Root
From Purdue Genomics Database Facility
darnoz
Contents |
Root
T. Aoyama, N. onodera, T. Nishiyama
(t_aoyama@nibb.ac.jp, tomoakin@kenroku.kanazawa-u.ac.jp)
Bryophytes lack roots, and the origin of and relationship between lycopod and angiosperm roots are controversial (Schneider et al., 2002). Putative orthologues of transcription factors involved in root development, such as PLTs, SHR, and SCR, were found in both S. moellendorffii and P. patens. Determining the functions of these genes in these species will provide insights into root evolution. The A. thaliana PLT1 land plant orthologous group contained PLTs, ANT, and BBM, which function in the regulation of cell division and differentiation in roots (Aida et al., 2004), lateral organs (Mizukami and Fischer, 2000), and shoot meristems (Boutilier et al., 2002), respectively. This suggests that the expansion of angiosperm genes in the PLT clade is related to an increase in the tissue and organ complexity of the diploid plant body in the angiosperm lineage after the divergence of S. moellendorffii.
Lateral Root
T. Aoyama, S. Miyazaki, T. Maruyama, R. Sotooka, T. Fujita, N. Sumikawa, M. Kubo, N. Shinohara, T. Hirai, N. Sugimoto, N. Onodera and Y. Hiwatashi, and T. Nishiyama
(t_aoyama@nibb.ac.jp, tomoakin@kenroku.kanazawa-u.ac.jp)
NAC1 is a member of NAC transcription factors and promotes lateral root formation in response to auxin signal (Xie et al., 2000). Putative orthologues of NAC1 were found only in angiosperms. However, those of all the other A. thaliana genes involved in lateral root development examined were found in both S. moellendorffii and P. patens.
References
Aida, M., Beis, D., Heidstra, R., Willemsen, V., Blilou, I., Galinha, C., Nussaume, L., Noh, Y.S., Amasino, R., and Scheres, B. (2004). The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119, 109-120.
Boutilier, K., Offringa, R., Sharma, V.K., Kieft, H., Ouellet, T., Zhang, L., Hattori, J., Liu, C.M., van Lammeren, A.A., Miki, B.L., Custers, J.B., and van Lookeren Campagne, M.M. (2002). Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell 14, 1737-1749.
Mizukami, Y., and Fischer, R.L. (2000). Plant organ size control: AINTEGUMENTA regulates growth and cell numbers during organogenesis. Proc. Natl. Acad. Sci. USA 97, 942-947.
Schneider, H., Pryer, K.M., Cranfill, R., Smith, A.R., and Wolf, P.G. (2002). Evolution of vascular plant body plans: a phylogenetic perspecrive. In Developmental Genetics and Plant Evolution, Q.C. Cronk, R.M. Bateman, and J.A. Hawkins, eds (London: Taylor & Francis), pp. 330-364.
Xie, Q., Frugis, G., Colgan, D., and Chua, N.H. (2000). Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development. Genes Dev. 14, 3024-3036.
Table of gene numbers
| Gene functions | Gene | Gene used as a query | The number of putative orthologs | |||
|---|---|---|---|---|---|---|
| Arabidopsis thaliana | Oryza sativa | Selaginalla moellendorffii (a) | Physcomitrella patens | |||
| Root | PLT1 and 2 | ANT | 8 | 11 | 1 (2) | 3 |
| Root | SHR | SHR | 1 | 2 | 3 (6) | 2 |
| Root | SCR | SCR | 1 | 2 | 2 (4) | 3 |
| Root | WOX5 | WUS | 16 | 10 | 9 (16) | 3 |
| Lateral root | NAC1 | NAC1 | 3 | 10 | 0 | 0 |
| Lateral root | SINAT5 | SINAT5 | 6 | 5 | 2 (4) | 2 |
| Lateral root | AIR3 | AIR3 | 3 | 5 | 10 (10) | 1 |
| Lateral root | PAS2 | PAS2 | 1 | 5 | 1 (2) | 1 |
| Lateral root | ATNRT2.1/LIN1 | ATNRT2.1 | 7 | 4 | 2 (4) | 8 |
| Lateral root | ALF4 | ALF4 | 1 | 1 | 1 (1) | 2 |
| Lateral root | RPD1 | RPD1 | 15 | 17 | 10 (20) | 4 |
| Auxin signalling | IAA1 to 20, 26 to 34 | IAA31 | 29 | 30 | 4 (7) | 2 |
| Auxin carriers | BIG1 | BIG1 | 1 | 1 | 1 (2) | 2 |
| Auxin carriers | AUX1 | AUX1 | 4 | 4 | 2 (4) | 4 |
| Auxin signalling | ARF5/MP, NPH4/BIPOSTO, ARF6, 8, 16, and 19 | NPH4 | 5 | 8 | 3 (5) | 6 |
| Light signalling | HY5 and HYH | HY5 | 2 | 3 | 2 (4) | 2 |
| Seed | ABI5 | ABI5 | 7 | 5 | 4 (8) | 1 |
| Abscisic acid signalling | ABI1 | ABI1 | 9 | 10 | 3 (6) | 2 |
| Auxin signalling | TIR1 | TIR1 | 6 | 6 | 2 (4) | 4 |
| Abscisic acid biosynthesis | ABA1/ZEP | ABA1 | 1 | 2 | 1 (2) | 2 |
| Seed | ABI4 | At2g40220 | 9 | 5 | 4 (6) | 7 |
footnote: The number of putative orthologs here refers to number of genes that is included in a clade that corresponds to all genes derived from a single gene in the last common ancestor of P. patens, S. moellendrffii, A. thaliana, and O. sativa based on phylogenetic analyses. The alignments and trees are available through http://moss.nibb.ac.jp/treedb/ (a) number of putative loci at first and number of putative alleles detected in parentheses. That is, 1 (2), indicates we found two sequences that likely represent two alleles of one locus. See http://wiki.genomics.purdue.edu/index.php/Evolution_of_developmental_genes#Methods for brief methods.
| protein id | gene name | annotated by |
| ANT related genes | ||
|---|---|---|
| 1154 | ANT-1 | |
| 107288 | ANT-2 | |
| SHORT ROOT related genes | ||
| 450138 | SHR1-1 | |
| 129615 | SHR1-2 | |
| 450140 | SHR2-1 | |
| 442953 | SHR2-2 | |
| 450144 | SHR3-1 | |
| 412418 | SHR3-2 | |
| SCARECROW related genes | ||
| 449930 | SCR1-1 | |
| 432115 | SCR1-2 | |
| 450947 | SCR2-1 | |
| 116328 | SCR2-2 | |
| SINAT5 related genes | ||
| 97849 | SINAT5A-1 | |
| 119614 | SINAT5A-2 | |
| 98090 | SINAT5B-1 | |
| 268881 | SINAT5B-2 | |
| AIR3 related genes | ||
| 172478 | AIR3L1-1 | |
| 97661 | AIR3L1-2 | |
| 407350 | AIR3L2-1 | |
| 95668 | AIR3L2-2 | |
| 236400 | AIR3L3-1 | |
| 236650 | AIR3L3-2 | |
| 412516 | AIR3L4-1 | |
| 413072 | AIR3L4-2 | |
| 181997 | AIR3L5-1 | |
| 154795 | AIR3L5b-1 | |
| 179856 | AIR3L5b-2 | |
| 444992 | AIR3L6-1 | |
| 116988 | AIR3L6-2 | |
| 437460 | AIR3L7-1 | |
| 408319 | AIR3L7-2 | |
| 125066 | AIR3L8-1 | |
| 417801 | AIR3L8-2 | |
| 107351 | AIR3L9A-1 | |
| 425827 | AIR3L9A-2 | |
| 107394 | AIR3L9B-1 | |
| 425830 | AIR3L9B-2 | |
| PAS2 related genes | ||
| 122503 | PAS2-1 | |
| 125223 | PAS2-2 | |
| ATNRT related genes | ||
| 168278 | NRT2.1-1 | |
| 443813 | NRT2.1-2 | |
| 136730 | NRT2.2-1 | |
| 138351 | NRT2.2-2 | |
| ALF4 related genes | ||
| 444363 | ALF4-1 | |
| 426228 | ALF4-2 | |
| RPD related genes | ||
| 438174 | EMB1692-1 | |
| 428028 | EMB1692-2 | |
| 413758 | RPDL1-1 | |
| 416507 | RPDL1-2 | |
| 409264 | RPD1L2-1 | |
| 411330 | RPD1L2-2 | |
| 451376 | RPD1L3-1 | |
| 451377 | RPD1L3-2 | |
| 417170 | RPD1L4a-1 | |
| 417174 | RPD1L4b-1 | |
| 430354 | RPD1L4a-2 | |
| 430356 | RPD1L4b-2 | |
| 440300 | RPD1L5-1 | |
| 411311 | RPD1L5-2 | |
| 422954 | RPD1L6-1 | |
| 428942 | RPD1L6-2 | |
| 451379 | RPD1L7a-1 | |
| 451386 | RPD1L7a-2 | |
| 451388 | RPD1L8-1 | |
| 451389 | RPD1L8-2 | |
| Aux/IAA genes | ||
| 451390 | IAA33-1 | |
| 451391 | IAA33-2 | |
| 167506 | IAA1-1 | |
| 450582 | IAA1-2 | |
| 168183 | IAA2-1 | |
| 179441 | IAA2-2 | |
| 172524 | IAA3-1 | |
| 187180 | IAA3-2 | |
| NPH4 related auxin response factors (ARF) | ||
| 179736 | NPH4A-1 | |
| 451392 | NPH4A-2 | |
| 451395 | NPH4B-1 | |
| 451397 | NPH4B-2 | |
| 181404 | NPH4C-1 | |
| 182255 | NPH4C-2 | |
| ABI5 related genes | ||
| 227594 | ABI5A-1 | |
| 451399 | ABI5A-2 | |
| 91900 | ABI5B-1 | |
| 94516 | ABI5B-2 | |
| 266892 | ABI5C-1 | |
| 443424 | ABI5C-2 | |
| 177659 | ABI5D-1 | |
| 428822 | ABI5D-2 | |
| ABI4 related genes | ||
| 420500 | ABI4-1 | |
| 427925 | ABI4-2 | |
| BIG1 ortholog | ||
| 141341 | BIG1-1 | |
| 153843 | BIG1-2 | |
| AUX related genes | ||
| 439204 | AUX1A-1 | |
| 176094 | AUX1A-2 | |
| 165624 | AUX1B-1 | |
| 112710 | AUX1B-2 | |
| TIR1 related genes | ||
| 170974 | TIR1A-1 | |
| 178850 | TIR1A-2 | |
| 168175 | TIR1B-1 | |
| 179436 | TIR1B-2 | |
| ABI1 related genes | ||
| 174627 | ABI1A-1 | |
| 451367 | ABI1A-2 | |
| 178598 | ABI1B-1 | |
| 179532 | ABI1B-2 | |
| 150390 | ABI1C-1 | |
| 54775 | ABI1C-2 | |
