Accelerate to discover

Back to filter

Related topics

Advancing Alzheimer's disease rsearch with IncuCyte S3 for Neuroscience

Sartorius

Nov 12, 2019

IncuCyte S3 Live-Cell Analysis System for Neuroscience: enables real-time automated measurements of the dynamic changes...

Webinar recording: Analysis of extracellular vesicles by AMNIS imaging flow cytometer

Luminex

Nov 4, 2019

Although conventional flow cytometry is limited to measure small particles down to approximately 300 nm – 500 nm, an...

Targeted mitochondrial DNA extraction and enrichment using the SageHLS

Sage Science

Oct 31, 2019

Sage Science introduced a novel approach for enriching mitochondrial DNA for sequence analysis without PCR or gradient...

Oncolytic chimeric orthopoxvirus causes regression of pancreatic cancer at a single low dose

Spectral Instruments Imaging

Oct 24, 2019

Pancreatic ductal adenocarcinoma (PDAC) has been increasing by 0.5% per year in the United States. This study describes...

Nov 13, 2019

Bionano ICS software upgrade: 2600 Gbp with new instrument control software for Bionano Saphyr

BioNano Genomics

Oct 24, 2019

Upgrade to Instrument Control Software v4.9 for higher throughput. Saphyr Instrument Control Software (ICS) v4.9 is the...

New code dedicated to esophageal procedures with Confocal Laser Endomicroscopy

Mauna Kea Technologies

Oct 21, 2019

Announcement of the creation of a new specific procedural code to be added to the Common Classification of Medical...

Flow cytometry technology in an affordable instrument - Discover Guava Muse

Luminex

Oct 21, 2019

Sophisticated cell analysis doesn’t have to be complicated or costly. With the Guava Muse cell analyzer, you can now...

Nov 13, 2019

Cytek Biosciences hits flow cytometry milestone: 40 color analysis from a single sample

Cytek Biosciences

Oct 17, 2019

Cytek Aurora turning aspirations into realizations: 40 Colors, One Tube. Until recently, developing fluorescence-based...

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