The widespread occurrence of repetitive stretches of DNA in genomes of organisms across
the tree of life imposes fundamental challenges for sequencing, genome assembly, and …

Reconstructing the tree of life remains a central goal in biology. Early methods, which relied
on small numbers of morphological or genetic characters, often yielded conflicting …

A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of
genomic research. Through generating deep coverage ultralong Oxford Nanopore …

Effective utilization of wild relatives is key to overcoming challenges in genetic improvement
of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher …

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 …

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 …

Motivation Protein-to-genome alignment is critical to annotating genes in non-model
organisms. While there are a few tools for this purpose, all of them were developed over 10 …

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 elucidate grapevine evolution and domestication histories with 3525 cultivated and wild
accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape …

Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions
between parental genomes in a polyploid nucleus, frequently involving subgenome …