Genomic resources in plant breeding for sustainable agriculture
Climate change during the last 40 years has had a serious impact on agriculture and
threatens global food and nutritional security. From over half a million plant species, cereals …
threatens global food and nutritional security. From over half a million plant species, cereals …
Unlocking plant genetics with telomere-to-telomere genome assemblies
Contiguous genome sequence assemblies will help us to realize the full potential of crop
translational genomics. Recent advances in sequencing technologies, especially long-read …
translational genomics. Recent advances in sequencing technologies, especially long-read …
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for
the 26 inbreds that serve as the founders for the maize nested association mapping …
the 26 inbreds that serve as the founders for the maize nested association mapping …
[HTML][HTML] GFF utilities: GffRead and GffCompare
GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats
used by bioinformatics programs to represent and exchange information about various …
used by bioinformatics programs to represent and exchange information about various …
Gapless assembly of maize chromosomes using long-read technologies
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the
ultimate challenges in genomics. We use two independent assemblies and an optical map …
ultimate challenges in genomics. We use two independent assemblies and an optical map …
Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand
antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of …
antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of …
Plant mitochondrial genome map (PMGmap): A software tool for the comprehensive visualization of coding, noncoding and genome features of plant mitochondrial …
X Zhang, H Chen, Y Ni, B Wu, J Li… - Molecular Ecology …, 2024 - Wiley Online Library
Tools for visualizing genomes are essential for investigating genomic features and their
interactions. Currently, tools designed originally for animal mitogenomes and plant …
interactions. Currently, tools designed originally for animal mitogenomes and plant …
A proposed metric set for evaluation of genome assembly quality
Quality control is essential for genome assemblies; however, a consensus has yet to be
reached on what metrics should be adopted for the evaluation of assembly quality. N50 is …
reached on what metrics should be adopted for the evaluation of assembly quality. N50 is …
[HTML][HTML] GAEP: a comprehensive genome assembly evaluating pipeline
Y Zhang, HW Lu, J Ruan - Journal of Genetics and Genomics, 2023 - Elsevier
With the rapid development of sequencing technologies, especially the maturity of third-
generation sequencing technologies, there has been a significant increase in the number …
generation sequencing technologies, there has been a significant increase in the number …
Effect 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 …
generation of reference-quality assemblies for complex genomes. Still, an assessment of …