Young sex chromosomes are very active

Posted 23 July 2013 by M. Wilson Sayres

Sex chromosomes are fascinating, and we still have so much to learn about how they originate and change over time. This last week I had the pleasure of talking to one of the leaders in the field, Deborah Charlesworth, about explaining sex chromosome evolution and genetics. I hope she'll forgive me for this simplification of a recent beautiful genetic analysis from her lab.

I study sex chromosomes in mammals (X and Y), but lots of other wonderful species have evolved chromosomal sex determination (instead of, say, using temperature or environmental cues to determine males and females).

One of those species is a lovely plant called Silene latifolia, also called a White Campion.

The plant, Silene latifolia, with sex chromosomes

This plant has very young sex chromosomes. Whereas the sex chromosomes in mammals look very different from each other (the X is large and full of genes, while the Y is small and gene-poor), the X and Y chromosomes of the Silene latifolia look more similar to each other. Moreover, while there is good evidence that the mammalian sex chromosomes started to differentiate from one another about 160 million years ago, the X and Y of Silene latifolia only started differentiating from one another 10-20 million years ago. This time can be estimated by comparing the number of differences between genes with one partner on the X and one partner on the Y (the longer the time since they started differentiating, the more differences will have accumulated between the once-identical X and Y sequences), and also by identifying which closely-related species have (or do not have) the same sex chromosome system. The very young sex chromosomes in Silene latifolia are exciting because they let us look at some of the changes that occur during the very early stages of sex chromosome evolution.

Bergero et al. (2013) studied the sex chromosomes of Silene latifolia, and compared those regions with a closely-related species without sex chromosomes (Silene vulgaris, the ugly stepsister-species), to learn about some

Just a quick reminder. The autosomes (non-sex chromosomes) can swap DNA anywhere. Most sex chromosomes, especially young sex chromosomes have a region that still swaps bits of DNA between the X and Y - this is called the pseudo-autosomal region, or PAR. The rest of the sex chromosomes, the sex-specific regions, cannot swap bits of DNA.

Bergero et al. (2013) did a lot of molecular genetics to better understand the sex-specific and the pseudoautosomal regions of the beautiful S. latifolia sex chromosomes. They found:

1. Single ancient source of the original S. latifolia X chromosome.
First, Bergero et al. (2013) found that the genes in the sex-specific regions are found in a single location in the sister species, suggesting that this sex-specific region evolved from a single ancestral autosomal ancestor (green blocks).

Like many sex chromosomes, the S. latifolia sex chromosomes have a sex-specific region and a pseudoautosomal region (not sex-specific).

2. Two independent additions to the S. latifolia X chromosome.
Looking at the pseudoautosomal region (PAR), Bergero et al. (2013) found that the genes in the S. latifolia PAR are found to reside in two unique regions on the autosomes in the sister species. Moreover, both of these sets of PAR genes are found in a different location from where the sex-specific genes cluster, suggesting they were added at different times (first the block of blue genes, and second the block of red genes).

There appears to have also been some rearrangement of the genes in the red and blue regions, but for simplicity, I'll keep them as blocks here.

3. X-Y differentiation is still very active.

Lastly, even though the additions (blue and red) were recent, Bergero et al. (2013) found some evidence that a portion of the additional blocks of genes that have a few unique X-variants and a few unique Y-variants, suggesting that the X-Y swapping stopped recently, or is in the process of stopping. This means that these regions are just now accumulating differences between the X and Y.

Sex chromosomes (some even younger than S. latifolia) exist in many other plants (e.g. papaya and strawberry). These systems let us learn how quickly sex chromosomes can evolve, and can shed light on how our own, old, sex chromosomes change over time.

2013 Jun 7. [Epub ahead of print]

Expansion of the Pseudoautosomal Region and Ongoing Recombination Suppression in the Silene latifolia Sex Chromosomes.

Bergero R, Qiu S, Forrest A, Borthwick H, Charlesworth D.

Source

University of Edinburgh, Institute of Evolutionary Biology.

6 Comments

John Harshman · 23 July 2013

There's an interesting literature on the homomorphic sex chromosomes of paleognath birds, showing among other things that cessation of recombination happened at different times in different regions, and also that different taxa have accumulated cessation events independently in different regions. Googling "ratite sex chromosome evolution" gets a fair number of relevant hits, if you aren't already acquainted.

M. Wilson Sayres · 23 July 2013

Yep, I wrote about them. :)

http://pandasthumb.org/archives/2013/04/emu-a-large-bir.html

Sylvilagus · 24 July 2013

Thanks so much for these posts. As a non-biologist I find this fascinating, educational and relatively easy to understand while still stretching my mind. A question: the degree of swapping and the timing of when swapping stopped correlate with location in the last diagram. Does transformation into a sex specific non swapping region have something to do with spatial distribution? Does it start at one end and move down the chromosome, as if some process were working its way down? Or is this merely an artifact of the timing of addition onto the chromosome, with newer added to the bottom progressively? But then why added only on to that one end? The progression down the chromosome puzzles me.

Actually, that was more than one question wasn't it?

M. Wilson Sayres · 24 July 2013

Sylvilagus said: Thanks so much for these posts. As a non-biologist I find this fascinating, educational and relatively easy to understand while still stretching my mind. A question: the degree of swapping and the timing of when swapping stopped correlate with location in the last diagram. Does transformation into a sex specific non swapping region have something to do with spatial distribution? Does it start at one end and move down the chromosome, as if some process were working its way down? Or is this merely an artifact of the timing of addition onto the chromosome, with newer added to the bottom progressively? But then why added only on to that one end? The progression down the chromosome puzzles me. Actually, that was more than one question wasn't it?

From what we currently understand, the expansion of the non-swapping proceeds out from either side of the region that currently doesn't swap. In this case, the first event (likely an inversion) appears to have occurred at or near the very end of the chromosome, so the only direction for it to continue is down the chromosome. We observe something similar in mammals, where all "strata" appear contiguous, with the oldest at one end, and the most recent at the other. However, this isn't always the case. In papaya, for example, the first strata appeared in the middle of the Y chromosome, so we expect the swapping to be stopped on either side of it. Chicken also appears to have non-linear strata, but this may have been due to rearrangements that happened in the chicken lineage.

https://www.google.com/accounts/o8/id?id=AItOawkJ0_Ke3ZSt4RDHdFbEAoEX-DzWA0cEwuY · 25 July 2013

What advantage does having sex chromosomes confer in this case?

M. Wilson Sayres · 25 July 2013

https://www.google.com/accounts/o8/id?id=AItOawkJ0_Ke3ZSt4RDHdFbEAoEX-DzWA0cEwuY said: What advantage does having sex chromosomes confer in this case?

There doesn't have to be an advantage. But, in this case, there likely is. In species with separate sexes, sex can be determined many ways including behavioral, environmental, or genetic. In the case of genetic sex determination, sex chromosomes don't necessarily evolve. But, if a sexually antagonistic allele (beneficial in one sex and harmful in the other) arises near the allele that determines sex, it would be advantageous to link those together, so that they always occur together. So, if an event occurs (like an inversion) that links these two alleles together and suppresses recombination between these two alleles and their counterparts on the other chromosome, so that the sexually antagonistic allele doesn't show up in the opposite sex where it is harmful, it might be quickly fixed in the population.