The genomes of hybrid plants and animals are complex. A biologist has discovered a method for determining their parent species. If you’ve ever had a garden, you’ve probably come across hybrids, which range from disease-resistant tomatoes to Stargazer lilies
Hybrids, which are common in agriculture and nature, have chromosomes from two or more parent species. These disparate parental chromosomes become doubled in some cases, including strawberries, goldfish, and several other species, a condition known as allopolyploidy.
Binghamton University Assistant Professor of Biological Sciences Adam Session and Daniel S. Rokhsar, a professor of genetics, evolution, and development at the University of California, Berkeley, outline a method to trace these genomes back to the polyploid hybrid’s parent species in “Transposon signatures of allopolyploid subgenome evolution,” a recent article published in the journal Nature Communications.
Unlike previous methods that rely on comparisons with related non-hybrid species to determine polypoid ancestry, the authors’ method allows them to discover distinct ancestries by examining genomic patterns in the hybrid itself.
Each ancestral genome contains a distinct set of repetitive elements. So if we find sets of chromosomes in a polypoid that carry different repetitive elements, that proves hybrid ancestry and allows us to figure out which chromosomes were inherited together coming from the various progenitor species.
Adam Session
“Each ancestral genome contains a distinct set of repetitive elements,” Session said. “So if we find sets of chromosomes in a polypoid that carry different repetitive elements, that proves hybrid ancestry and allows us to figure out which chromosomes were inherited together coming from the various progenitor species.”
In the article, they apply the method to some well-studied cases of polyploid hybrids, such as tobacco, cotton, and cyprinid fish, such as goldfish and carp. They also use it to tease out the disputed ancestors of other hybrids, such as false flax and strawberries.
“In many cases, the ancestors of living polyploids are not known. Using our method, we can figure out the ancestral origin of different chromosomes just by studying the polyploid genome itself, and divide the chromosomes into sets, or ‘sub-genomes,’ derived from its various ancestors,” he said. “In addition to identifying the subgenomes, we can also tell you the order in which they were put together.”
Polyploidization, or the duplication of genomes in a hybrid that stabilises its ancestry, is much more common in plants than in animals, Session explained, because plants can tolerate multiple copies of their genomes better. Polyploidization is more common in animal species, though it does occur in some fish and amphibians. The authors demonstrate for the first time in the case of goldfish that they share the same duplicated gene sequences as common carp, and thus a common hybrid ancestor.
Mammals do not have polyploidy, but hybridization is still possible. Consider mules, which are a cross between horses and donkeys: Male mules are sterile, but female mules can mate with either parent species. However, the distinct hybrid type cannot be stably propagated in the absence of genomic duplication.
Cotton is a tetraploid, with four copies of each chromosome, two from each of two ancestors, whereas false flax is a hexaploid, with six chromosomes derived from three parent species. An octoploid, such as strawberry, has four ancestral species because it has eight copies of each chromosome.
Polyploids have a complex biology that is still being unravelled, and determining the sub-genome structure of their genomes is a significant step forward. The genes contributed by each of the parental species evolve in their new polyploid context over millions of years. Some redundant genes are lost or inactivated, while others develop new functions or interact in novel ways with their counterparts in other sub-genomes. According to the new research, the order in which parental species are introduced into the emerging polyploid mix in a higher polyploid like strawberry can have a significant impact on how these evolutionary processes occur. The authors stated that determining the impact of these duplicates on the evolving polyploid is an ongoing challenge.
“Understanding polyploid genome evolution as a whole is important to the wider field of plant biology,” Session said. “Many important crops like maize and emerging biofuel crops like miscanthus and switchgrass are affected by this process, and we hope to take advantage of their genomic flexibility to breed new and improved varieties.”
