De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive But Compact Genome

Abstract Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

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De novo assembly and annotation of the North American bison ( Bison bison ) reference genome and subsequent variant identification

Animal Genetics ◽

10.1111/age.13060 ◽

2021 ◽

Author(s):

L. K. Dobson ◽

A. Zimin ◽

D. Bayles ◽

E. Fritz‐Waters ◽

D. Alt ◽

...

Keyword(s):

North American ◽

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Bison Bison ◽

The North ◽

Variant Identification

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Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

10.1101/200287 ◽

2017 ◽

Author(s):

Nadia M Davidson ◽

Alicia Oshlack

Keyword(s):

Differential Expression ◽

De Novo Assembly ◽

Reference Genome ◽

Reference Data ◽

De Novo ◽

Rna Seq ◽

Software Pipeline ◽

Standard Methods ◽

A Genome ◽

Genome Annotations

AbstractBackgroundRNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in particular for species where the reference genome or the annotation is incomplete. However, tools for integrating assembled transcriptome with reference annotation are lacking.FindingsNecklace is a software pipeline that runs genome-guided and de novo assembly and combines the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome out of the assembled and reference data. Reads are subsequently aligned and counted in preparation for differential expression testing.ConclusionsNecklace allows a comprehensive transcriptome to be built from a combination of assembled and annotated transcripts which results in a more comprehensive transcriptome for the majority of organisms. In addition RNA-seq data is mapped back to this newly created superTranscript reference to enable differential expression testing with standard methods. Necklace is available from https://github.com/Oshlack/necklace/wiki under GPL 3.0.

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Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab272 ◽

2021 ◽

Author(s):

Myung-Shin Kim ◽

Taeyoung Lee ◽

Jeonghun Baek ◽

Ji Hong Kim ◽

Changhoon Kim ◽

...

Keyword(s):

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Anthocyanin Biosynthesis ◽

Genetic Maps ◽

Soybean Cultivar ◽

Gene Arrangement ◽

Sequencing Data ◽

Crop Species ◽

Satellite Repeats

Abstract Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

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Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut

PLoS ONE ◽

10.1371/journal.pone.0173300 ◽

2017 ◽

Vol 12 (3) ◽

pp. e0173300 ◽

Cited By ~ 8

Author(s):

Alix Armero ◽

Luc Baudouin ◽

Stéphanie Bocs ◽

Dominique This

Keyword(s):

Oil Palm ◽

Related Species ◽

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Translational Genomics

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De novo assembly of a chromosome‐level reference genome of red‐spotted grouper ( Epinephelus akaara ) using nanopore sequencing and Hi‐C

Molecular Ecology Resources ◽

10.1111/1755-0998.13064 ◽

2019 ◽

Vol 19 (6) ◽

pp. 1461-1469 ◽

Cited By ~ 12

Author(s):

Hui Ge ◽

Kebing Lin ◽

Mi Shen ◽

Shuiqing Wu ◽

Yilei Wang ◽

...

Keyword(s):

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Nanopore Sequencing ◽

Epinephelus Akaara ◽

Chromosome Level

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De novo assembly and annotation of a highly contiguous reference genome of the fathead minnow (Pimephales promelas) reveals an AT-rich repetitive genome with compact gene structure

10.1101/2021.02.24.432777 ◽

2021 ◽

Cited By ~ 1

Author(s):

John Martinson ◽

David C. Bencic ◽

Gregory P. Toth ◽

Mitchell S. Kostich ◽

Robert W. Flick ◽

...

Keyword(s):

Gene Structure ◽

Fathead Minnow ◽

Reference Genome ◽

De Novo ◽

Gene Annotation ◽

Pimephales Promelas ◽

Single Copy ◽

Model Organisms ◽

Coding Regions ◽

Genomic Resource

ABSTRACTThe Fathead Minnow (FHM) is one of the most important and widely used model organisms in aquatic toxicology. The lack of a high-quality and well-annotated FHM reference genome, however, has severely hampered the efforts using modem ‘omics approaches with FHM for environmental toxicogenomics studies. We present here a de novo assembled and nearly complete reference of the fathead minnow genome. Compared to the current fragmented and sparsely annotated FHM genome assembly (FHM1), the new highly contiguous and well-annotated FHM reference genome (FHM2) represents a major improvement, having 95.1% of the complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) and a scaffold N50 of 12.0 Mbps. The completeness of gene annotation for the FHM2 reference genome was demonstrated to be comparable to that of the zebrafish (ZF) GRCz11 reference genome. In addition, our comparative genomics analyses between FHM and ZF revealed highly conserved coding regions between two species while discovering much more compact gene structure in FHM than ZF. This study not only provides insights for assembling a highly repetitive AT-rich genome, but also delivers a critical genomic resource essential for toxicogenomics studies in environmental toxicology.

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Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus)

Genome ◽

10.1139/gen-2016-0202 ◽

2017 ◽

Vol 60 (9) ◽

pp. 743-755 ◽

Cited By ~ 21

Author(s):

Sorel Fitz-Gibbon ◽

Andrew L. Hipp ◽

Kasey K. Pham ◽

Paul S. Manos ◽

Victoria L. Sork

Keyword(s):

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Sequence Data ◽

Draft Genome ◽

Reduced Representation ◽

Advantages And Disadvantages ◽

Mapping Sequence ◽

Wide Range ◽

Short Read Sequence

The emergence of next generation sequencing has increased by several orders of magnitude the amount of data available for phylogenetics. Reduced representation approaches, such as restriction-sited associated DNA sequencing (RADseq), have proven useful for phylogenetic studies of non-model species at a wide range of phylogenetic depths. However, analysis of these datasets is not uniform and we know little about the potential benefits and drawbacks of de novo assembly versus assembly by mapping to a reference genome. Using RADseq data for 83 oak samples representing 16 taxa, we identified variants via three pipelines: mapping sequence reads to a recently published draft genome of Quercus lobata, and de novo assembly under two sets of locus filters. For each pipeline, we inferred the maximum likelihood phylogeny. All pipelines produced similar trees, with minor shifts in relationships within well-supported clades, despite the fact that they yielded different numbers of loci (68 000 – 111 000 loci) and different degrees of overlap with the reference genome. We conclude that both the reference-aligned and de novo assembly pipelines yield reliable results, and that advantages and disadvantages of these approaches pertain mainly to downstream uses of RADseq data, not to phylogenetic inference per se.

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