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

Mapping Intimacies ◽

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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MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

Genome Biology ◽

10.1186/s13059-021-02507-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Marek Cmero ◽

Breon Schmidt ◽

Ian J. Majewski ◽

Paul G. Ekert ◽

Alicia Oshlack ◽

...

Keyword(s):

Differential Expression ◽

De Novo Assembly ◽

De Novo ◽

Splice Variants ◽

Differential Expression Analysis ◽

New Disease ◽

Fusion Genes ◽

Rna Seq ◽

Novel Variants ◽

Transcriptional Variants

AbstractCalling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.

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Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

10.1101/2021.11.23.469778 ◽

2021 ◽

Author(s):

Xinxin Yi ◽

Jing Liu ◽

Shengcai Chen ◽

Hao Wu ◽

Min Liu ◽

...

Keyword(s):

Nitrogen Fixation ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Genome Wide ◽

A Genome ◽

Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

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Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

Microbiology Resource Announcements ◽

10.1128/mra.00726-20 ◽

2020 ◽

Vol 9 (37) ◽

Author(s):

Samuel O’Donnell ◽

Frederic Chaux ◽

Gilles Fischer

Keyword(s):

Chlamydomonas Reinhardtii ◽

Genome Size ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Content Type ◽

Oxford Nanopore ◽

A Genome ◽

Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

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Author Correction: De novo assembly of the Platycladus orientalis (L.) Franco transcriptome provides insight into the development and pollination mechanism of female cone based on RNA-Seq data

Scientific Reports ◽

10.1038/s41598-019-53777-z ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Wei Zhou ◽

Qi Chen ◽

Xiao-Bing Wang ◽

Tyler O. Hughes ◽

Jian-Jun Liu ◽

...

Keyword(s):

De Novo Assembly ◽

De Novo ◽

Rna Seq ◽

Female Cone ◽

Pollination Mechanism ◽

Platycladus Orientalis ◽

Insight Into

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Towards a reference genome that captures global genetic diversity

Nature Communications ◽

10.1038/s41467-020-19311-w ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Karen H. Y. Wong ◽

Walfred Ma ◽

Chun-Yu Wei ◽

Erh-Chan Yeh ◽

Wan-Jia Lin ◽

...

Keyword(s):

Genetic Diversity ◽

Reference Genome ◽

Regulatory Elements ◽

Human Populations ◽

Single Individual ◽

Rna Seq ◽

Human Reference Genome ◽

Reference Sequences ◽

Genome Annotations ◽

Unmapped Reads

Abstract The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity.

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De novo assembly of the cattle reference genome with single-molecule sequencing

GigaScience ◽

10.1093/gigascience/giaa021 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 35

Author(s):

Benjamin D Rosen ◽

Derek M Bickhart ◽

Robert D Schnabel ◽

Sergey Koren ◽

Christine G Elsik ◽

...

Keyword(s):

Single Molecule ◽

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Future Research ◽

Protein Coding ◽

Single Molecule Sequencing ◽

Assembly Accuracy ◽

Genomic Tools

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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