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Article
Open AccessEffect of sequence depth and length in long-read assembly of the maize inbred NC358
Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is...
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Article
Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF...
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Article
Open AccessThe maize W22 genome provides a foundation for functional genomics and transposon biology
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short...
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Article
Open AccessExtensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes
Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corres...
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Article
Open AccessGenomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that de...
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Article
Open AccessImproved maize reference genome with single-molecule technologies
An improved reference genome for maize, using single-molecule sequencing and high-resolution optical map**, enables characterization of structural variation and repetitive regions, and identifies lineage exp...
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Article
Open AccessUnveiling the complexity of the maize transcriptome by single-molecule long-read sequencing
Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-mo...
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Article
Open AccessWhole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica
The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic varia...
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Article
Open AccessA new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
The challenges of accurate gene prediction and enumeration are further aggravated in large genomes that contain highly repetitive transposable elements (TEs). Yet TEs play a substantial role in genome evolutio...
