Researchers are developing software with improved genome sequencing capabilities for better plant breeding

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A new software tool with enhanced genome sequencing capabilities has been developed by the University of Adelaide, increasing the speed and accuracy with which researchers can improve plants through breeding.

These improvements will enable farmers to grow more resilient crops in a dynamically changing climate and landscape.

The tool, called CoreDetector, was created to efficiently perform more computationally challenging genome sequencing tasks, such as aligning large and evolutionarily diverse plant genomes.

“Whole genome alignments of species remain an important method for determining structural and sequence variations of populations,” said Dr Julian Taylor of the University of Adelaide, who co-led the project.

“Few tools have the functionality to handle large and evolutionarily diverse genomes, but CoreDetector leverages the power of computational parallelization to take on the cumbersome task of pairwise sequence alignment between population member genomes.

“The tool can be applied to a wide range of species – from kilobyte bacterial genomes to gigabyte plant genomes, such as wheat – and even supports diploid organisms, such as humans and other animals.”

CoreDetector’s underlying research was published in Bioinformaticsand the software is also published on GitHub, making it free and accessible to anyone who can benefit from it.

This will provide immediate benefits to the plant pre-breeding and breeding research community, especially those working with more complex plant genomes.

The software is Java-based and easily portable between operating systems.

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“As high-throughput sequencing technologies become more sophisticated and more species can be sequenced, we believe open access to CoreDetector will continue to enable rapid advances in genetic research of diverse populations,” said the university’s Dr. Fruzangohar, who also co-led of the research. project.

“This will provide an efficient genome sequence analysis tool for plant breeders and researchers, which can form part of an analytical pipeline for improving our genetic understanding of biological organisms.”

Dr. Taylor and Dr. Fruzangohar are members of the Biometry Hub, within the university’s School of Agriculture, Food and Wine. The Hub was created to provide a space for researchers to collaboratively develop statistical models and computational tools, such as CoreDetector, to answer industry-relevant biological questions.

Although CoreDetector has only recently been made publicly available, Dr. Taylor and Dr. Fruzangohar is already working on the next iteration of the technology.

“We aim to extend the theoretical and computational framework of CoreDetector to obtain the core genome plus additional sequences of a population. This complete set of sequences is known as the pan-genome,” said Dr. Taylor.

“We plan to collaborate with other bioinformaticians from external organizations involved in pan-genome research and develop an advanced heuristic algorithm to efficiently construct pan-genomes of populations.”

More information:
Mario Fruzangohar et al, CoreDetector: a flexible and efficient program for core genome alignment of evolutionarily diverse genomes, Bioinformatics (2023). DOI: 10.1093/bioinformatics/btad628

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