A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species
This article has been Reviewed by the following groups
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
- Evaluated articles (GigaScience)
Abstract
We generated a reference genome for the Ural Owl ( Strix uralensis ) based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. The primary assembly had a size of 1.38 gigabase pairs (Gb), while the alternative assembly (i.e., the second haplotype) had a size of 1.3 Gb. The corresponding N50 was 90.1 Mb for the primary assembly and 17.0 Mb for the alternate assembly. The primary assembly achieved a compleasm BUSCO completeness of 99.94%, indicative of a high-quality genome. In addition, cell culture of progressive passages was evaluated as a tool for genetic resources. To this aim, a cell culture of the same Ural Owl individual was established from skin tissue. At passages 5 and 10, cells were harvested and investigated for possible nucleotide variants by analysing the karyotype and single nucleotide polymorphisms (SNPs) to investigate the effect of cell culture on mutation. Karyotyping confirmed the number of chromosomes and no large variants were observed, while SNP analysis revealed a minor presence of short variants over cell passages. The established reference genome is a valuable resource for ongoing conservation efforts but also generally for avian genomics research. Cell culture, on the other hand, requires more research to determine if progressive passages can be safely used in genomic research.
Article activity feed
-
AbstractBackground Reference genomes have a wide range of applications. Yet, we are from a complete genomic picture for the tree of life. We here contribute another piece to the puzzle by providing a high-quality reference genome for the Ural Owl (Strix uralensis), a species of conservation concern and efforts affected by habitat destruction and climate change.Results We generated a reference genome assembly for the Ural Owl based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. It figures amongst the best avian genome assemblies currently available (BUSCO completeness of 99.94 %). The primary assembly had a size of 1.38 Gb with a scaffold N50 of 90.1 Mb, while the alternative assembly had a size of 1.3 Gb and a scaffold N50 of 17.0 Mb. We show an exceptionally high repeat content (21.07 %) that is …
AbstractBackground Reference genomes have a wide range of applications. Yet, we are from a complete genomic picture for the tree of life. We here contribute another piece to the puzzle by providing a high-quality reference genome for the Ural Owl (Strix uralensis), a species of conservation concern and efforts affected by habitat destruction and climate change.Results We generated a reference genome assembly for the Ural Owl based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. It figures amongst the best avian genome assemblies currently available (BUSCO completeness of 99.94 %). The primary assembly had a size of 1.38 Gb with a scaffold N50 of 90.1 Mb, while the alternative assembly had a size of 1.3 Gb and a scaffold N50 of 17.0 Mb. We show an exceptionally high repeat content (21.07 %) that is different from those of other bird taxa with repeat extensions. We confirm a Strix characteristic chromosomal fusion and support the observation that bird microchromosomes have a higher density of genes, associated with a reduction in gene length due to shorter introns. An analysis of gene content provides evidence of changes in the keratin gene repertoire as well as modifications of metabolism genes of owls. This opens an avenue of research if this is related to flight adaptations. The population size history of the Ural Owl decreased over long periods of time with increases during the Eemian interglacial and stable size during the last glacial period. Ever since it is declining to its currently lowest effective population size. We also investigated cell culture of progressive passages as a tool for genetic resources. Karyotyping of passages confirmed no large variants, while a SNP analysis revealed a low presence of short variants across cell passages.Conclusions The established reference genome is a valuable resource for ongoing conservation efforts, but also for (avian) comparative genomics research. Further research is needed to determine whether cell culture passages can be safely used in genomic research.
This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giaf106), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:
Reviewer 2: Luohao Xu
This manuscript provides a high-quality genome of Ural owl which is of evolutionary and ecological importance, as well as cell cultures that is worth exploration for endangered species. But Oral owl does not seem to be an endangered species?
One chromosomal fusion was identified, but it is very important to specific which chromosome. The chromosomes are very conserved in birds. The authors should follow the chromosome nomenclature according to chicken chromosome homology (http://pnas.org/doi/10.1073/pnas.2216641120).
"bird microchromosomes have a higher density of genes" is already known for 20 years, so no need to confirm again.
It is very speculative to link karatin gene expansions to flight adaptions. I suggest to revise this statement throughout the manuscript.
The first paragraph lacks any citations. And the statements are not fully accurate because there are already reference genomes in Strigiformes (owls), some of which were generated by the bioEarch project.
L120, I don't think this is true?
L131, remove million?
L158, again, the authors need to make sure that those chromosomes are homologous to chicken chromosomes. It is known that the 10 smallest microchromosomes are difficult for assembly due to HiFi sequencing dropout (Huang 2023 PNAS). I am curious whether the 10 smallest microchromosomes (or dot chromosomes) have been correctly assembled? The figure 3 does not seem to show this information.
For the 17 lost genes, are they lost in all reference genomes, or just "supported by more than one reference genome" (L260)?
It is not surprising to me that kerain, immune and olfactory receptor genes are independently expanded in different bird lineages.
L284-285, this statement is not true, because females also have a Z chromosome. Maybe the sequence coverage of the Z chromosome can be used to confirm the sex.
L361, cite B10K publications.
L370, "identified" should be "confirmed"?
L378, this is a bit misleading, because it is clear that barn owls have microchromosomes.
L382, "mainly composed of centromeric satellite DNA", and L387-388 are not true. LINEs the LTRs should still be the major repeat contents.
L395-396, "In birds, microchromosomes possibly originate from chromosome fission.", this is not true, again see Huang 2023 PNAS.
The paragraph starting from L394 is already well know. No need to discuss this. Overall, the discussion part needs to be streamlined, including the paragraph at L434 and L455
-
AbstractBackground Reference genomes have a wide range of applications. Yet, we are from a complete genomic picture for the tree of life. We here contribute another piece to the puzzle by providing a high-quality reference genome for the Ural Owl (Strix uralensis), a species of conservation concern and efforts affected by habitat destruction and climate change.Results We generated a reference genome assembly for the Ural Owl based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. It figures amongst the best avian genome assemblies currently available (BUSCO completeness of 99.94 %). The primary assembly had a size of 1.38 Gb with a scaffold N50 of 90.1 Mb, while the alternative assembly had a size of 1.3 Gb and a scaffold N50 of 17.0 Mb. We show an exceptionally high repeat content (21.07 %) that is …
AbstractBackground Reference genomes have a wide range of applications. Yet, we are from a complete genomic picture for the tree of life. We here contribute another piece to the puzzle by providing a high-quality reference genome for the Ural Owl (Strix uralensis), a species of conservation concern and efforts affected by habitat destruction and climate change.Results We generated a reference genome assembly for the Ural Owl based on high-fidelity (HiFi) long reads and chromosome conformation capture (Hi-C) data. It figures amongst the best avian genome assemblies currently available (BUSCO completeness of 99.94 %). The primary assembly had a size of 1.38 Gb with a scaffold N50 of 90.1 Mb, while the alternative assembly had a size of 1.3 Gb and a scaffold N50 of 17.0 Mb. We show an exceptionally high repeat content (21.07 %) that is different from those of other bird taxa with repeat extensions. We confirm a Strix characteristic chromosomal fusion and support the observation that bird microchromosomes have a higher density of genes, associated with a reduction in gene length due to shorter introns. An analysis of gene content provides evidence of changes in the keratin gene repertoire as well as modifications of metabolism genes of owls. This opens an avenue of research if this is related to flight adaptations. The population size history of the Ural Owl decreased over long periods of time with increases during the Eemian interglacial and stable size during the last glacial period. Ever since it is declining to its currently lowest effective population size. We also investigated cell culture of progressive passages as a tool for genetic resources. Karyotyping of passages confirmed no large variants, while a SNP analysis revealed a low presence of short variants across cell passages.Conclusions The established reference genome is a valuable resource for ongoing conservation efforts, but also for (avian) comparative genomics research. Further research is needed to determine whether cell culture passages can be safely used in genomic research.
This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giaf106), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:
Reviewer 1: Jianbo Jian
The authors provide a high-quality reference genome for the Ural Owl (Strix uralensis), these genomic resources are valuable for conservation and evolution. The manuscript is well-written, and the scientific story with cell culture for conservation is interesting. I have some questions or comments as following: 1、 in abstract， the N50 is contig or scaffold？ 2、For the GenomeScope analysis, the estimated genome size is 1.29 Gb with low heterozygosity (0.2%). The assembled genome size is 1.38 Gb. Could there be duplicated genome sequences in the assembly, or did the genome survey evaluation exclude some k-mers? What were the parameters used in GenomeScope2 (e.g., was the -h parameter set to its default value)? 3、How do you perform the decontamination？ 4、For the Hi-C contact map, due to some chromosomes are considerably larger while others are much smaller, it is suggested that the larger chromosomes could be displayed independently from the smaller ones to enhance clarity and interpretation.
-
