Table 2.
Features of Plant Comparative Genomics Tools
| Tool | Speciesa | Gene Families | Phylogenetic Trees | WGDotplots | Inter Species Colinearity | Functional Annotation | Genome Browser | Comments |
|---|---|---|---|---|---|---|---|---|
| PLAZA | 9 (Ath, Cpa, Ptr, Vvi, Osa, Sbi, Ppa, Olu & Cre) | X | X | X | X | X | X | Multispecies colinearity views (Skyline Plot and Multiplicon view), Ks dating tool, family-wise similarity heat map and Workbench |
| Genome Cluster Database | 2 (Ath & Osa) | X | X | X | Chromosome map and link with Arabidopsis expression data | |||
| GreenPhylDB | 2 (Ath & Osa) | X | X | X | Manual curation of a subset of families | |||
| OrthologID | 3+2 (Ath, Ptr & Osa + Ppa and Cre as outgroup) | X | X | Diagnostic characters per orthologous group | ||||
| Plant Genome Duplication Database | 7 (Ath, Cpa, Ptr, Mtr, Vvi, Osa & Sbi) | X | X | Genome-wide mapping tool for homologous sequences and syntenic locus search | ||||
| Phytozomeb | 14 (Ath,Aly,Cpa, Ptr, Vvi, Mtr, Gma, Osa, Bdi, Sbi, Zma, Smo, Ppa & Cre) | X | ± | X | ||||
| PlantTribes | 5 (Ath, Cpa, Ptr, Mtr & Osa) | X | X | Link with Arabidopsis expression data | ||||
| CoGec | 14 (Ath, Cpa, Ptr, Mtr, Lja, Vvi, Osa, Sbi, Zma, Ppa, Smo, Olu, Cre, Vca) | X | X | X | X | DNA-based sequence comparisons (conserved noncoding sequences) | ||
| SynBrowse | 3 (Ath, Mtr, Lja) | X | Synteny browser based on GBrowse (no intraspecies colinearity) | |||||
| Gramened | 6 (Ath, Osa, Ptr, Vvi, Sbi & Zma) | X | X | ± | ± | X | X | Based on the Ensembl pipeline |
a
Species names are abbreviated: Arabidopsis lyrata (Aly), Arabidopsis thaliana (Ath), Brachypodium distachyon (Bdi), Carica papaya (Cpa), Chlamydomonas reinhardtii (Cre), Glycine max (Gma), Lotus japonica (Lja), Medicago trunculata (Mtr), Ostreococcus lucimarinus (Olu), Oryza sativa (Osa), Physcomitrella patens (Ppa), Populus trichocarpa (ptr), Sorghum bicolor (Sbi), Selaginella moellendorffi (Smo), Vitis vinifera (Vvi), Volvox carteri (Vca), and Zea mays (Zma).
b
Phytozome has a synteny viewer instead of a genuine colinearity pipeline.
c
CoGe includes also viral, prokaryotic, and other, nonplant, eukaryotic genomes.
d
Gramene has some features to visualize macrocolinearity based on marker maps.