Journal
GENOME BIOLOGY
Volume 23, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-022-02764-1
Keywords
False duplication; Assembly error; Phasing error; De novo assembly; Vertebrate genome project
Funding
- Marine Biotechnology Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) - Ministry of Ocean and Fisheries (MOF), Republic of Korea [20180430]
- Howard Hughes Medical Institute (HHMI)
- Program for Agriculture Science and Technology Development of the Rural Development Administration (RDA), Republic of Korea [PJ0133402]
- National Research Foundation of Korea (NRF) - Korea government (MSIT) [2021R1A2C2094111]
- Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health [1ZIAHG200398]
- National Research Foundation of Korea [2021R1A2C2094111] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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This study quantifies false duplications in previous genome assemblies for platypus, zebra finch, and Anna's Hummingbird, and highlights the need for more advanced assembly methods and cautious gene gain analysis. The main source of false duplications is heterotype duplications, while a minor source is sequencing errors. The study emphasizes the importance of accurately separating haplotypes and sequence errors in genome assemblies.
Background False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna's Hummingbird, and their new counterparts of the same species generated by the Vertebrate Genomes Project, of which the Vertebrate Genomes Project pipeline attempted to eliminate false duplications through haplotype phasing and purging. These assemblies are among the first generated by the Vertebrate Genomes Project where there was a prior chromosomal level reference assembly to compare with. Results Whole genome alignments revealed that 4 to 16% of the sequences are falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These lead to overestimated gene family expansions. The main source of the false duplications is heterotype duplications, where the haplotype sequences were relatively more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source is sequencing errors. Ancient ATP nucleotide binding gene families have a higher prevalence of false duplications compared to other gene families. Although present in a smaller proportion, we observe false duplications remaining in the Vertebrate Genomes Project assemblies that can be identified and purged. Conclusions This study highlights the need for more advanced assembly methods that better separate haplotypes and sequence errors, and the need for cautious analyses on gene gains.
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