprinopsis cinerea okayama7#130]
  1. Expression values are expressed as normalized read number. ‘Fold change’ is calculated as FR reads/ISR 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.