LIFE SCIENCE

The recommended index system for genome assembly quality evaluation was released


Recently, Wang Peng, a researcher at the Institute of Tropical Crop Variety Resources of the Chinese Academy of Tropical Agricultural Sciences, and Wang Fei, a doctor from Shanghai Institute of Technology, proposed a CC ratio (contig/chromosome logarithmic ratio) index to evaluate genome assembly continuity, and established a suggested index system for genome assembly quality evaluation. The system covers five aspects, including continuity, completeness, accuracy, heterozygosity, and organelle genome, with a total of 14 indicators, which solves the problem that there has been no comprehensive and unified assembly quality evaluation system in the field of genome for a long time. The paper was published as a cover article in the internationally renowned journal Trends in Genetics.

The paper was published as a cover article in Trends in Genetics. Photo courtesy of China Institute of Thermal Sciences

Genomics is an internationally popular discipline, but there has long been a debate in the academic circles about how to scientifically and comprehensively evaluate the quality of genome assembly. Since the completion of the Human Genome Project, scholars have proposed a number of indicators, but there has been no widely recognized genome assembly quality evaluation system.

The authors analyze the limitations of N50 in evaluating assembly continuity, as well as the problems of BUSCO indicators in evaluating genome integrity, and point out the widespread neglect of assembly accuracy, especially assembly structure, in genomic projects. In addition, organelle genomes such as mitochondria and chloroplasts are an indispensable part of the eukaryotic genome, and heterozygosity is a common problem in eukaryotic genomes, and most current genome projects lack the evaluation of the quality of these aspects. For these reasons, the authors established a quality evaluation system that established standards for the quality evaluation of genome assembly.

Wang Peng is the first and corresponding author, and Wang Fei is the co-corresponding author. This work is supported by the basic scientific research business funds of the central public welfare scientific research institutes and the national key research and development plan. (Source: Zhang Qingdan, China Science News)

Related paper information:https://doi.org/10.1016/j.tig.2022.10.005



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