Tag Archives: corn

Corn: 85% not corn, and missing big pieces

popcornSo I’m all excited about the genome festival that I’m seeing, related to the publication of the new sequence version of corn. You can access the main paper in Science, and there’s a very neat diagram in figure 1 that is like looking across time at the sequence data and into the corn nebula.  But the thing that cracked me up was this line from the abstract:

Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome.

That means 85% of corn isn’t corn!!  And what business do those elements have messing with the genomes??  I am told all the time that messing with plant genomes is wrong and unnatural.  Heh.

For full coverage of the big news today I’ll point you to James and the Giant Corn (appropriately enough) who seems to be the CNN (Corn News Network) of 24-hour coverage of many aspects of the work.

I spent my morning looking over the PLoS Maize Special Collection papers, including the intriguing appetizer:  10 Reasons to be Tantalized by the B73 Maize Genome.  But I spent longer looking at the CNVs and PAVs paper.  I’ve been thinking about CNVs a lot  lately, and was interested to see this covered in a non-mammalian species.

Figure 1 is a nice example of how to use VISTA for effective displays in comparative genomics.  (If you haven’t used VISTA before you might check out our sponsored free tutorial on that–we are currently working with the VISTA team to update that with their new features too.)

There’s a really striking segment of chromosome 6 that appears to be present in one of the strains they examine and absent in the other (illustrated in figure 4).  And it looks like it has genes that are expressed and active in the B73 strain.  The ongoing investigation of that is pretty intriguing as well.

The structural variations are not evenly distributed across the genomes.  Some places have large occurrences, and some are untouched.  It’s clear that just in these two strains there’s a lot more structural diversity than in other species that have been examined:

In the human, rat, dog, mouse, macaque and chimpanzee genomes the average number of CNVs between two individuals is between 15 and 75 [43]–[48]. A high resolution study of eight human genomes [49] revealed only several hundred insertions and deletions, including CNV and PAV sequences, in the comparison of any two human genomes. In contrast, even after very stringent filtering we identified >3,700 CNV or PAV sequences that represent at least 2,000 events between these two maize genomes.

Emphasis mine.  Plants are so much more flexible, apparently….

This is going to lead to some neat clues on heterosis (or hybrid vigor) as the research proceeds with these new tools.  What a great time to be a plant scientist.  There are some very exciting projects coming along with the tools of genomics.

What I couldn’t locate was any reference to a CNV database (like DGV or CHOP CNV) where you can examine the whole set.  I’ll dig through the supplement data to see if I can find out more on that.  But I wanted get this post out to celebrate the very nice work and collection of papers on this project. Congrats to the teams involved!

References:

Springer, N., Ying, K., Fu, Y., Ji, T., Yeh, C., Jia, Y., Wu, W., Richmond, T., Kitzman, J., Rosenbaum, H., Iniguez, A., Barbazuk, W., Jeddeloh, J., Nettleton, D., & Schnable, P. (2009). Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content PLoS Genetics, 5 (11) DOI: 10.1371/journal.pgen.1000734

Schnable, P., Ware, D., Fulton, R., Stein, J., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T., Minx, P., Reily, A., Courtney, L., Kruchowski, S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., Rock, S., Belter, E., Du, F., Kim, K., Abbott, R., Cotton, M., Levy, A., Marchetto, P., Ochoa, K., Jackson, S., Gillam, B., Chen, W., Yan, L., Higginbotham, J., Cardenas, M., Waligorski, J., Applebaum, E., Phelps, L., Falcone, J., Kanchi, K., Thane, T., Scimone, A., Thane, N., Henke, J., Wang, T., Ruppert, J., Shah, N., Rotter, K., Hodges, J., Ingenthron, E., Cordes, M., Kohlberg, S., Sgro, J., Delgado, B., Mead, K., Chinwalla, A., Leonard, S., Crouse, K., Collura, K., Kudrna, D., Currie, J., He, R., Angelova, A., Rajasekar, S., Mueller, T., Lomeli, R., Scara, G., Ko, A., Delaney, K., Wissotski, M., Lopez, G., Campos, D., Braidotti, M., Ashley, E., Golser, W., Kim, H., Lee, S., Lin, J., Dujmic, Z., Kim, W., Talag, J., Zuccolo, A., Fan, C., Sebastian, A., Kramer, M., Spiegel, L., Nascimento, L., Zutavern, T., Miller, B., Ambroise, C., Muller, S., Spooner, W., Narechania, A., Ren, L., Wei, S., Kumari, S., Faga, B., Levy, M., McMahan, L., Van Buren, P., Vaughn, M., Ying, K., Yeh, C., Emrich, S., Jia, Y., Kalyanaraman, A., Hsia, A., Barbazuk, W., Baucom, R., Brutnell, T., Carpita, N., Chaparro, C., Chia, J., Deragon, J., Estill, J., Fu, Y., Jeddeloh, J., Han, Y., Lee, H., Li, P., Lisch, D., Liu, S., Liu, Z., Nagel, D., McCann, M., SanMiguel, P., Myers, A., Nettleton, D., Nguyen, J., Penning, B., Ponnala, L., Schneider, K., Schwartz, D., Sharma, A., Soderlund, C., Springer, N., Sun, Q., Wang, H., Waterman, M., Westerman, R., Wolfgruber, T., Yang, L., Yu, Y., Zhang, L., Zhou, S., Zhu, Q., Bennetzen, J., Dawe, R., Jiang, J., Jiang, N., Presting, G., Wessler, S., Aluru, S., Martienssen, R., Clifton, S., McCombie, W., Wing, R., & Wilson, R. (2009). The B73 Maize Genome: Complexity, Diversity, and Dynamics Science, 326 (5956), 1112-1115 DOI: 10.1126/science.1178534

Tip of the Week: Fun in the Grass

GrameneShotToday’s tip of the week introduces you to Gramene, a great database of grass genomes including rice, corn, oats, millet, wheat and others. The database is full of serious data and genomic analysiscornbread for gramene fun tools for the grasses, but today we are going to show you something fun you could do with Gramene… plan your dinner. After quickly showing you that there is a wealth of data on a large number of species, we’ll point you to some information on how to cook those genomes.

http://www.gramene.org/

Corn genome released

corn.jpgSometimes it feels like “another day, another genome….” ’round here. But this one is big. Corn is such a major commodity–important in history, for our current food supply, and for the future. Today researchers announced the completion of the maize draft genome. You can view it here:

The Maize Genome Browser http://www.maizesequence.org/index.html

The browser appears to be based on the Ensembl framework. So I would expect you can do the same kinds of searches, displays, and custom BioMart queries that you may recognize from other databases. But I can’t seem to find the BioMart link just yet…? It also links to Gramene, another important place to find plant genomic information.

From the press release at EurekAlert (excerpts):

A team of scientists led by Washington University in St. Louis has begun to unlock the genetic secrets of corn, a crop vital to U.S. agriculture. The researchers have completed a working draft of the corn genome, an accomplishment that should accelerate efforts to develop better crop varieties to meet society’s growing demands for food, livestock feed and fuel…

The draft covers about 95 percent of the corn genome, and scientists will spend the remaining year of the grant refining and finalizing the sequence….

Corn is only the second crop after rice to have its genome sequenced, and scientists will now be able to look for genetic similarities and differences between the crops, Quatrano adds….

Happy hunting, genomics folks!

PS: Did you know that Gramene has recipies? How many species browsers have that?? Actually, if you know, go ahead and post them!

Edit: It looks like this browser at Maize Sequence is based on the July 2005 release of the genome data that they had at the time. Hey, where’s the new one??  That’s what I get for posting before I’m done with my coffee…