![]() ![]() These findings demonstrate the necessity of sequencing technology that reads through GC-rich regions and generates long reads longer than the repeat units in a genome, to obtain the complete gene landscape. The main causes for these false losses were the inability or difficulty of short-read technologies to sequence through high GC content regions and difficulty in assembling repeat regions. Additionally, we discovered a strong bias of missing sequences and other errors in 5′ regulatory regions or protein-coding genes and long non-coding RNAs. ![]() We found thousands of genes completely or partially missing as false gene losses in the previous assemblies, many located in newly identified chromosomes. These species included a mammal (platypus), two birds (zebra finch, Anna’s hummingbird), and a fish (climbing perch). Here, we performed a more thorough evaluation of the new VGP references relative to previous popular reference assemblies. The resulting assemblies have among the highest contiguity metrics for vertebrate species to date, and preliminary analyses by the authors of this study discovered some sequences and genes missing in previous assemblies of the same species. The Phase 1 pipeline developed by the VGP included generating haplotype-phased contigs with PacBio continuous long reads (CLR) and scaffolding the contigs with 10X Genomics linked reads, Bionano Genomics optical maps, and Arima Genomics Hi-C reads. Utilizing and further developing these technologies, the Vertebrate Genomes Project (VGP) aims to generate as complete and error-free reference genome sequences as possible, ultimately of all extant vertebrate species. More recently, the development of long-read sequencing platforms (e.g., Pacific Biosciences and Oxford Nanopore), long-range scaffolding data (e.g., Bionano optical maps and Hi-C), and new algorithms, allow the generation of more complete and accurate higher-quality assemblies. Except for human and a few model species, many of these assemblies have been generated using cost-effective platforms with short reads that are a few hundred (<200 bp, mainly Illumina reads) to a thousand bp (~1 kbp, Sanger reads) in length. However, their completeness and accuracy varies. Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.Ī multitude of reference genome assemblies of diverse vertebrates have been reported in the literature. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies. The impact of missing sequences is biased towards GC-rich 5′-proximal promoters and 5′ exon regions of protein-coding genes and long non-coding RNAs. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna’s hummingbird), and a fish (climbing perch). A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. ![]()
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