A new, less expensive, and faster method now has been developed and used to determine the DNA sequence of the male-specific Y chromosome in the gorilla. The technique will allow better access to genetic information of the Y chromosome of any species and thus can be used to study male infertility disorders and male-specific mutations. It also can aid in conservation genetics efforts by helping to trace paternity and to track how males move within and between populations in endangered species, like gorillas.
A paper describing the method and the discovery resulting from its use in comparing the sequence of the gorilla Y chromosome to the sequences of the human and chimpanzee Y chromosomes will be published on March 2, 2016 in the Advance Online edition of the journal Genome Research. The article also will be published in the April 2016 print issue of the journal.
The Y chromosome of mammals is incredibly difficult to sequence for a number of reasons. One reason is that the Y chromosome is present in only one copy and makes up only about one to two percent of the total genetic material found in a cell of a male. To reduce this difficulty, the researchers used an experimental technique called flow-sorting to preferentially select the Y chromosome for sequencing based on the chromosome’s size and genetic content.
The Y chromosome, like all DNA, is composed of a series of molecules called “bases” that are represented by the letters A, T, C, and G. Current genetic sequencing technologies produce “reads” of sequence that are much shorter than the entire length of the chromosome. These reads need to be placed in order and pieced together by finding places where they overlap into longer and longer chunks. The research team used two different sequencing technologies to help with this assembly of the DNA sequence of the Y chromosome.
One sequencing technology used by the researchers produces massive amounts of very short reads—about 150 to 250 bases in length. Using this method, the researchers sequenced enough reads to cover the entire length of the Y chromosome about 450 times. The researchers assembled these short reads into longer chunks that they then further connected using the second sequencing technology that produces longer reads—about seven thousand bases in length on average.
Another reason that determining the genetic sequence of the Y chromosome is so difficult is that it is composed of an unusually high number of repeated sequences—regions where the sequence of As, Ts, Cs, and Gs are identical, or nearly identical, for thousands or millions of bases in a row. Many of these repeats, including some genes, appear as back-to-back series of the same repeated sequence or as long palindromes which, like the word “racecar,” read the same forward and backward. The researchers used an experimental technique—”droplet digital polymerase chain reaction”—to determine the number of copies of the genes that appear in these series.
To demonstrate the utility of the gorilla Y chromosome sequence they generated, the researchers designed genetic markers that can be used to differentiate the genetic relatedness among male gorillas and thus to aid in conservation genetics efforts targeted at preserving this endangered species.