Grad students graduating with PhDs right now probably entered grad school at point A, or earlier. People at the end of their first post-doc (and potentially in a position to apply for faculty positions and start training new graduate students themselves) would have entered grad school at point B or earlier.

Today there are a mere 10 published plant genomes out of the more than quarter million named plant species in the world. But even ten genomes is a huge amount of data to deal with for a plant genomics community that largely came of age during the long genome drought of 2002-2006. What is the genome drought? The rice genome was published in April 2002. It was only the second plant genome to be sequenced, and the last plant genome to be published until the poplar genome came out in September of 2006, a gap of more than four years. Two genomes, especially of species as distantly related as arabidopsis and rice doesn’t make for a lot of compelling comparative genomics (Although there was certainly some really cool stuff being discovered in this time period.)

Does that matter? Probably not, but it’s important to remember that the people earning their PhDs today probably entered grad school (and chose a lab and field of study) during that two-plant-genome era (see point A) and less opportunity for exciting research mean less grant money and less ability to attract grad students. The youngest people applying for faculty positions today (assuming they only did one, quite successful, post-doc), also entered grad school in the two genome era (see point B), if not the previous single genome era.

I’m talking about this mostly to make the point that I think comparative genomics as a field of study is getting a lot more exciting as more genomes become avaliable, which is likely to attract more graduate students in that key first year when they join a lab and begin to specialize. Which means as we move farther away from the time of the long genome drought, we will hopefully* start to see a lot more well trained people doing plant genomics.

Which is a good thing because the other point this graph should make (not that I think many people need to be reminded of it), is that the pace of sequencing plant genomes is accelerating, and SOMEONE needs to analyze the huge quantities of data that are already starting to flow through the plant biology community.

This should be the last plant genome themed post for a while, but please continue to let me know if you know/hear about more plant genome projects. jcs98 (@) jamesandthegiantcorn.com

*If the hypothetical end to the also-hypothetical-and-possibly-the-result of-wishful-thinking-on-my-part shortage of plant comparative genomicists could hold off long enough for me to be really in demand when/if I finish grad school, that would be great.

Libe slope in Ithaca, NY. Behind you are student dorms. At the top of the hill, campus starts. Photo: foreverdigital, flickr (click to see in original context)

When I was an undergraduate, there were exactly two sequenced plant genomes, rice and arabidopsis. And sure maybe I didn’t have to walk “ten miles to school, barefoot, in the snow, uphill, both ways”* the one way I did have to walk uphill (sometimes in the snow but always with shoes), was very uphill. But where was I?

Oh yeah, plant genome sequences. Kids getting into plant genomics these days don’t realize how easy they’ve got it. By my count (which may be low but I’m getting to that) there are ten published plant genomes, with several more unpublished genomes that are available in various states of completion, and lots more on the way.

Which brings me to what I was doing yesterday instead of writing an update for this website: trying to document the published plant genomes, the unpublished genomes that are available, and which new genomes we can expect to see published in the near future.

Please, if you find mistakes or know of additional flowering plant genomes I should mention, let me know! jcs98 (@) jamesandthegiantcorn.com.

If you don’t work in biology, it might be interesting to see which plants have sequenced genomes and how they’re related to each other.

*An explanation of this phrase.

But where was I? Oh yeah, gene counts. 32,690 high confidence genes*. Of those, how many have been studied individually?

While I don’t know that anyone knows the precise answer to that question, one indicator is how many maize genes were named before the maize genome was sequenced. People have been naming maize genes since before even the structure of DNA was known, based on the effect mutant version of the gene have on corn plants (for example: waxy1 or yellow stripe1). Later names might be based on the function of the gene (alcohol dehydrogenase1 or superoxide dismutase4), or anything else we know about the gene (wound induced protein1 or male flower specific18). The point being, if someone bothered to name a gene sometime during the last century of maize genetics, it was likely because they were studying it (to a greater or lesser extent). MaizeGDB keeps records of most of the named genes in maize and (excluding chloroplast and mitochondrial genes) I was able to find records of 1181 named genes in maize.

That’s less than 4% of the number of high confidence genes found within the maize genome, and at least a few of the named genes aren’t found within that group (see the first footnote for more details). Why is that number so low?

1. Each of the genes that has been studied in any detail probably represents some grad student’s doctoral thesis. While the tools have gotten better, the expectations for what is involved in characterizing a gene have risen too. I don’t have any statistics on how many maize genetics students earn their PhDs every year (and many of them will have worked on other kinds of projects than characterizing some new mutant gene), but it’s certainly not the thousands that would be required to characterize every gene in the genome in a short period of time.
2. Perhaps more importantly, the first genes to be studied are the ones with the best mutant phenotypes. To be a good mutant to study, breaking a gene should create something obviously different about the plant (it’s purple, or the tassel produces seeds like an ear instead of pollen, or the plants grow along the ground instead of standing upright), but not be so vital that embryos containing broken versions of the gene don’t develop at all. From a project that to knock out every gene in another plant Arabidopsis thaliana we know that many genes can be broken without any obvious effect on the plants that carry broken copies. That doesn’t mean there won’t be still be interesting things wrong with the plants when they’re studied in more detail, but such mutants were less likely to be identified early on. As for genes mutations are usually lethal, they can be studied (a friend in a lab downstairs is working with just such a mutant) but it certainly adds a whole new layer of difficulty to any research project so the genes better be involved in something interesting enough to justify the extra pain and suffering involved.

Now the situation isn’t nearly as grim as it might sound. Nature re-uses related genes over and over again both between and within species, so any time a researcher studies a new gene in detail, that information doesn’t just inform our knowledge of one particular gene in one particular species. Like a candle in a dark room, the information created by the study of a single gene will illuminate, to a greater or lesser extent, nearby genes (genes that have similar sequences to the gene being studied directly.) So even for a gene that’s never been studied in maize, we can make guesses about its function based on any related genes that have benefited from detailed study (either other genes in maize, in other grasses like barley or rice, other plants like arabidopsis or snapdragon, or even in animals or bacteria). While no geneticist worth their pollenating apron wouldn’t need experimental data before being CERTAIN of a gene’s function, knowing something about the functions of related genes is an excellent starting point.

I just finished some “free time” science looking at the classical genes of maize genetics (which displaced the time I normally spend writing for this site), so expect a couple more posts on related topics later this week.

*The good folks at maizesequence.org also produced a set of all the sequences they thought MIGHT be genes which, in addition to the filtered genes, includes ~70,000 more sequences that might or might not be genes. Many of these potential genes are computationally predicted, by programs that look at the underlying characteristics of the DNA sequence itself (how they work is outside my expertise and above my pay grade), but I can personally vouch for the fact that at least some of those “possible” maize genes are the real thing so the true number of genes contained within the maize genome is at least somewhat greater than the 32,690 reported with high confidence. This fact isn’t in any way a criticism of the people involved in sequencing and annotating the maize genome. The vast majority of the high confidence genes (called the filtered gene set) are real, and most of the other 70,000 genes (those included only in the working gene set (which also includes the genes from the filtered gene set)) are probably figments of a computer program’s imagination. Anywhere they chose to draw the line between the two groups was going to put some genes in the wrong category, and they did everything they could to minimize those miscategorizations.

**This doesn’t mean that the genes don’t have important jobs. You can imagine, for example, that genes involved in a plant’s ability to survive disease, water shortages, cold stress or heat stress all won’t create obvious problems for plants grown in the relatively pampered conditions we biologists try to provide for our research subjects when we aren’t actively studying what happens when we stress plants.

Sorry to harp on the same topic a second time, this video is just SO MUCH BETTER than the previous one and I needed to show it off.

Brachypodium distachyon (photo courtesy of Devin O'Conner)

Sorry this is late going up. -James

This morning Nature officially published the paper* describing the sequence of the Brachypodium distachyon genome. This publication brings the number of grass genomes available for comparative analysis to four. In celebration I’m going to list four reasons to be excited about the publication of this genome.

The location of Brachypodium within the grass family tree.

Brachy (as I will refer to the species from here on) is a member of the Pooideae a sub-family of grasses from which no sequenced grasses have come. For the work we do in my lab this is exciting because it adds more depth to our analysis of changes in the grass genomes. The more distantly related grasses we can compare at the whole genome level, the better we can infer what the ancestral species that gave rise to all the grasses might have been like at a genome level. The most we know, or can make educated guesses about that species, the better position we are in to say what changed along the evolutionary paths leading to grasses like maize, rice, and sorghum. The choice of the Pooideae wasn’t at random, or even because of the sub-family’s distant relationship to other sequenced grasses.

Family tree of the sequenced grasses. As you can see, corn (green) and sorghum (blue) are quite closely related, and while brachypodium (red) is more closely related to rice (orange) than it is to the sorghum/corn pair, it's still pretty far away from anything else yet sequenced. Tree visualized in Mesquite ( http://mesquiteproject.org/ ) and is an approximation at best.

As I’ve said many times, both on this site and elsewhere, it is the unrivalled productivity of three grasses (grains) that underpin our civilization. Without corn/maize, rice, and wheat, it might have been that human societies would never have been able to produce enough surplus food so that farmers could support philosophers and copper workers and all that great surplus people who do things other than bring food from the ground. Of the big three grains, rice was the second genome ever sequences and the genome of maize/corn was published this past November. Wheat stands alone as a genome so complex the very though of trying to assemble it makes grown bioinformaticians cry (I’m obviously taking some dramatic license here). As you may have guessed, wheat (and its close relatives barley, rye, and oats) also belong to the Pooideae. Prior to the publication of the brachy genome, wheat geneticists would have to go all the way to rice to find the most closely related species with a sequenced genome. So while the publication of the brachypodium genome may not be of huge excitement to wheat geneticists (the relationship between brachypodium and wheat still last shared a common ancester more than 30 million years ago), it’s still an improvement from their previous situation. (Though it may be cold comfort wheat geneticists, remember the rest of us plant folks are in awe of you.)

Brachypodium Really is the Arabidopsis of the Grass World.

It can be said as an insult, implying that like Arabidopsis, brachy is small and boring, but being small really does have its advantages for research. A lot more brachypodium plants can fit into a given square foot than can corn or sorghum. And from my own experience, brachy takes much better to life in a growth chamber than any other grass species I’ve worked with, which means instead of doing genetics out in a field, with all the costs**, limitations***, and risks**** that entails. Brachy researchers can just grow their plants in growth chambers down the hall (or downstairs) from their labs, a convenience arabidopsis researchers have been enjoying for decades. Personally I think those limitations build character and encourage the development of good habits like planning out one’s research in advance (including fallbacks and alternative avenues), but I’d also be thrilled to see more labs get into grass genetics so on the balance I consider brachy’s arabidopsis-like nature to be a Good Thing.

Brachypodium has a very NICE genome.

A dotplot showing the conserved order of genes in the chromosomes of rice (Oryza sativa) and Brachypodium distachyon. The darker blue diagonal lines represent orthologous genes. The light-blue/cyan lines homeologous regions (ones that were created when the ancestor of all sequenced grasses doubled its whole genome. The regions have evolved independently since but enough duplicated copies of genes are still in the same order that they're easy to spot.) Tree generated using CoGe's Synmap tool ( synteny.cnr.berkeley.edu/CoGe/SynMap.pl ), with color coding based on synonymous substitution rates.

Brachy has only five chromosomes, and, as you can see in the dotplot comparing brachy to rice, the genes line up in long straight syntenic stretches. Even the light blue regions which result from a whole genome duplication in the ancestor of all grasses are relatively long and well defined. You’ll also notice brachypodium only has five chromosomes, to rice’s 12. (Maize/corn and sorghum both have 10)

Transposons, the “jumping genes” that make working in maize so complicated, are a much smaller proportion of the total genome in Brachypodium than in other systems weighing in at less than 27% of the total genome which in total is only 271 megabases long (less than 15% the size of the 2.3 gigabase corn genome which is 85% transposons, which … mumble…carry the one …. means corn has 26.7 TIMES more transposon sequence than brachy, and I sure want to learn more about how brachy keeps its transposons in check.)

The Author List

Publishing a good genome paper is an enormous undertaking, involving collaborations between dozens of research groups across the country or sometimes around the world. Of the, by my count, 135 names attached to the paper paper I can count old employers, current collaborators, science friends and acquaintances, one relative and (at least) one regular reader of this site.

One of those 135 names is also my own. This is from work I did back during my second rotation last winter doing manual verification and analysis of flowering time genes in the brachypodium genome sequence. A very small part of the work that in turn went into a small section of the paper, but this is the first time my name has actually been attached to a peer reviewed publication, EVER! (My undergraduate work made it onto a couple of poster abstracts but no papers, and none the projects I’ve worked on since joining my lab have made it to print yet.)

Random thought:

-Brachypodium is the first sequenced grass that hasn’t been domesticated as a crop. I would expect at least a couple of papers will eventually be published that capitalize on that distinction.

*The International Brachypodium Initiative, “Genome Sequencing and analysis of the model grass Brachypodium distachyon” DOI: 10.1038/nature08747 The genome sequence itself can be accessed at here among other places.

**Especially on urban and suburban campuses, land for a cornfield represents a substantial investment.

***No growing plants in winter unless you’ve got enough green house space (and even then they may not be happy enough to flower), or the money to run a winter field somewhere warm like Hawaii or Puerto Rico. And no way to fix it in August if you realize you didn’t plant enough plants to do get everything you need done.

****The number of people will break into a building to pull plants out of a growth chamber because they (usually mistakenly) have decided they plants are genetically engineered and need to be kills is much lower than the number who will do the same thing to an unguarded cornfield.

One of the earliest fruits of my work to define relationships between syntenic genes* was a list of sorghum genes and corn genes in one or both of the two related regions of the corn genome (each region in sorghum corresponds to two in corn because the ancestors of corn completely doubled their genome in the time after the ancestors of corn and sorghum went their separate ways.)

But this is not the post where I explain my research projects. That post would be confusing and densely written at the best of times, which two AM in the morning certainly isn’t. Tonight my goal is simply to introduce the embedded video below, which explains how any researchers who want to can check out the relationships I’ve identified between genes in the two duplicate regions of maize, and the genes of the sorghum genome can do so using the MaizeGDB genome browser, and CoGe’s own GenomeViewer application. Video below. If you’re going to watch, I recommend selecting the highest resolution youtube offers you.

To play around with the panel of genes shown at the end of the video, click here. Note that I misspoke during the video voice over, saying the Brachypodium genome hadn’t been sequenced (obviously it has since I ran a BLAST search of it during the video), what I meant to say was that the paper describing the Brachypodum distachyon genome has not yet been published.

The video itself was more an experiment than anything else. At a bare minimum it has convinced me that I need to either invest money in better video editing software, or invest time in checking out the best open source video editors. I did the editing on an ancient version of iMovie that was choking on the high resolution videos I was trying to edit (why many of the transitions are less smooth than I would like.) Ideally I’d also like to hire voice actors to read my lines more clearly, and with fewer ‘uhhs’ than I can manage myself. Since I wasn’t able to do that, please forgive the times when my voice becomes unintelligible, the voice overs were primarily recorded between midnight and 2 am local time.

If you’re interested in using the particular aspect of CoGe I’m advertising today, check out the written tutorial on CoGepedia, or ask me any questions you have directly.

*Genes arranged in the same order in different genomes, or different parts of the same genome

Corngrass1 a dominant mutant that keeps maize from making the transition to adult growth. The stalk of a normal maize plant is shown to the left for comparison. According to George Chuck, in some genetic backgrounds where they never flower, corngrass plants are potentially immortal, as cuttings of the stalk can be transplanted to new soil and simply continue to grow. (Normally corn plants are annuals, they stop growing once the end of their stalk turns into a tassel and eventually die off even if they're grown in temp. controlled greenhouses.) Photo courtesy of MaizeGDB.org

Just got back from a great talk given by George Chuck, who works on microRNAs that control the transitions between the juvinile and adult phases of plant development in maize at the USDA’s Plant Gene Expression Center. In trying to figure out why it was such a great talks (besides the obvious, that he had exciting data to present).

The obvious ones I could spot where:

• History. One of the mutants he was working on, corngrass1, was first discovered in a sweetcorn field before many in the audience had even been born, and he was able to tie the history of the mutant in with the history of the debate about corn’s relationship to teosinte the wild grass from which we now know corn was domesticated.
• Context. Starting out by discussing phase change in model organisms like C. elegans, as well as phase change in humans (more commonly known as puberty) before bringing it back to corn.
• Tiny unexpected things. The one datapoint he presented to suggest the system he’d found in corn might also be functioning in eudicts wasn’t the usual model system for eudicts (Arabidopsis thaliana, the first plant to have its genome sequenced). It was watermelon. “I’ve always wanted a reason to work with watermelons.” It was only the second time I’ve seen any biologic data on watermelons. (The first was the result of a fascinating discussion with my roommate about phloem loading in the cucurbits (a group of species that includes melons, squash, pumpkins and cucumbers).)
• I’m sure there were lots of other things I didn’t even notice. Like housekeeping, it’s what’s left undone or done badly is much easier to notice than what is taken care of perfectly. <– I don’t know how the analogy to housekeeping entered my vocabulary, sounds more like something a person who was alive for the 1950s would use.

Studying plant genetics (and probably a lot of other scientific fields as well) means seeing a lot of presentations that are difficult to follow, even though they’re presenting fascinating data, but it also means seeing the occasion speaker who has mastered both the concepts and methods of his or her field as well the techniques used hook an audience.

This isn’t true just of public speaking. I’ve heard people complain (though I haven’t formed an opinion of my own on the subject), that the papers that get published in Science and Nature, the two most prestigious scientific journals out there, don’t always represent the biggest scientific breakthroughs, but rather great science that’s been done by people who are the best at writing papers accessible and interesting to people not working in the exact same field as the authors. I’m still too unexperienced as a scientist to know if this is a real bias, or just represents bitterness by people whose papers don’t get accepted, but you can see how it would make sense if it were true, can’t you?

Science and Nature are both read by highly educated scientists across a wide range of disciplines. If you and I both make discoveries of equal scientific merit, but my paper is written up in such a way that NO one outside of plant science will be able to make heads or tails of it, and yours has a chance of being read and understood by people working in everything from the phylogenetics of archaea to human medicine, and maybe even get a few anthropologists interested enough to skim the figures, obviously your paper should have a higher priority for being published in journals that reach the widest audiences (like Science and Nature).

It really isn’t fair, but people who can do the research, and then turn around and effectively communicate their results clearly do have an advantage in science. That’s why I’m trying to make notes of what keeps me engaged during the best talks. My one attempt so far to present the results of my own research was an only slightly mitigated disaster.

As just for the record, unless you’ve already decided you want a 100% teaching position, great communication skills are NOT a substitute for actually producing interesting data. They’re complementary goods, not substitutes.

But first of all, let’s do this the right way this time. Here’s the paper in Nature describing the soybean genome. Here’s one of the places you can download the entire sequence from. Hopefully that establishes, beyond a reasonable doubt, that the soybean genome has, in fact, been published.

The soybean genome has doubled twice since its last common ancestor with other published genomes like grape and arabidopsis. The genome paper dates the more recent duplication as ~13 million years old and the older as ~59 million years old. When I look at homeologous* regions in soybean from the most recent genome duplication, they look more conserved than comparable regions in corn which also underwent a whole genome duplication relatively recently (the maize genome paper estimated the date at 5-12 million years ago), when one would expect a slightly older duplication to be either less conserved, or at most indistigushable from the younger. Dating genome duplications is difficult to do precisely, it’s possible the maize duplication is older and the soybean younger than current measurements suggest. It’s also possible the difference is exaggerated because comparing homeologous maize chromosomes runs into issues with the waves of transposons that have washed over the maize genome in the past ten million years. The favorite explanation I’ve thought of so far is that the different selective pressures and/or reproductive strategies of the wild ancestors of corn and soybean favored or permitted higher loss of duplicate genes in maize or selected for the avoidance of any gene loss in soybean. No idea how to test any of these ideas though…

Comparison of four homologous regions in soybean resulting from the two tetraploidies described in the soybean genome paper. Top two and bottom two are related by the recent tetraploidy, and the top and bottom pairs are related by the older tetraploidy. To load this figure live in CoGe (where you can examine the quality of the blast hits, the identity of the genes and generally have fun) visit: http://tinyurl.com/ydh95oh

After a whole genome duplication, every single gene exists as two separate copes on two different chromosomes. Generally speaking two things can happen to a pair of genes. One possibility is that both copies will be retained for either dosage reasons** or because one copy will take on a new function a change called neofunctionalization, or because each of the new gene copies has specialized in part of the job of the original gene, a change called subfunctionalization. The other, generally more common fate of duplicated genes is that one disappears from the genome. Plant genomes are dynamic places (especially compared to animal genomes, but more on that later) and sequences that don’t provide some benefit aren’t preserved for long***. A lot of my own research has to do with how a genome sheds duplicate genes, and the biases in which kinds of genes are lost and which are preserved and I find it fascinating stuff.

Anyway, to all those involved in sequencing the soybean genome, thank you for giving me even more fascinating information to study.

Previous in depth post on soybeans.

*Homeologous regions are areas of the genome that started out as duplicate copies of the same part of the genome after a whole genome duplication, but have since been evolving on their own, usually in different directions.

**If one set of genes produces a protein that works together with many other genes, doubling all of them at once has no stong effect, but if only one gene loses its extra copy, the ratios of the different proteins could end up out of balance, harming the plant. Since it’s highly unlikely that one copy of all the genes involved would be deleted at the same time, the result is that deletions or serious mutations of any of the copies of any of the genes get selected against, and the plant keeps two copies of all the genes involved for longer than other types of genes.

Think of the genome as a restaurant where there’s one person for every job (we’ll simplify it down to just a hostess, and waitress and a cook). Though it wouldn’t in the real work, hypothetically this ratio works out perfectly, the hostess can seat people fast enough to keep the waitress busy but not overwelm her and the cook is constantly cooking but orders aren’t finished late.. If suddenly the owners decide to hire another person for every job so now there are two cooks, two hostesses, and two waiteresses, everything stays in balance. Twice as many people are seated, which is just enough to be handled by two waitresses, and two cooks exactly handle the doubling of orders. But if any one of our six hypothetical people calls in sick the system breaks down. If the hostess calls in sick not enough people are seated and the waitresses, and cooks spend a lot of time just standing around. If one of the waitresses is out, the one waitress has to try to deal with twice as many constomers as she can actually handle, customers aren’t happy because of the poor quality service, and the cooks and dishwashers are still underutilized. If one of the cooks doesn’t show up, people are seated and their orders get taken promptly, but food arrives late, the cook is stressed out, and the customers are unhappy again. If a cook, a waitress, and a hostess all didn’t show up on the same day, everything would be still be in balance, but since sick days (like knock out mutations of genes) occure independently of each other, anyone not showing up to work will be bad for the restuarant, and losing a gene that functions in a complex will be bad for a plant.

***Before anyone points out transposons as a counterexample of sequences that last a long time without, usually, providing a benefit to a plant, keep in mind that because transposons are self replicating, they generate lots of copies. Most of those copies don’t last for millions of years, and almost all those that do are mangled enough by point mutations and insertion deletions that they can no longer function. Similarly when scaning through the genome it’s common to spot pseudogenes. Bits of sequence that used to be a gene, but have been destroyed by

If I worked with arabidopsis or brachypodium, I’d probably have plants flowering this week that I’d be missing. Without the chance to make the crosses I needed to continue my research I might be set back a month or more while I waiting for new plants to grow. If I was mostly doing wet lab work, I wouldn’t fall as far behind assuming I’d gotten all my projects properly refrigerated or frozen before leaving for Thanksgiving, but the whole week I was gone would still be a complete loss.

Fortunately, I now study comparative genomics, which means, while I won’t get as much done this week as I normally would have, I’m definitely going to continue working. I’ve already shown off my workstation in the lab.

And here is where I’ll be working most of this week.

I’ve been advised, by people who’ve been doing a lot longer than I have, that working on a laptop long-term is a great way to burn out your hands (carpel tunnel), but for a week it’s no big deal. I can get more work done from here, thousands of miles away, than from an apartment a few blocked from the job, because the faster internet connection means I’m better able to access my own workstation (the first computer pictured), two of the my lab’s servers, and even a Linux box I left running in my apartment, all of which was using for different parts on my work on Monday.

If you look closely you’ll also notice one other difference between the permanent and temporary digs. Just for this week, I have a window!

The plant in question is studied internationally and while in America “corn” means those cool looking plants that you see me standing in front of one third of the time when you visit this blog, in british english the same word means any grain. I’ve never heard it explicitly said, but I assume the reason the geneticists who study the plant originally called it maize was to avoid confusion from those mixed definitions. It’s also possible “corn” was still considered a slang term back then, and not the sort of name a well educated scientist should be using regardless.

As a result of growing up in the midwest surrounded by corn and getting interested in comparative genomics by way of maize genetics, terms like “corn geneticist” and “corn genome” don’t sound right to my ear and ones like “maize plant” or “maize is selling for $5 a bushel” sound even worse. On the other hand, the sentence “Sequencing the maize genome is going to provide even more powerful tools to corn breeders” sounds fine, but I realize it can be confusing to people whose life experiences are different from my own.*

*An even weirder one: Back when I was still doing science that required writing with pen and paper instead of doing everything on the computer, without thinking about it I’d either cross my sevens or not depending on whether I was writing a number in a scientific context.

A crossed 7.

Theoretically a crossed 7 is easier to distinguish from a 1, especially on tassel bags and row stakes that are going to be outside, exposed to the elements for months. (And where a mistake has the potential to ruin a year or years of work. It’s not like maize geneticists can run down to Walmart and buy more seeds carrying the genotypes they’ve spent years putting together.)