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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...for the study of conserved sequences. Species of the Andropogoneae tribe have diverged in a relatively short time frame, sharing a common ancestor ∼16–20 million years ago (Vicentini et al. 2008). Andropogoneae species include maize, sorghum, sugarcane, and silvergrass, some of the most productive grain, sugar...
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Research: The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
- Thomas E. Hughes,
- Jane A. Langdale,
- and Steven Kelly
Genome Res. August 2014 24: 1348-1355; Published in Advance April 30, 2014, doi:10.1101/gr.172684.114
..., Depamphilis CW, Wall PK, Soltis PS. 2009. Polyploidy and angiosperm diversification. Am J Bot 96: 336–348. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V, Bennetzen JL, Messing J. 2004a. Close split of sorghum and maize progenitors. Genome Res 14: 1916–1923. Swigonova Z, Lai J, Ma J, Ramakrishna W, Llaca V...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
...rice, have permitted the alignment of genes derived from common ancestral grass chromosomes ( Swigonova et al. 2004 ). It appears that the two progenitors of maize and the progenitor of sorghum were n = 5 species that diverged about 11.9 million years ago (Mya). The two maize progenitors are believed...
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LETTER: Gene Loss and Movement in the Maize Genome
- Jinsheng Lai,
- Jianxin Ma,
- Zuzana Swigoňová,
- Wusirika Ramakrishna,
- Eric Linton,
- Victor Llaca,
- Bahattin Tanyolac,
- Yong-Jin Park,
- O-Young Jeong,
- Jeffrey L. Bennetzen,
- and Joachim Messing
Genome Res. October 2004 14: 1924-1931; doi:10.1101/gr.2701104
.... 2002 . Mosaic organization of orthologous sequences in grass s. Genome Res. 12 : 1549 -1555. ↵ Swigonova, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004 . Close split of maize and sorghum progenitors. Genome Res. (this issue). ↵ Tikhonov, A.P., SanMiguel, P...
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Research: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
- Michael Regulski,
- Zhenyuan Lu,
- Jude Kendall,
- Mark T.A. Donoghue,
- Jon Reinders,
- Victor Llaca,
- Stephane Deschamps,
- Andrew Smith,
- Dan Levy,
- W. Richard McCombie,
- Scott Tingey,
- Antoni Rafalski,
- James Hicks,
- Doreen Ware,
- and Robert A. Martienssen
Genome Res. October 2013 23: 1651-1662; Published in Advance June 5, 2013, doi:10.1101/gr.153510.112
...on false-positive detection of large methylation state changes in the RILs by analyzing regions where both B73 and Mo17 are either highly methylated or hypomethylated and the RIL is in the opposite state. The median size of the CG HDMRs is 508 bases. We split the maize into nonoverlapping 500-base regions...
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LETTER: Characterization of the Maize Endosperm Transcriptome and Its Comparison to the Rice Genome
- Jinsheng Lai,
- Nrisingha Dey,
- Cheol-Soo Kim,
- Arvind K. Bharti,
- Stephen Rudd,
- Klaus F.X. Mayer,
- Brian A. Larkins,
- Philip Becraft,
- and Joachim Messing
Genome Res. October 2004 14: 1932-1937; doi:10.1101/gr.2780504
...organization of orthologous sequences in grass s. Genome Res. 12 : 1549 -1555. ↵ Swigoňová, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004 . Close split of sorghum and maize progenitors. Genome Res. (this issue). ↵ Van der Hoeven, R., Ronning, C., Giovannoni, J., Martin...
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LETTER: Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome
- Blake C. Meyers,
- Scott V. Tingey,
- and Michele Morgante
Genome Res. October 1, 2001 11: 1660-1676; Published in Advance September 20, 2001, doi:10.1101/gr.188201
...sequences indicated that elements most abundant in the genome are less abundant at the transcript level than are more rare retrotransposons. Additional phylogenies also demonstrated that rice and maize retrotransposon families are frequently more closely related to each other than to families within...
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Methods: Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries
- John Emberton,
- Jianxin Ma,
- Yinan Yuan,
- Phillip SanMiguel,
- and Jeffrey L. Bennetzen
Genome Res. October 2005 15: 1441-1446; doi:10.1101/gr.3362105
.... ↵ Swigonová, Z., Lai, J., Ma, J., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004 . Close split of sorghum and maize progenitors. Genome Res. 14 : 1916 -1923. ↵ Van Deynze, A.E., Sorrells, M.E., Park, W.D., Ayres, N.M., Fu, H., Cartinhour, S.W., Paul, E., and McCouch, S.R. 1998 . Anchor...
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Chicken Special/Letters: The repetitive landscape of the chicken genome
- Thomas Wicker,
- Jon S. Robertson,
- Stefan R. Schulze,
- F. Alex Feltus,
- Vincent Magrini,
- Jason A. Morrison,
- Elaine R. Mardis,
- Richard K. Wilson,
- Daniel G. Peterson,
- Andrew H. Paterson,
- and Robert Ivarie
Genome Res. January 2005 15: 126-136; Published in Advance July 15, 2004, doi:10.1101/gr.2438004
...provided representative sequences from DNA families comprising 15% of the sorghum . CBCS has also been used on a smaller scale by others for repeat analysis ( Ho and Leung 2002 ). We report here on the application of a combination of CBCS and bioinformatics to characterize the repetitive landscape...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
...of plant comparisons because of the sets of closely related s that have been fully sequenced since early 2010 (rice, sorghum, maize, Brachypodium). We conducted a reconstruction of the AGK, in terms of ancestral gene order, as well as several intermediary ancestral s, delineating today’s species from...

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