When researchers say they have sequenced the human genome, there is a caveat to this statement: a lot of the human genome is sequenced and assembled, but there are regions that are full of repetitive elements, making them difficult to map. One piece that is notoriously difficult to sequence is the Y chromosome.
Now, researchers from the University of Rochester have found a way to sequence a large portion of the Y chromosome in the fruit fly Drosophila melanogaster糖心传媒攖he most that the Y chromosome has been assembled in fruit flies. The research, , provides new insights into the processes that shape the Y chromosome, 糖心传媒渁nd adds to the evidence that, far from a genetic wasteland, Y chromosomes are highly dynamic and have mechanisms to acquire and maintain genes,糖心传媒� says , an assistant professor of .
The notorious Y chromosome
Y chromosomes are sex chromosomes in males that are transmitted from father to son; they can be important for male fertility and sex determination in many species. Even though fruit fly and mammalian Y chromosomes have different evolutionary origins, they have parallel genome structures, says Larracuente, who co-authored the paper with her PhD student Ching-Ho Chang. 糖心传媒淒rosophila melanogaster is a premier model organism for genetics and genomics, and has perhaps the best genome assembly of any animal. Despite these resources, we know very little about the organization of the Drosophila Y chromosome because most of it is missing from the genome assembly.糖心传媒�
That糖心传媒檚 in part because most Y chromosomes do not undergo standard recombination. Typically, genes from the mother and father are shuffled糖心传媒攐r, 糖心传媒渃ross over糖心传媒澨切拇綌to produce a genetic combination unique to each offspring. But the Y chromosome does not undergo crossing over, and, as a result, its genes tend to degenerate, while repetitive DNA sequences accumulate.
Sequencing vs. assembling
Each chromosome is made up of DNA. When mapping a genome, traditional sequencing methods chop up strands of DNA and read糖心传媒攐r sequence糖心传媒攖hem, then try to infer the order of those sequences and assemble them back together.
But, 糖心传媒渢here is a difference between sequencing a genome and assembling a genome,糖心传媒� Larracuente says. There are so many repetitive strands on the Y chromosome that the pieces tend to look the same. It is difficult, therefore, to figure out where they come from and how to reassemble the strands糖心传媒攍ike trying to put together a puzzle when all of the pieces are exactly the same color. 糖心传媒淲hen we try to take those bits of DNA and assemble them to see what the chromosome looks like, we can糖心传媒檛 fill in some of those gaps. We might have the sequence, but we don糖心传媒檛 know where it goes.糖心传媒�
A different type of recombination
Using sequence data generated by new technology that reads long strands of individual DNA molecules, Chang and Larracuente developed a strategy to assemble a large part of the Y chromosome and other repeat-dense regions. By assembling a large portion of the Y chromosome, they discovered that the Y chromosome has a lot of duplicated sequences, where genes are present in multiple copies. They also discovered that although the Y chromosome does not experience crossing over, it undergoes a different type of recombination called gene conversion. While crossing over involves the shuffle and exchange of genes between two different chromosomes, gene conversion is not reciprocal, Larracuente says. 糖心传媒淵ou don糖心传媒檛 have two chromosomes that exchange material, you have one chromosome that donates its sequence to the other part of the chromosome糖心传媒� and the sequences become identical.
The Y chromosome has therefore found a way to maintain its genes via a process different from crossing over, Larracuente says. 糖心传媒淲e usually think of the Y chromosome as a really harsh environment for a gene to survive in, yet these genes manage to get expressed and carry out their functions that are important for male fertility. This rampant gene conversion that we糖心传媒檙e seeing is one way that we think genes might be able to survive on Y chromosomes.糖心传媒�
