Piercing the dark matter: bioinformatics of long-range sequencing and mapping

FJ Sedlazeck, H Lee, CA Darby, MC Schatz - Nature Reviews Genetics, 2018 - nature.com
Several new genomics technologies have become available that offer long-read sequencing
or long-range mapping with higher throughput and higher resolution analysis than ever …

Next-generation sequencing technologies

WR McCombie, JD McPherson… - Cold Spring …, 2019 - perspectivesinmedicine.cshlp.org
Although DNA and RNA sequencing has a history spanning five decades, large-scale
massively parallel sequencing, or next-generation sequencing (NGS), has only been …

[HTML][HTML] Multiple wheat genomes reveal global variation in modern breeding

S Walkowiak, L Gao, C Monat, G Haberer, MT Kassa… - Nature, 2020 - nature.com
Advances in genomics have expedited the improvement of several agriculturally important
crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely …

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

T Zhu, L Wang, H Rimbert, JC Rodriguez… - The Plant …, 2021 - Wiley Online Library
Until recently, achieving a reference‐quality genome sequence for bread wheat was long
thought beyond the limits of genome sequencing and assembly technology, primarily due to …

Long-read sequence assembly: a technical evaluation in barley

M Mascher, T Wicker, J Jenkins, C Plott, T Lux… - The Plant …, 2021 - academic.oup.com
Sequence assembly of large and repeat-rich plant genomes has been challenging,
requiring substantial computational resources and often several complementary sequence …

[HTML][HTML] GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

TR Ranallo-Benavidez, KS Jaron, MC Schatz - Nature communications, 2020 - nature.com
An important assessment prior to genome assembly and related analyses is genome
profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate …

Shifting the limits in wheat research and breeding using a fully annotated reference genome

International Wheat Genome Sequencing Consortium … - Science, 2018 - science.org
INTRODUCTION Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth,
contributing about a fifth of the total calories consumed by humans. Consequently, wheat …

Genomic architecture and introgression shape a butterfly radiation

NB Edelman, PB Frandsen, M Miyagi, B Clavijo… - Science, 2019 - science.org
We used 20 de novo genome assemblies to probe the speciation history and architecture of
gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete …

The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat

C Sun, Z Dong, L Zhao, Y Ren… - Plant biotechnology …, 2020 - Wiley Online Library
The rapid development and application of molecular marker assays have facilitated genomic
selection and genome‐wide linkage and association studies in wheat breeding. Although …

The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons

J Bally, H Jung, C Mortimer, F Naim… - Annual review of …, 2018 - annualreviews.org
A decade ago, the value of Nicotiana benthamiana as a tool for plant molecular biologists
was beginning to be appreciated. Scientists were using it to study plant-microbe and protein …