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Whole-genome duplicate (WGD) genes are retrieved from (Bowers et al., 2003) and (Schnable et al., 2011) for Arabidopsis and maize, respectively. Duplicates derived from tandem duplication (TD) are identified if duplicate genes have BLASTp e-value <= 1e-5 and are located within 100 Kbp on the same chromosome. For tandem gene clusters for than two memebrs, two genes were randomly selected.

This is based on previous studies (Blanc and Wolfe, 2004; Liu et al., 2011). Basically, we identied ortholog-paralog triplet using several outgroup species. We then calculated Ka, Ks, Ka/Ks for each pair of ortholog and paralog in the triplet, based on which the relative divergence is calculated. For example, the Ka divergence is calculated as (Ka[paralog2]-Ka[paralog1])/(Ka[paralog2]+Ka[paralog1])

Arabidopsis Root (Hsu et al. 2016)
Arabidopsis Shoot (Hsu et al. 2016)
Arabidopsis seedling (normal/control) (Juntawong et al. 2014)
Arabidopsis seedling (hypoxia) (Juntawong at al. 2014)
Arabidopsis leaves (Lukoszek et al. 2016)
Maize seedling (normal/control) (Lei et al. 2015)
Maize seedling (drought) (Lei et al. 2015)

Please see the reference section on this page for the references.

RF is abbreviation of ribosome footprint. RF abundance is defined as the abundance of ribosome-associated reads mapped in ribo-seq, as widely used in many studies. To calculate RF for each gene, we calculated FPKM for each gene using Cufflinks. RF fold difference was calculated as RF2/RF1, and the result was transformed into a log2-based value. Relative divergence of RF abundance is calculated as (RF2-RF1)/(RF1+RF2).

TE refers to trasnlational efficiency. It is calculated as the ratio of ribosome footprints to mRNA fragments (Ingolia et al., 2009). TE fold difference was calculated as TE2/TE1, and the result was transformed into a log2-based value. Relative divergence of TE is calculated as (TE2-TE1)/(TE1+TE2).

Wang S, Chen Y. Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize. Frontiers in plant science. 2019;10:534.

Please write to Sishuo Wang for any suggestions or bug reports. Your help is always appreciated!

References

1. Hsu PY, Calviello L, Wu HYL, Li FW, Rothfels CJ, Ohler U, Benfey PN (2016) Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proceedings Of the National Academy Of Sciences Of the United States Of America 113: E7126-E7135
2. Juntawong P, Girke T, Bazin J, Bailey-Serres J (2014) Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proceedings Of the National Academy Of Sciences Of the United States Of America 111: E203-E212
3. Lei L, Shi JP, Chen J, Zhang M, Sun SL, Xie SJ, Li XJ, Zeng BA, Peng LZ, Hauck A, Zhao HM, Song WB, Fan ZF, Lai JS (2015) Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress. Plant Journal 84: 1206-1218
4. Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691
5. Liu SL, Baute GJ, Adams KL (2011) Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana. Genome Biol Evol 3: 1419-1436
6. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-23
7. Lukoszek R, Feist P, Ignatova Z (2016) Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-Seq. BMC Plant Biol 16: 221
1. Pixabay
2. Arabidopsis thaliana image: Dawid Skalec