scholarly journals De novo assembly of a chromosome-scale reference genome for the northern flicker Colaptes auratus

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jack P Hruska ◽  
Joseph D Manthey
Keyword(s):  
Mutation Rate ◽  
Genome Assembly ◽  
De Novo ◽  
Single Copy ◽  
De Novo Genome Assembly ◽  
Phenotypic Differentiation ◽  
The Family ◽  
Northern Flicker ◽  
Long Read ◽  
Colaptes Auratus

Abstract The northern flicker, Colaptes auratus, is a widely distributed North American woodpecker and a long-standing focal species for the study of ecology, behavior, phenotypic differentiation, and hybridization. We present here a highly contiguous de novo genome assembly of C. auratus, the first such assembly for the species and the first published chromosome-level assembly for woodpeckers (Picidae). The assembly was generated using a combination of short-read Chromium 10× and long-read PacBio sequencing, and further scaffolded with chromatin conformation capture (Hi-C) reads. The resulting genome assembly is 1.378 Gb in size, with a scaffold N50 of 11  and a scaffold L50 of 43.948 Mb. This assembly contains 87.4–91.7% of genes present across four sets of universal single-copy orthologs found in tetrapods and birds. We annotated the assembly both for genes and repetitive content, identifying 18,745 genes and a prevalence of ∼28.0% repetitive elements. Lastly, we used fourfold degenerate sites from neutrally evolving genes to estimate a mutation rate for C. auratus, which we estimated to be 4.007 × 10−9 substitutions/site/year, about 1.5× times faster than an earlier mutation rate estimate of the family. The highly contiguous assembly and annotations we report will serve as a resource for future studies on the genomics of C. auratus and comparative evolution of woodpeckers.

scholarly journals De Novo Assembly of a Chromosome-Scale Reference Genome for the Northern Flicker Colaptes auratus

2020 ◽  
Author(s):  
Jack P. Hruska ◽  
Joseph D. Manthey
Keyword(s):  
Mutation Rate ◽  
Genome Assembly ◽  
De Novo ◽  
Single Copy ◽  
Phenotypic Differentiation ◽  
The Family ◽  
Northern Flicker ◽  
Long Read ◽  
Colaptes Auratus ◽  
Comparative Evolution

ABSTRACTThe northern flicker, Colaptes auratus, is a widely distributed North American woodpecker and a long-standing focal species for the study of ecology, behavior, phenotypic differentiation, and hybridization. We present here a highly contiguous de novo genome assembly of C. auratus, the first such assembly for the species and the first published chromosome-level assembly for woodpeckers (Picidae). The assembly was generated using a combination of short-read Chromium 10x and long-read PacBio sequencing, and further scaffolded with chromatin conformation capture (Hi-C) reads. The resulting genome assembly is 1.378 Gb in size, with a scaffold N50 of 43.948 Mb and a scaffold L50 of 11. This assembly contains 87.4 % - 91.7 % of genes present across four sets of universal single-copy orthologs found in tetrapods and birds. We annotated the assembly both for genes and repetitive content, identifying 18,745 genes and a prevalence of ~ 28.0 % repetitive elements. Lastly, we used four-fold degenerate sites from neutrally evolving genes to estimate a mutation rate for C. auratus, which we estimated to be 4.007 × 10−9 substitutions / site / year, about 1.5x times faster than an earlier mutation rate estimate of the family. The highly contiguous assembly and annotations we report will serve as a resource for future studies on the genomics of C. auratus and comparative evolution of woodpeckers.

scholarly journals Accurate long-read de novo assembly evaluation with Inspector

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Chen ◽  
Yixin Zhang ◽  
Amy Y. Wang ◽  
Min Gao ◽  
Zechen Chong
Keyword(s):  
Genome Assembly ◽  
De Novo Assembly ◽  
In Silico ◽  
Large Scale ◽  
De Novo ◽  
Small Scale ◽  
De Novo Genome Assembly ◽  
Consensus Sequences ◽  
Assembly Evaluation ◽  
Long Read

AbstractLong-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations. Notably, Inspector can correct the assembly errors based on consensus sequences derived from raw reads covering erroneous regions. Based on in silico and long-read assembly results from multiple long-read data and assemblers, we demonstrate that in addition to providing generic metrics, Inspector can accurately identify both large-scale and small-scale assembly errors.

scholarly journals Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

2020 ◽  
Author(s):  
David Porubsky ◽  
◽  
Peter Ebert ◽  
Peter A. Audano ◽  
Mitchell R. Vollger ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Assembly ◽  
De Novo ◽  
Error Rates ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
De Novo Genome Assembly ◽  
Parental Data ◽  
Human Genome Assembly ◽  
Long Read

AbstractHuman genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.

scholarly journals De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 69 ◽  
Author(s):  
Nagesh Kancharla ◽  
Saakshi Jalali ◽  
J. Narasimham ◽  
Vinod Nair ◽  
Vijay Yepuri ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Genome Assembly ◽  
Jatropha Curcas ◽  
Quantitative Trait ◽  
De Novo ◽  
Mapping Population ◽  
Single Copy ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
Sequencing Technologies

Jatropha curcas is an important perennial, drought tolerant plant that has been identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of J. curcas generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for Jatropha Mosaic Virus (JMV) resistance. In this study, we generated scaffolds of 265.7 Mbp in length, which correspond to 84.8% of the gene space, using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Additionally, 96.4% of predicted protein-coding genes were captured in RNA sequencing data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide simple sequence repeat (SSR) markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 207 polymorphic SSR markers were employed to construct a genetic linkage map for JMV resistance, using an interspecific F2 mapping population involving susceptible J. curcas and resistant Jatropha integerrima as parents. Quantitative trait locus (QTL) analysis led to the identification of three minor QTLs for JMV resistance, and the same has been validated in an alternate F2 mapping population. These validated QTLs were utilized in marker-assisted breeding for JMV resistance. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha, and serves as source for the development of agronomically improved virus-resistant and oil-producing lines.

scholarly journals Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Yaoxi He ◽  
Xin Luo ◽  
Bin Zhou ◽  
Ting Hu ◽  
Xiaoyu Meng ◽  
...  
Keyword(s):  
Rhesus Macaque ◽  
Genome Assembly ◽  
De Novo ◽  
Gene Annotation ◽  
Large Body ◽  
Phenotypic Traits ◽  
Structural Variants ◽  
De Novo Genome Assembly ◽  
Chinese Rhesus Macaque ◽  
Long Read

Abstract We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). We improve gene annotation by generating more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to ape genomes. Many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a subset that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. The rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies.

scholarly journals A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

GigaScience ◽  
2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Sarah B Kingan ◽  
Julie Urban ◽  
Christine C Lambert ◽  
Primo Baybayan ◽  
Anna K Childers ◽  
...  
Keyword(s):  
Invasive Species ◽  
Genome Assembly ◽  
De Novo ◽  
Fragment Size ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Lycorma Delicatula ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome

ABSTRACT Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. Results The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. Conclusions We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

scholarly journals A high-quality, long-read de novo genome assembly to aid conservation of Hawaii’s last remaining crow species

2018 ◽  
Author(s):  
Jolene T. Sutton ◽  
Martin Helmkampf ◽  
Cynthia C. Steiner ◽  
M. Renee Bellinger ◽  
Jonas Korlach ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Captive Breeding ◽  
De Novo ◽  
Bird Species ◽  
Population Level ◽  
Model Systems ◽  
Population Declines ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Long Read

AbstractGenome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, and to apply these results to conservation management. Here we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the Alala. As the only remaining native crow species in Hawaii, the Alala survived solely in a captive breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies, and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the Alala genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important for conservation applications, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications.

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 LongStitch: High-quality genome assembly correction and scaffolding using long reads

2021 ◽  
Author(s):  
Lauren Coombe ◽  
Janet X Li ◽  
Theodora Lo ◽  
Johnathan Wong ◽  
Vladimir Nikolic ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Model Organisms ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Long Reads ◽  
Long Read ◽  
Genomic Regions ◽  
Genome Assemblies

Background Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information. Long reads are better able to span repetitive genomic regions compared to short reads, and thus have tremendous utility for resolving problematic regions and helping generate more complete draft assemblies. Here, we present LongStitch, a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tigmint-long and ARKS-long are misassembly correction and scaffolding utilities, respectively, previously developed for linked reads, that we adapted for long reads. Here, we describe the LongStitch pipeline and introduce our new long-read scaffolder, ntLink, which utilizes lightweight minimizer mappings to join contigs. LongStitch was tested on short and long-read assemblies of three different human individuals using corresponding nanopore long-read data, and improves the contiguity of each assembly from 2.0-fold up to 304.6-fold (as measured by NGA50 length). Furthermore, LongStitch generates more contiguous and correct assemblies compared to state-of-the-art long-read scaffolder LRScaf in most tests, and consistently runs in under five hours using less than 23GB of RAM. Conclusions Due to its effectiveness and efficiency in improving draft assemblies using long reads, we expect LongStitch to benefit a wide variety of de novo genome assembly projects. The LongStitch pipeline is freely available at https://github.com/bcgsc/longstitch.

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