Table 3.
List of top 30 downregulated genes (p < 0.05) on NL1-I and BCMV-S2 virus treatments, respectively
| NL1-I | Log2 fold change | Annotation | BCMV-S2 | Log2 fold change | Annotation |
|---|---|---|---|---|---|
| Phvul.001G050500 | −2.68 | Adenine Phosphoribosyltransferase | Phvul.001G021700a | −2.38 | Protein kinase superfamily (0.010) |
| Phvul.001G091600 | −3.65 | Homocitrate synthase-related | Phvul.001G091600 | −4.08 | HOMOCITRATE SYNTHASE-RELATED |
| Phvul.001G138800 a | −3.31 | dsRNA-binding protein 3 (DRB3) (0.007) | Phvul.001G091700a | −3.24 | ARABIDOPSIS HEAVY METAL ATPASE 8 (0.029) |
| Phvul.001G165900 | −2.75 | ABC-2 type transporter | Phvul.001G138800 a | −2.68 | dsRNA-binding protein 3 (DRB3) (0.007) |
| Phvul.001G206500a | −2.79 | Hexokinase 3 (0.006) | Phvul.001G151900 | −2.87 | Terpene synthase family, metal binding domain |
| Phvul.001G239100a | −3.00 | Encodes a microRNA that targets several TIR1/AFB family members (0.003) | Phvul.001G165800 | −3.38 | ABC transporter |
| Phvul.002G153600 | −2.80 | Hydroxymethylglutaryl-CoA synthase | Phvul.001G165900 | −3.05 | ABC-2 type transporter |
| Phvul.002G193300 | −3.00 | Oxidoreductase, 20G-Fe(II) oxygenase family protein | Phvul.001G166200 | −2.42 | ABC-2 type transporter |
| Phvul.002G216900 | −3.24 | Squalene Monooxygenase | Phvul.001G206700 | −2.53 | ABC transporter |
| Phvul.002G259700 a | −3.15 | Transposable element gene (0.092) | Phvul.001G251300 | −2.34 | TREHALOSE-6-PHOSPHATE SYNTHASE |
| Phvul.002G268800 | −3.79 | EamA-like transporter family | Phvul.001G263900 | −2.36 | Protein of unknown function (DUF1264) |
| Phvul.002G297200 a | −3.35 | RING/U-box superfamily protein (0.055) | Phvul.002G059500 | −2.33 | LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE |
| Phvul.002G297300 a | −3.53 | Mediator complex subunit Med23 (0.075) | Phvul.002G150200 | −2.74 | Drug transmembrane transporter activity |
| Phvul.003G159200 | −2.91 | Plasma membrane H + −transporting ATPase | Phvul.002G216900 | −2.48 | SQUALENE MONOOXYGENASE |
| Phvul.003G192800 | −2.81 | H+/oligopeptide symporter | Phvul.002G227500a | −2.69 | Encodessl dehydroquinate-shikimate dehydrogenase enzyme (2e-08) |
| Phvul.003G218900 | −3.27 | Protease inhibitor/seed storage/LTP family | Phvul.002G259700 a | −2.32 | Transposable element gene (0.092) |
| Phvul.003G248200 | −2.98 | Alpha/Beta Hydrolase Fold-Containing Protein | Phvul.002G294200 | −2.80 | AAA-FAMILY ATPASE |
| Phvul.003G278200 | −3.03 | Glucose dehydrogenase/choline dehydrogenase/mandelonitrile Lyase | Phvul.002G297200 a | −2.55 | RING/U-box superfamily protein (0.055) |
| Phvul.004G142000 | −3.17 | Synaptic vesicle and related transporters | Phvul.002G297300 a | −3.13 | Mediator complex subunit Med23 (0.075) |
| Phvul.005G001000 | −3.24 | Cellulose synthase | Phvul.003G060100 | −2.92 | Dehydrogenases with different specificities |
| Phvul.005G005000 | −2.83 | ATP binding | Phvul.003G082300 | −2.36 | OXIDOREDUCTASE, 2OG-FE(II) OXYGENASE FAMILY PROTEIN |
| Phvul.005G005400 | −2.69 | UDP-glucoronosyl and UDP-glucosyl transferase | Phvul.003G278200 | −2.59 | Glucose dehydrogenase/choline dehydrogenase/mandelonitrile lyase |
| Phvul.005G032500 | −3.68 | Dirigent-like protein | Phvul.005G001000 | −2.49 | Cellulose synthase |
| Phvul.005G032600 | −3.28 | Dirigent-like protein | Phvul.005G005400 | −2.47 | UDP-glucoronosyl and UDP-glucosyl transferase |
| Phvul.005G069400 | −3.09 | NA | Phvul.005G032500 | −3.09 | Dirigent-like protein |
| Phvul.005G145700 | −2.72 | DVL family | Phvul.005G032600 | −2.73 | Dirigent-like protein |
| Phvul.005G159600 | −3.25 | GTP-binding protein | Phvul.005G159600 | −2.94 | GTP-binding protein |
| Phvul.005G166200 | −4.20 | Phosphorelay signal transduction system | Phvul.006G195500 | −2.54 | Helix-loop-helix DNA-binding domain, transcription regulator activity |
| Phvul.005G170300 | −3.09 | Aquaporin (major intrinsic protein family) | Phvul.007G209700 | −3.09 | ABC transporter |
| Phvul.006G034000 | −2.71 | NAD dependent epimerase/dehydratase family | Phvul.007G275800 | −2.38 | Hemopexin |
The gene names in bold are common between the two treatments. Gene annotations were retrieved for common bean genome in Phytozome. The unannotated genes were functionally classified using TAIR (indicated by a, the e-value of TAIR match is indicated in the brackets). "NA" represents no functional characterization of gene is available