De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

Abstract Motivation Solanum sitiens is a self-incompatible wild relative of tomato, characterized by salt and drought-resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S.pennellii and S.chilense. Therefore, the availability of a reference genome for S.sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. Results A high-quality de novo genome and transcriptome assembly for S.sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (∼159× coverage) and PacBio long reads (∼44× coverage), generating a total of ∼262 Gbp of DNA sequence. A reference genome of 1245 Mbp, arranged in 1483 scaffolds with an N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31 164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S.lycopersicum, containing several drought-resistance-related genes, such as beta-amylase 1 and YUCCA7. Availability and implementation S.sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI’s Sequence Read Archive, under the BioProject number ‘PRJNA633104’. All the commands and scripts necessary to generate the assembly are available at the following github repository: https://github.com/MCorentin/Solanum_sitiens_assembly. Supplementary information Supplementary data are available at Bioinformatics online.

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De novo genome assembly and transcriptome analysis for the drought and salt resistant Solanum sitiens

10.1101/2020.06.14.151043 ◽

2020 ◽

Author(s):

C. Molitor ◽

T.J. Kurowski ◽

P.M. Fidalgo de Almeida ◽

P. Eerolla ◽

D.J. Spindlow ◽

...

Keyword(s):

Drought Resistance ◽

Crop Production ◽

Reference Genome ◽

De Novo ◽

Transcriptome Assembly ◽

Crop Improvement ◽

Single Copy ◽

Analysis Tool ◽

High Quality ◽

De Novo Genome Assembly

AbstractSolanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a high-quality reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. Here, we present a de novo genome and transcriptome assembly for S. sitiens (Accession LA1974). A hybrid assembly strategy was followed using Illumina short reads (∼159X coverage) and PacBio long reads (∼44X coverage), generating a total of ∼262 Gbp of DNA sequence; in addition, ∼2,670 Gbp of BioNano data was obtained. A reference genome of 1,245 Mbp, arranged in 1,481 scaffolds with a N50 of 1,826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT); this is within the range of current high-quality reference genomes for other tomato wild relatives. Additionally, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as beta-amylase 1 and YUCCA7.In addition, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and perform a de novo transcriptome. Some of the protein clusters unique to S. sitiens were associated with genes involved in drought and salt resistance, including GLO1 and FQR1.This first reference genome for S. sitiens will provide a valuable resource to progress QTL studies to the gene level, and will assist molecular breeding to improve crop production in water-limited environments.

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

Genes ◽

10.3390/genes10010069 ◽

2019 ◽

Vol 10 (1) ◽

pp. 69 ◽

Cited By ~ 9

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.

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dnAQET: a framework to compute a consolidated metric for benchmarking quality of de novo assemblies

BMC Genomics ◽

10.1186/s12864-019-6070-x ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Gokhan Yavas ◽

Huixiao Hong ◽

Wenming Xiao

Keyword(s):

Quality Assessment ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Quality Score ◽

De Novo Genome Assembly ◽

Genome Assemblies ◽

Reference Genomes ◽

Better Than

Abstract Background Accurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome research. Although many quality metrics have been proposed and software tools for calculating those metrics have been developed, the existing tools do not produce a unified measure to reflect the overall quality of an assembly. Results To address this issue, we developed the de novo Assembly Quality Evaluation Tool (dnAQET) that generates a unified metric for benchmarking the quality assessment of assemblies. Our framework first calculates individual quality scores for the scaffolds/contigs of an assembly by aligning them to a reference genome. Next, it computes a quality score for the assembly using its overall reference genome coverage, the quality score distribution of its scaffolds and the redundancy identified in it. Using synthetic assemblies randomly generated from the latest human genome build, various builds of the reference genomes for five organisms and six de novo assemblies for sample NA24385, we tested dnAQET to assess its capability for benchmarking quality evaluation of genome assemblies. For synthetic data, our quality score increased with decreasing number of misassemblies and redundancy and increasing average contig length and coverage, as expected. For genome builds, dnAQET quality score calculated for a more recent reference genome was better than the score for an older version. To compare with some of the most frequently used measures, 13 other quality measures were calculated. The quality score from dnAQET was found to be better than all other measures in terms of consistency with the known quality of the reference genomes, indicating that dnAQET is reliable for benchmarking quality assessment of de novo genome assemblies. Conclusions The dnAQET is a scalable framework designed to evaluate a de novo genome assembly based on the aggregated quality of its scaffolds (or contigs). Our results demonstrated that dnAQET quality score is reliable for benchmarking quality assessment of genome assemblies. The dnQAET can help researchers to identify the most suitable assembly tools and to select high quality assemblies generated.

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GraphSeq: Accelerating String Graph Construction for De Novo Assembly on Spark

10.1101/321729 ◽

2018 ◽

Author(s):

Chung-Tsai Su ◽

Ming-Tai Chang ◽

Yun-Chian Cheng ◽

Yun-Lung Li ◽

Yao-Ting Wang

Keyword(s):

Genome Assembly ◽

De Novo Assembly ◽

De Novo ◽

Data Representation ◽

Important Application ◽

Supplementary Information ◽

De Novo Genome Assembly ◽

String Graph ◽

Computing Framework ◽

Variant Identification

AbstractSummary: De novo genome assembly is an important application on both uncharacterized genome assembly and variant identification in a reference-unbiased way. In comparison with de Brujin graph, string graph is a lossless data representation for de novo assembly. However, string graph construction is computational intensive. We propose GraphSeq to accelerate string graph construction by leveraging the distributed computing framework.Availability and Implementation: GraphSeq is implemented with Scala on Spark and freely available at https://www.atgenomix.com/blog/graphseq.Supplementary information: Supplementary data are available at Bioinformatics online.

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Assemblytics: a web analytics tool for the detection of assembly-based variants

10.1101/044925 ◽

2016 ◽

Cited By ~ 5

Author(s):

Maria Nattestad ◽

Michael C Schatz

Keyword(s):

Genome Assembly ◽

Related Species ◽

Reference Genome ◽

De Novo ◽

Web Analytics ◽

Structural Variants ◽

De Novo Genome Assembly ◽

Interactive Visualizations ◽

Web App ◽

Filtering Approach

Summary: Assemblytics is a web app for detecting and analyzing structural variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor filtering approach to increase robustness to repetitive elements, and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species. Multiple interactive visualizations enable in-depth explorations of the genomic distributions of variants. Availability and Implementation: http://qb.cshl.edu/assemblytics, https://github.com/marianattestad/assemblytics Contact: [email protected]

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Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C

GigaScience ◽

10.1093/gigascience/giaa027 ◽

2020 ◽

Vol 9 (4) ◽

Cited By ~ 5

Author(s):

Matt A Field ◽

Benjamin D Rosen ◽

Olga Dudchenko ◽

Eva K F Chan ◽

Andre E Minoche ◽

...

Keyword(s):

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Gene Annotation ◽

Draft Genome ◽

Single Copy ◽

Canis Lupus Familiaris ◽

German Shepherd ◽

German Shepherd Dog ◽

First Choice

Abstract Background The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. Findings Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. Conclusions GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.

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The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C data

10.1101/2021.04.05.438426 ◽

2021 ◽

Author(s):

Hui-Su Kim ◽

Asta Blazyte ◽

Sungwon Jeon ◽

Changhan Yoon ◽

Yeonkyung Kim ◽

...

Keyword(s):

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Gene Prediction ◽

Chromosomal Mapping ◽

Autosomal Snps ◽

Contig Assembly ◽

De Novo Genome Assembly ◽

Human Reference Genome ◽

The Baltic

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly constructed using 57× of ultra-long nanopore reads and 47× of short paired-end reads. We also utilized 72 Gb of Hi-C chromosomal mapping data to maximize the assembly′s contiguity and accuracy. LT1′s contig assembly was 2.73 Gbp in length comprising of 4,490 contigs with an N50 value of 13.4 Mbp. After scaffolding with Hi-C data and extensive manual curation, we produced a chromosome-scale assembly with an N50 value of 138 Mbp and 4,699 scaffolds. Our gene prediction quality assessment using BUSCO identify 89.3% of the single-copy orthologous genes included in the benchmarking set. Detailed characterization of LT1 suggested it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,000 short indels, and 12,330 large structural variants. These data are shared as a public resource without any restrictions and can be used as a benchmark for further in-depth genomic analyses of the Baltic populations.

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

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa026 ◽

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.

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