SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (<i>Hirundo rustica rustica</i>)

Formenti, Giulio; Chiara, Matteo; Poveda, Lucy; Françoijs, Kees−Jan; Bonisoli‐Alquati, Andrea; Canova, Luca; Gianfranceschi, L.; Horner, David Stephen; Saino, Nicola

doi:10.1101/374512

Cited by 6 publications

(3 citation statements)

References 52 publications

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“…Additionally, new scaffolding technologies, such as Bionano Genomics and high-throughput chromatin interaction mapping (Hi-C), allow the contigs to be assembled to the chromosome level (Burton et al, 2013;Lam et al, 2012). Recently, these technologies have been successfully applied in many genome projects (Formenti et al, 2019;Lind et al, 2019;Zhu et al, 2019), including several fishes (Cai et al, 2019;Ge et al, 2019;Gong et al, 2018;He et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

Zheng

Shao

Liu

et al. 2021

Molecular Ecology Resources

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The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

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Section: Introductionmentioning

confidence: 99%

Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

Zheng

Shao

Liu

et al. 2021

Molecular Ecology Resources

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“…We also removed reads shorter than 32 bp (MINLEN:32) or with an average quality score below 30 (AVGQUAL:30). We mapped the filtered read data to the European barn swallow (Hirundo rustica rustica) reference genome (Formenti et al, 2019) using bwa "mem" version 0.7.17 with default settings. We then sorted output BAM files and quantified mapping statistics using the samtools version 1.10 "sort" and "stat" tools, respectively.…”

Section: Variant Calling and Filteringmentioning

confidence: 99%

Sex‐linked genetic diversity and differentiation in a globally distributed avian species complex

et al. 2021

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Sex chromosomes often bear distinct patterns of genetic variation due to unique patterns of inheritance and demography. The processes of mutation, recombination, genetic drift and selection also influence rates of evolution on sex chromosomes differently than autosomes. Measuring such differences provides information about how these processes shape genomic variation and their roles in the origin of species. To test hypotheses and predictions about patterns of autosomal and sex‐linked genomic diversity and differentiation, we measured population genetic statistics within and between populations and subspecies of the barn swallow (Hirundo rustica) and performed explicit comparisons between autosomal and Z‐linked genomic regions. We first tested for evidence of low Z‐linked genetic diversity and high Z‐linked population differentiation relative to autosomes, then for evidence that the Z chromosome bears greater ancestry information due to faster lineage sorting. Finally, we investigated geographical clines across hybrid zones for evidence that the Z chromosome is resistant to introgression due to selection against hybrids. We found evidence that the barn swallow mating system, demographic history and linked selection each contribute to low Z‐linked diversity and high Z‐linked differentiation. While incomplete lineage sorting is rampant across the genome, our results indicate faster sorting of ancestral polymorphism on the Z. Finally, hybrid zone analyses indicate barriers to introgression on the Z chromosome, suggesting that sex‐linked traits are important in reproductive isolation, especially in migratory divide regions. Our study highlights how selection, gene flow and demography shape sex‐linked genetic diversity and underlines the relevance of the Z chromosome in speciation.

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“…The homogenate was passed through a 100 um nylon filter, fixed on ice for 30 minutes in 2 mL 100% ethanol, and centrifuged for 5 minutes at 2000 g. The resulting pellet was re-suspended in homogenization buffer and added to pre-warmed agarose to make 0.8% agarose plugs. High molecular weight DNA was extracted from the agarose plugs, labelled, stained, and imaged on a Bionano Saphyr system 40 . Further detail on de novo optical map assembly is given in Supplementary Note 2.…”

Section: Bionano Dna Isolation and Assemblymentioning

confidence: 99%

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

Tearle

et al. 2019

Preprint

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We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosomelevel genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. The very high quality of the assemblies from both sub-species enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought. MainAbout 10,000 years ago, cattle were domesticated from the aurochs which ranged across Eurasia and North Africa but are now extinct 1 . Modern day cattle belong to two subspecies, the humped zebu or indicine breeds (Bos taurus indicus) and the humpless taurine breeds (Bos taurus taurus), which arose from independent domestication events of genetically distinct aurochs populations 2 .During the last century, taurine breeds have been intensively selected for production traits, particularly milk and/or meat yield and quality, and generally have higher fertility than indicine breeds. European taurine breeds, such as Angus, have excellent carcass and meat quality, high fertility, and reach puberty early. These breeds have been imported by farmers around the world to improve or replace less-productive breeds. However, while European taurine animals are well adapted to temperate environments, they do not thrive and perform in hot, humid tropical environments with high disease and parasite burden.Indicine breeds originate from the Indus valley and later spread to Africa and across southeast Asia 3 . Between 1854 and 1926, the four indicine breeds, Ongole, Krishna, Gir and Gujarat, were imported into the United States and crossed with European taurine cattle to create the Brahman breed. Current US Brahman cattle retain ~10% of their genome of taurine origin 4 . Brahman have short, thick, glossy coat that reflects sunlight and loose skin that increases the body surface area exposed for cooling. While the Brahman are less productive and have lower fertility than taurine breeds, they have desirable traits, such as heat tolerance, and lower susceptibility to parasites such as ticks, and are disease and drought resistant 5 .We previously demonstrated a novel trio binning approach to assemble haplotypes of diploid individuals at the contig level. The quality of the contigs exceeded those of the best livestock reference genomes 6 . Here we present chromosome-level taurine (Angus) and indicine (Brahman) cattle ge...

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SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)

Cited by 6 publications

References 52 publications

Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

Sex‐linked genetic diversity and differentiation in a globally distributed avian species complex

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

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