What Lurks in This Flower’s Bizarrely Large Y Chromosome?

The vast majority of plants are hermaphrodites, with both male and female reproductive parts. Oaks, some orchids, the potted spider plant in your office — they’re all capable of reproducing without a member of another sex nearby.

“It makes sense if you are an organism that can’t run around and find mates,” said Deborah Charlesworth, a population geneticist at the University of Edinburgh who has studied the reproductive strategies of plants for decades.

But some plants have taken a different approach. They have evolved sex chromosomes, the bits of DNA that make individual plants either male or female. In that club are organisms like the ginkgo, whose females produce stinky fruits, while males are stink-free. Or consider the asparagus, whose females produce red berries and thinner stalks than males.

Some of these species are stranger yet: Their sex chromosomes are bizarrely outsized. The diminutive white campion plant, for instance, packs a Y chromosome that is bigger than the entire genome of the puffer fish or that of the fruit fly. In the journal Science on Thursday, collaborating researchers, including Dr. Charlesworth, have published a full sequence of the white campion’s beefy Y chromosome, allowing a closer look at its contents and evolutionary history.

DNA sequencing is commonplace these days. But in the 1990s, when fast sequencing technology was new and fueling a revolution in biology, scientists could not use it effectively on the Y chromosomes of plants, said Gabriel Marais, a biologist at Université Claude Bernard Lyon 1 in France and a senior author of the new paper.

That’s because the techniques used to sequence the rest of the genome do not work well on Y chromosomes, which tend to have many of the same sequences repeated over and over. Slicing up the Y chromosome, sequencing the fragments and trying to piece them together like a puzzle — which works so well with the rest of the genome — yields so many identical pieces that it is impossible to assemble the larger picture.

In the last decade, however, the arrival of another form of sequencing has made it possible to try again.

No slicing and dicing is required, allowing long, intact stretches of the chromosomes to be deciphered. In the new paper, Dr. Marais and his colleagues used the technique on the white campion’s Y. Then, they sequenced the sex chromosomes of male plants they found that exhibited mutations and pinpointed genes playing different roles in making them male. Some genes suppressed female traits. Others encouraged male ones, influencing processes like flower development and pollen production.

The findings may explain why the white campion’s Y chromosome is such a mammoth: Preserving these genes and others like them might have taken priority over keeping the chromosome compact, Dr. Charlesworth said. Much of the Y’s bulk is made up of pieces of DNA that have a tendency to duplicate themselves, in an endless copy-and-paste fest.

In many organisms, X and Y chromosomes can jettison extra material during DNA-swapping sessions with each other. But the campion lost much of its ability to tidy up large parts of its sex chromosomes this way long ago, perhaps in part because swapping could endanger the integrity of these genes. Over time, this idea goes, more and more material would have built up, leading to an outlandishly large chromosome hoard.

Understanding how plants that have developed two sexes determine which plant becomes male or female has implications beyond scientific curiosity. Many crop plants fall into that category, including figs, papayas, grapes and others. Cannabis has a particularly ancient system for determining sex, Dr. Charlesworth noted, two or three times older than that in white campion.

Curiously, the researchers were able to deduce that there have been several bursts of growth in the chromosome’s existence over the last 11 million years. What drove those bursts is still a mystery. They hope that future work, as well as identifying more genes driving sex differences, may illuminate more about how this Y chromosome grew so gigantic.