Landscape of next-generation sequencing technologies

TP Niedringhaus, D Milanova, MB Kerby… - Analytical …, 2011 - ACS Publications
DNA sequencing is in the throes of an enormous technolog-ical shift marked by dramatic
throughput increases, a precipitously dropping per-base cost of raw sequence, and an …

Technological advances in maize breeding: past, present and future

C Andorf, WD Beavis, M Hufford, S Smith… - Theoretical and applied …, 2019 - Springer
Maize has for many decades been both one of the most important crops worldwide and one
of the primary genetic model organisms. More recently, maize breeding has been impacted …

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

B Wang, E Tseng, M Regulski, TA Clark, T Hon… - Nature …, 2016 - nature.com
Zea mays is an important genetic model for elucidating transcriptional networks.
Uncertainties about the complete structure of mRNA transcripts limit the progress of research …

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

Y Dong, M Xie, YU Jiang, N Xiao, X Du, W Zhang… - Nature …, 2013 - nature.com
Abstract We report the∼ 2.66-Gb genome sequence of a female Yunnan black goat. The
sequence was obtained by combining short-read sequencing data and optical mapping data …

A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome

MW Ganal, G Durstewitz, A Polley, A Bérard… - PloS one, 2011 - journals.plos.org
SNP genotyping arrays have been useful for many applications that require a large number
of molecular markers such as high-density genetic mapping, genome-wide association …

Improved maize reference genome with single-molecule technologies

Y Jiao, P Peluso, J Shi, T Liang, MC Stitzer, B Wang… - Nature, 2017 - nature.com
Complete and accurate reference genomes and annotations provide fundamental tools for
characterization of genetic and functional variation. These resources facilitate the …

Genome-wide analysis of bZIP-encoding genes in maize

K Wei, J Chen, Y Wang, Y Chen, S Chen, Y Lin… - DNA …, 2012 - academic.oup.com
In plants, basic leucine zipper (bZIP) proteins regulate numerous biological processes such
as seed maturation, flower and vascular development, stress signalling and pathogen …

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

JD Washburn, MK Mejia-Guerra… - Proceedings of the …, 2019 - National Acad Sciences
Deep learning methodologies have revolutionized prediction in many fields and show
potential to do the same in molecular biology and genetics. However, applying these …

Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation

CJ Underwood, K Choi, C Lambing, X Zhao… - Genome …, 2018 - genome.cshlp.org
Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the
spindle allowing segregation. During meiosis, centromeres are suppressed for inter …

Molecular phylogenetic and expression analysis of the complete WRKY transcription factor family in maize

KF Wei, J Chen, YF Chen, LJ Wu, DX Xie - DNA research, 2012 - academic.oup.com
The WRKY transcription factors function in plant growth and development, and response to
the biotic and abiotic stresses. Although many studies have focused on the functional …