Accelerate to discover

Back to filter

Related topics

Bruker announces acquisition of preclinical and molecular imaging research software provider PMOD

Bruker Biospin

Aug 19, 2019

The PMOD software is widely used for the analysis of positron emission tomography (PET) studies in neurology,...

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

Sage Science

Aug 16, 2019

The BluePippin was used for High Pass DNA size selection prior to library construction. ONT Promethion was used for...

Fluxion Biosciences launches custom liquid biopsy NGS panel development

Fluxion Biosciences

Aug 14, 2019

Fluxion a leading developer of precision solutions for life science research and diagnostics, announced that can...

Superior flow cytometry data with NEW Curiox Laminar Wash systems - centrifuge - less washing

Curiox

Aug 12, 2019

The Laminar Wash technology provides an advantage to scientists in processing suspension cells for flow cytometry....

Aug 20, 2019

Next-generation cytogenetics is here

BioNano Genomics

Aug 9, 2019

On ESHG 2019 conference several oral and poster presentations compared Bionano optical mapping to clinical cytogenetics...

Electroporation using Lumascope: A sustainable method for Adipogenous Mesenchymal Stem Cells

Etaluma

Aug 7, 2019

Human mesenchymal stem cells derived from adipose tissue (AD-hMSCs) represent a promising source for tissue engineering...

The best way to fragment DNA for genomic and paired end library construction

Digilab

Aug 5, 2019

Digilab NextGen Shear DNA Shearing offers the simplest, most reproducible, and most controllable method available for...

Aug 20, 2019

New Cytek Full Spectrum Viewer tool, a powerful guide for your fluorochrome choices

Cytek Biosciences

Aug 2, 2019

Want to see which fluorochromes have unique signatures and which are identical? Then the Cytek Full Spectrum Viewer...

Show all topics (10)

The amaranth genome: Genome, transcriptome, and physical map assembly

Sep 15, 2016

Amaranth (Amaranthus hypochondriacus L.) is an emergingpseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2n = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N50 of 371 kb.
Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which Copia-like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (A. hypochondriacus, A. caudatus, and A. cruentus) and their putative progenitor (A. hybridus) were resequenced.

A single nucleotide polymorphism (SNP) phylogeny supported the classification of A. hybridus as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for A. hypochondriacus using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N50 of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet (Beta vulgaris L.) and estimated, using Ks analysis, the age of the most recent polyploidization event in amaranth.

Read more

Scientific paper
Product news

Related technologies: Genome mapping

Get more info

Regina Fillerová

Field application specialist

Regina

Fillerová

+420 731 127 718

Send Message

Brand profile

BioNano Genomics

A revolutionary NanoChannel technology for Genome mapping of extremely long DNA without amplification, providing long-range contiguity and eliminating PCR bias.

Related products

Genome maps of extremely long DNA without amplification, providing long-range contiguity and eliminating PCR bias

show detail

We supply and support Life-Science Technologies in the territory of Central and Eastern Europe.

Czech Republic

Slovakia

Hungary

Poland

Croatia

Slovenia

Serbia

Romania

Bulgaria

Latvia

Lithuania

Estonia

Russia

Ukraine

Belarus

Turkey