Improving draft genome contiguity with reference-derived <i>in silico</i> mate-pair libraries

Grau, José Horacio; Hackl, Thomas; Koepfli, Klaus‐Peter; Hofreiter, Michael

doi:10.1093/gigascience/giy029

Cited by 22 publications

(32 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We assembled 2,350,959,615 base pairs (bp) of the narwhal nuclear genome (2,156,711,577 bp excluding missing data [N's]) with a scaffold N50 of 1,483,363 bp and contig N50 of 10,481 bp, in a total of 21,007 scaffolds. We used ∼100× coverage of multiple short insert and ∼32× of mate paired Illumina libraries and in silico mate paired libraries (Grau et al., 2018) constructed using the beluga reference genome (Jones et al., 2017) (Genbank: GCA_002288925.2) (Table S1). Investigations into the completeness of the assembly using Benchmarking Universal Single-Copy Orthologs (BUSCO) analyses and the mammalian BUSCO gene set showed a high level of complete BUSCO scores (93%) (Table S2), indicating a fairly complete and high-quality genome.…”

Section: Resultsmentioning

confidence: 99%

Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size

et al. 2019

View full text Add to dashboard Cite

Summary The narwhal ( Monodon monoceros ) is a highly specialized endemic Arctic cetacean, restricted to the Arctic seas bordering the North Atlantic. Low levels of genetic diversity have been observed across several narwhal populations using mitochondrial DNA and microsatellites. Despite this, the global abundance of narwhals was recently estimated at ∼170,000 individuals. However, the species is still considered vulnerable to changing climates due to its high specialization and restricted Arctic distribution. We assembled and annotated a genome from a narwhal from West Greenland. We find relatively low diversity at the genomic scale and show that this did not arise by recent inbreeding, but rather has been stable over an extended evolutionary timescale. We also find that the current large global abundance most likely reflects a recent rapid expansion from a much smaller founding population.

show abstract

Section: Resultsmentioning

confidence: 99%

Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size

et al. 2019

View full text Add to dashboard Cite

show abstract

“…However, as the assembly was scaffolded using in silico mate-pair libraries generated by a closely related species, it also has some limitations. The assembly could contain some mis-assemblies caused by changes in the genomic architecture of the fin and minke whale after they diverged ~10.5Ma [2] meaning it may be inadequate for the study of gene copy number variation, chromosomal structural variation, and synteny between species [13].…”

Section: Discussionmentioning

confidence: 99%

“…We trimmed Illumina adapter sequences from reads and removed reads shorter than 30bp using skewer [12]. From these trimmed reads we constructed in-silico mate paired library reads with insert sizes 1kb, 2kb, 5kb, 10kb, and 20kb using the repeatmasked minke whale genome as a reference (GCA_000493695.1) [11] and Cross-Species Scaffolding, specifying default parameters (100bp reads of ~10x coverage) [13]. Specific read numbers and information can be found in S1 Table.…”

Section: Methodsmentioning

confidence: 99%

Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids

2019

View full text Add to dashboard Cite

Fin whales (Balaenoptera physalus) and blue whales (B. musculus) are the two largest species on Earth and are widely distributed across the world’s oceans. Hybrids between these species appear to be relatively widespread and have been reported in both the North Atlantic and North Pacific; they are also relatively common, and have been proposed to occur once in every thousand fin whales. However, despite known hybridization, fin and blue whales are not sibling species. Rather, the closest living relative of fin whales are humpback whales (Megaptera novaeangliae). To improve the quality of fin whale data available for analysis, we assembled and annotated a fin whale nuclear genome using in-silico mate pair libraries and previously published short-read data. Using this assembly and genomic data from a humpback, blue, and bowhead whale, we investigated whether signatures of introgression between the fin and blue whale could be found. We find no signatures of contemporary admixture in the fin and blue whale genomes, although our analyses support ancestral gene flow between the species until 2.4–1.3 Ma. We propose the following explanations for our findings; i) fin/blue whale hybridization does not occur in the populations our samples originate from, ii) contemporary hybrids are a recent phenomenon and the genetic consequences have yet to become widespread across populations, or iii) fin/blue whale hybrids are under large negative selection, preventing them from backcrossing and contributing to the parental gene pools.

show abstract

“…For example, the reliability of analyses such as operon structure identification, gene regulation, and comparative genomic studies is enhanced by the availability of complete genomes. Additionally, the finishing process can substantially improve the quality of data available to the community by identifying and correcting incorrect assemblies and low coverage regions [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…Currently, several features of sequencing data, particularly increased depth of coverage and error reduction in sequencing libraries, are useful for genome finishing steps. Thus, draft genomes can be combined with additional information from new sequencing and mapping studies to reduce the effort of the finalization process [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

ImproveAssembly - Tool for identifying new gene products and improving genome assembly

2018

View full text Add to dashboard Cite

The availability of biological information in public databases has increased exponentially. To ensure the accuracy of this information, researchers have adopted several methods and refinements to avoid the dissemination of incorrect information; for example, several automated tools are available for annotation processes. However, manual curation ensures and enriches biological information. Additionally, the genomic finishing process is complex, resulting in increased deposition of drafts genomes. This introduces bias in other omics analyses because incomplete genomic content is used. This is also observed for complete genomes. For example, genomes generated by reference assembly may not include new products in the new sequence or errors or bias can occur during the assembly process. Thus, we developed ImproveAssembly, a tool capable of identifying new products missing from genomic sequences, which can be used for complete and draft genomes. The identified products can improve the annotation of complete genomes and drafts while significantly reducing the bias when the information is used in other omics analyses.

show abstract

Improving draft genome contiguity with reference-derived in silico mate-pair libraries

Cited by 22 publications

References 40 publications

Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size

Narwhal Genome Reveals Long-Term Low Genetic Diversity despite Current Large Abundance Size

Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids

ImproveAssembly - Tool for identifying new gene products and improving genome assembly

Contact Info

Product

Resources

About