A Maize Pan-Transcriptome

Here I am adding to my neverending maize-related wish-list.

Based on the amount of RNA-Seq/Microarray data generated, The maize community should have significant amount of information to start compiling a Pan-transcriptome for some tissues/developmental stages of interest.

I know that some researchers at Michigan State University (Hansey/Hirsch CN) at have already started, but wondering if someone out there (Gramene? MaizeGDB?) is gathering a good portion of the information generated by the community and building a Pan-transcriptome of Maize. So far, Hansey and collaborators have generated and analyzed RNA-Seq from seedlings of 21 maize lines including the reference maize inbred line B73. So, here I will point out at references/resources that could be used to build a Zea mays Pan-transcriptome while I wish for the 10,001 maize genomes project to happen.

1. Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21(4):1053-69 (2009). #B73
2. Eveland AL, Satoh-Nagasawa N, Goldshmidt A, Meyer S, Beatty M, Sakai H, Ware D, Jackson D. Digital gene expression signatures for maize development. Plant Physiol. 154(3):1024-39 (2010). #B73
3. Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP. The developmental dynamics of the maize leaf transcriptome. Nat Genet 42(12):1060-7 (2010). #B73
4. Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM. Genome-wide atlas of transcription during maize development. Plant J 66(4):553-63 (2011).
5. Davidson, R. M. et al. Utility of RNA sequencing for analysis of maize reproductive transcriptomes. Plant Genome 4, 191–203 (2011). #B73
6. Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 23(12):4221-33 (2011) #B73xMo17
7. Zhang M, Zhao H, Xie S, Chen J, Xu Y, Wang K, Zhao H, Guan H, Hu X, Jiao Y, Song W, Lai J. Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc Natl Acad Sci U S A. 108(50):20042-7 (2011) #B73xMo17
8. Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Buell CR. Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS One 7(3):e33071 (2012).
9. Chang YM, Liu WY, Shih AC, Shen MN, Lu CH, Lu MY, Yang HW, Wang TY, Chen SC, Chen SM, Li WH, Ku MS. Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis. Plant Physiol 160(1):165-77 (2012). #B73
10. Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM. Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One 8(4):e61005 (2013). #B73
11. Fu J, Cheng Y, Linghu J, Yang X, Kang L, Zhang Z, Zhang J, He C, Du X, Peng Z, Wang B, Zhai L, Dai C, Xu J, Wang W, Li X, Zheng J, Chen L, Luo L, Liu J, Qian X, Yan J, Wang J, Wang G. RNA sequencing reveals the complex regulatory network in the maize kernel. Nat Commun 4:2832 (2013).
12. Li L, Petsch K, Shimizu R, Liu S, Xu WW, Ying K, Yu J, Scanlon MJ, Schnable PS, Timmermans MC, Springer NM, Muehlbauer GJ. Mendelian and non-Mendelian regulation of gene expression in maize. PLoS Genet 9(1):e1003202 (2013). #B73xMo17
13. Fordyce SL, Ávila-Arcos MC, Rasmussen M, Cappellini E, Romero-Navarro JA, Wales N, Alquezar-Planas DE, Penfield S, Brown TA, Vielle-Calzada JP, Montiel R, Jørgensen T, Odegaard N, Jacobs M, Arriaza B, Higham TF, Ramsey CB, Willerslev E, Gilbert MT. Deep sequencing of RNA from ancient maize kernels. PLoS One 8(1):e50961 (2013).
14. He G, Chen B, Wang X, Li X, Li J, He H, Yang M, Lu L, Qi Y, Wang X, Wang Deng X. Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 14(6):R57 (2013) #B73xMo17
15. Xin M, Yang R, Li G, Chen H, Laurie J, Ma C, Wang D, Yao Y, Larkins BA, Sun Q, Yadegari R, Wang X, Ni Z. Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. Plant Cell 25(9):3212-27 (2013). #B73xMo17

Thanks to the Maize eFP Browser we can access the Sekhon et al., 2011 microarray-data and the Li et al., 2010 RNA-Seq data as informative and beautiful pictograms. So, just imagine having the same information discriminated per allele/inbred line.

Finally, did you notice that, reference 10 here, was a popular one in the twitterverse back in May/2013.

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