scholarly journals High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

2018 ◽  
Author(s):  
Marijke Autenrieth ◽  
Stefanie Hartmann ◽  
Ljerka Lah ◽  
Anna Roos ◽  
Alice B. Dennis ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Bos Taurus ◽  
Demographic History ◽  
Harbour Porpoise ◽  
Population History ◽  
Whole Genome Sequence ◽  
Phocoena Phocoena ◽  
Total Size ◽  
High Level

AbstractThe harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found in waters across the Northern hemisphere. It occurs in coastal water and inhabits water basins that vary broadly in salinity, temperature, and food availability. These diverse habitats could drive differentiation among populations. Here we report the first harbour porpoise genome, assembled de novo from a Swedish Kattegat individual. The genome is one of the most complete cetacean genomes currently available, with a total size of 2.7 Gb and 50% of the total length found in just 34 scaffolds. Using the largest 122 scaffolds, we were able to validate a high level of homology to the chromosome-level genome assembly of the closest related species for which such resource was available, the domestic cattle (Bos taurus). The draft annotation comprises 22,154 predicted gene models, which we further annotated through matches to the NCBI nucleotide database, GO categorization, and motif prediction. To infer the adaptive abilities of this species, as well as their population history, we performed a Bayesian skyline analysis, and produced results that are concordant with the demographic history of this species, including expansion and fragmentation events. Overall, this genome assembly, together with the draft annotation, represents a crucial addition to the limited genetic markers currently available for the study of porpoises and Phocoenidae conservation, phylogeny, and evolution.

scholarly journals Applicability of the Mutation–Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans

2019 ◽  
Vol 36 (8) ◽  
pp. 1701-1710 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J Balick ◽  
Christopher Cassa ◽  
Jack A Kosmicki ◽  
Mark J Daly ◽  
...  
Keyword(s):  
Population Genetics ◽  
De Novo ◽  
Demographic History ◽  
Purifying Selection ◽  
Population History ◽  
Balance Model ◽  
Data Set ◽  
Stochastic Force ◽  
Drift Estimation ◽  
Human Genes

Abstract The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation–selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation–selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.

scholarly journals A high-quality de novo genome assembly from a single parasitoid wasp

2020 ◽  
Author(s):  
Xinhai Ye ◽  
Yi Yang ◽  
Zhaoyang Tian ◽  
Le Xu ◽  
Kaili Yu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Parasitoid Wasp ◽  
Genome Comparison ◽  
Single Individual ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Low Input ◽  
A Genome ◽  
High Level

AbstractSequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Although few studies sequenced a single small insect with about 100 ng DNA as input, it may still be challenging for many small organisms to obtain such amount of DNA from a single individual. Here, we use 20 ng DNA as input, and present a high-quality genome assembly for a single haploid male parasitoid wasp (Habrobracon hebetor) using Nanopore and Illumina. Because of the low input DNA, a whole genome amplification (WGA) method is used before sequencing. The assembled genome size is 131.6 Mb with a contig N50 of 1.63 Mb. A total of 99% Benchmarking Universal Single-Copy Orthologs are detected, suggesting the high level of completeness of the genome assembly. Genome comparison between H. hebetor and its relative Bracon brevicornis shows a high-level genome synteny, indicating the genome of H. hebetor is highly accurate and contiguous. Our study provides an example for de novo assembling a genome from ultra-low input DNA, and will be used for sequencing projects of small sized species and rare samples, haploid genomics as well as population genetics of small sized species.

scholarly journals A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection

2019 ◽  
Author(s):  
Mats E. Pettersson ◽  
Christina M. Rochus ◽  
Fan Han ◽  
Junfeng Chen ◽  
Jason Hill ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Genome Assembly ◽  
Large Scale ◽  
De Novo ◽  
Hybrid Approach ◽  
Ecological Adaptation ◽  
Atlantic Herring ◽  
Total Size ◽  
Bony Fishes ◽  
Chromosome Level

ABSTRACTThe Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining ade novoPacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.

scholarly journals A near complete genome for goat genetic and genomic research

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Ran Li ◽  
Peng Yang ◽  
Xuelei Dai ◽  
Hojjat Asadollahpour Nanaei ◽  
Wenwen Fang ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Genetic Research ◽  
Genomic Research ◽  
Dairy Goat ◽  
De Novo Genome Assembly ◽  
Important Species ◽  
Long Read ◽  
High Level

Abstract Background Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds. Results Here, we present a very high-quality de novo genome assembly, Saanen_v1, from a male Saanen dairy goat, with the first goat Y chromosome scaffold based on 117× PacBio long-read sequencing and 118× Hi-C data. Saanen_v1 displays a high level of completeness thanks to the presence of centromeric and telomeric repeats at the proximal and distal ends of two-thirds of the autosomes, and a much reduced number of gaps (169 vs. 773). The completeness and accuracy of the Saanen_v1 genome assembly are also evidenced by more assembled sequences on the chromosomes (2.63 Gb for Saanen_v1 vs. 2.58 Gb for ARS1), a slightly increased mapping ratio for transcriptomic data, and more genes anchored to chromosomes. The eight putative large assembly errors (1 to ~ 7 Mb each) found in ARS1 were amended, and for the first time, the substitution rate of this ruminant Y chromosome was estimated. Furthermore, sequence improvement in Saanen_v1, compared with ARS1, enables us to assign the likely correct positions for 4.4% of the single nucleotide polymorphism (SNP) probes in the widely used GoatSNP50 chip. Conclusions The updated goat genome assembly including both sex chromosomes (X and Y) and the autosomes with high-resolution quality will serve as a valuable resource for goat genetic research and applications.

scholarly journals Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Yu Xing ◽  
Yang Liu ◽  
Qing Zhang ◽  
Xinghua Nie ◽  
Yamin Sun ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Genetic Improvement ◽  
De Novo ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
High Quality ◽  
Chinese Chestnut ◽  
Castanea Mollissima

AbstractBackgroundThe Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.FindingsWe produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.ConclusionsThe high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

scholarly journals A de novo genome assembly and annotation of the southern flying squirrel (Glaucomys volans)

2021 ◽  
Author(s):  
Jesse F Wolf ◽  
Jeff Bowman ◽  
Sonesinh Keobouasone ◽  
Rebecca S Taylor ◽  
Paul J Wilson
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Demographic History ◽  
Secondary Contact ◽  
Glaucomys Volans ◽  
Widespread Species ◽  
Short Read ◽  
Flying Squirrel ◽  
Flying Squirrels ◽  
Southern Flying Squirrel

Northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels are widespread species distributed across much of North America. Northern flying squirrels are common inhabitants of the boreal forest, also occurring in coniferous forest remnants farther south, whereas the southern flying squirrel range is centered in eastern temperate woodlands. These two flying squirrel species exhibit a hybrid zone across a latitudinal gradient in an area of recent secondary contact. Glaucomys hybrid offspring are viable and can successfully backcross with either parental species, however, the fitness implications of such events are currently unknown. Some populations of G. sabrinus are endangered, and thus, interspecific hybridization is a key conservation concern in flying squirrels. We sequenced and assembled a de novo long-read genome from a G. volans individual sampled in southern Ontario, Canada, while four short-read genomes (2 G. sabrinus and 2 G. volans, all from Ontario) were re-sequenced on Illumina platforms. The final genome assembly consisted of approximately 2.40Gb with a scaffold N50 of 455.26Kb. Benchmarking Universal Single-Copy Orthologs reconstructed 3,742 (91.2%) complete mammalian genes, and genome annotation using RNA-seq identified the locations of 19,124 protein-coding genes. The four short-read individuals were aligned to our reference genome to investigate the demographic history of the two species. A Principal Component Analysis clearly separated re-sequenced individuals, while inferring population size history using the Pairwise Sequentially Markovian Coalescent model noted an approximate species split one million years ago, and a single, possibly recently introgressed individual.

scholarly journals Genome assembly of Vitis rotundifolia Michx. using third-generation sequencing (Oxford Nanopore Technologies)

2021 ◽  
Vol 182 (2) ◽  
pp. 63-71
Author(s):  
M. M. Agakhanov ◽  
E. A. Grigoreva ◽  
E. K. Potokina ◽  
P. S. Ulianich ◽  
Y. V. Ukhatova
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Third Generation ◽  
Vitis Rotundifolia ◽  
Third Generation Sequencing ◽  
Genome Sequence Assembly ◽  
Generation Sequencing

The immune North American grapevine species Vitis rotundifolia Michaux (subgen. Muscadinia Planch.) is regarded as a potential donor of disease resistance genes, withstanding such dangerous diseases of grapes as powdery and downy mildews. The cultivar ‘Dixie’ is the only representative of this species preserved ex situ in Russia: it is maintained by the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) in the orchards of its branch, Krymsk Experiment Breeding Station. Third-generation sequencing on the MinION platform was performed to obtain information on the primary structure of the cultivar’s genomic DNA, employing also the results of Illumina sequencing available in databases. A detailed description of the technique with modifications at various stages is presented, as it was used for grapevine genome sequencing and whole-genome sequence assembly. The modified technique included the main stages of the original protocol recommended by the MinION producer: 1) DNA extraction; 2) preparation of libraries for sequencing; 3) MinION sequencing and bioinformatic data processing; 4) de novo whole-genome sequence assembly using only MinION data or hybrid assembly (MinION+Illumina data); and 5) functional annotation of the whole-genome assembly. Stage 4 included not only de novo sequencing, but also the analysis of the available bioinformatic data, thus minimizing errors and increasing precision during the assembly of the studied genome. The DNA isolated from the leaves of cv. ‘Dixie’ was sequenced using two MinION flow cells (R9.4.1).

scholarly journals A de novo genome assembly and annotation of the southern flying squirrel (Glaucomys volans)

2021 ◽  
Author(s):  
J F Wolf ◽  
Jeff Bowman ◽  
Sonesinh Keobouasone ◽  
Rebecca S Taylor ◽  
Paul J Wilson
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Demographic History ◽  
Secondary Contact ◽  
Glaucomys Volans ◽  
Widespread Species ◽  
Short Read ◽  
Flying Squirrel ◽  
Flying Squirrels ◽  
Southern Flying Squirrel

Abstract Northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels are widespread species distributed across North America. Northern flying squirrels are common inhabitants of the boreal forest, also occurring in coniferous forest remnants farther south, whereas the southern flying squirrel range is centered in eastern temperate woodlands. These two flying squirrel species exhibit a hybrid zone across a latitudinal gradient in an area of recent secondary contact. Glaucomys hybrid offspring are viable and can successfully backcross with either parental species, however, the fitness implications of such events are currently unknown. Some populations of G. sabrinus are endangered, and thus, interspecific hybridization is a key conservation concern in flying squirrels. To provide a resource for future studies to evaluate hybridization and possible introgression, we sequenced and assembled a de novo long-read genome from a G. volans individual sampled in southern Ontario, Canada, while four short-read genomes (two G. sabrinus and two G. volans, all from Ontario) were resequenced on Illumina platforms. The final genome assembly consisted of approximately 2.40 Gb with a scaffold N50 of 455.26 Kb. benchmarking universal single-copy orthologs reconstructed 3742 (91.2%) complete mammalian genes and genome annotation using RNA-Seq identified the locations of 19,124 protein-coding genes. The four short-read individuals were aligned to our reference genome to investigate the demographic history of the two species. A principal component analysis clearly separated resequenced individuals, while inferring population size history using the pairwise sequentially Markovian coalescent model noted an approximate species split 1 million years ago, and a single, possibly recently introgressed individual.

scholarly journals Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

2020 ◽  
Vol 10 (11) ◽  
pp. 3897-3906
Author(s):  
Mikhail Yu. Ozerov ◽  
Martin Flajšhans ◽  
Kristina Noreikiene ◽  
Anti Vasemägi ◽  
Riho Gross
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Apex Predator ◽  
Protein Coding ◽  
Silurus Glanis ◽  
Draft Genome Assembly ◽  
Breeding Research ◽  
Aquaculture Production

The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.

scholarly journals Applicability of the mutation-selection balance model to population genetics of heterozygous protein-truncating variants in humans

2018 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J. Balick ◽  
Christopher Cassa ◽  
Jack Kosmicki ◽  
Mark J. Daly ◽  
...  
Keyword(s):  
Population Genetics ◽  
De Novo ◽  
Demographic History ◽  
Purifying Selection ◽  
Population History ◽  
Balance Model ◽  
Stochastic Force ◽  
Drift Estimation ◽  
Human Genes ◽  
Per Gene

AbstractThe fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation-selection balance, as has been proposed earlier [1]. Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC dataset [2]. Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation-selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.

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