A field guide to whole‐genome sequencing, assembly and annotation
Genome sequencing projects were long confined to biomedical model organisms and
required the concerted effort of large consortia. Rapid progress in high‐throughput …
required the concerted effort of large consortia. Rapid progress in high‐throughput …
Computational methods for transcriptome annotation and quantification using RNA-seq
High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the
transcriptome, allowing for the complete annotation and quantification of all genes and their …
transcriptome, allowing for the complete annotation and quantification of all genes and their …
A complete telomere-to-telomere assembly of the maize genome
J Chen, Z Wang, K Tan, W Huang, J Shi, T Li, J Hu… - Nature …, 2023 - nature.com
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of
genomic research. Through generating deep coverage ultralong Oxford Nanopore …
genomic research. Through generating deep coverage ultralong Oxford Nanopore …
Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits
Y Huang, J He, Y Xu, W Zheng, S Wang, P Chen… - Nature …, 2023 - nature.com
The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide,
such as sweet orange and lemon. The origin of Citrus species has long been debated and …
such as sweet orange and lemon. The origin of Citrus species has long been debated and …
Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here,
we developed a graph-based pan-genome by assembling ten chromosomal genomes with …
we developed a graph-based pan-genome by assembling ten chromosomal genomes with …
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 …
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics
Complete and accurate reference genomes and annotations provide fundamental resources
for functional genomics and crop breeding. Here we report a de novo assembly and …
for functional genomics and crop breeding. Here we report a de novo assembly and …
[HTML][HTML] Pan-genome of wild and cultivated soybeans
Y Liu, H Du, P Li, Y Shen, H Peng, S Liu, GA Zhou… - Cell, 2020 - cell.com
Soybean is one of the most important vegetable oil and protein feed crops. To capture the
entire genomic diversity, it is needed to construct a complete high-quality pan-genome from …
entire genomic diversity, it is needed to construct a complete high-quality pan-genome from …
Evolutionary analysis of a complete chicken genome
Z Huang, Z Xu, H Bai, Y Huang… - Proceedings of the …, 2023 - National Acad Sciences
Microchromosomes are prevalent in nonmammalian vertebrates [PD Waters et al., Proc.
Natl. Acad. Sci. USA 118 (2021)], but a few of them are missing in bird genome assemblies …
Natl. Acad. Sci. USA 118 (2021)], but a few of them are missing in bird genome assemblies …
A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding
Y Deng, S Liu, Y Zhang, J Tan, X Li, X Chu, B Xu… - Molecular plant, 2022 - cell.com
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …
gaps and a narrow genetic base hinder functional genomics and genetic improvement of …