Ohio University Assistant Professor of Environmental and Plant Biology Dr. Zhihua Hua has recently published two studies on how to convert genome sequencing data into meaningful biological information. One of the studies focuses on a new program he created that will allow biologists to find missing genes to better compare genomes in different plants, animals and humans, ultimately allowing scientists to better look at the evolution of certain genes.
The study demonstrates that while current genome programs leave 15% of genes undiscovered, this new program can discover them and gather a complete set. By gaining this whole set to study, researchers can compare multiple genomes of different organisms such as humans, rats and apes to see the evolution and differences between them.
“Genomics is one approach that allows us to identify and prioritize essential genes for further functional studies,” said Hua. “Therefore, by developing innovative genomic programs, we can effectively improve the problem-solving and discovery process in molecular biology and better compare genes."
The results of this program can help uncover previously unknown members of a gene family and help in analyzing the evolution of specific genes. This analysis can help scientists explore how genetic diseases have changed throughout history and look at similar organisms to see where the mutated genes come from and what they have in common.
Plant biologists can also take this information to compare the genetic makeup of diverse plants to help with efficiency when growing crops. By looking at the genes that make up specific plants, biologists can determine what does better in various environmental conditions, as well as study more about how certain crops evolved into others and how they could evolve further.
Hua developed this algorithm and program, called Closing-Target-Trimming (CTT), after he started looking for relatives of 700 F-box genes, which encode a protein that targets abnormal and unwanted proteins for degradation in all eukaryotic cells. From this study, he recognized that there were many undiscovered F-box members in sequenced genomes. The CTT program unveils the unreported genes by trimming away the genes that have been already reported.
He has been striving to transmit his research skills to students both in his lab and in his classes, as well as to the science community. Hua also recently published two programming packages, CTT and CTTdocker, that employ the Closing-Target-Trimming algorithm for discovering hidden superfamily members in any sequenced genomes.
This work has been recently published in two articles titled “Closing target trimming and CTTdocker programs for discovering hidden superfamily loci in genomes” and “Diversifying evolution of the ubiquitin-26S proteasome system in Brassicaceae and Poaceae” on PLoS ONE and International Journal of Molecular Sciences, respectively.