Víctor Llaca
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View article: Analyses of contiguous reference genomes of Amaranthus tuberculatus highlight the landscape of the sex-associated region and PEBP gene family diversity
Analyses of contiguous reference genomes of Amaranthus tuberculatus highlight the landscape of the sex-associated region and PEBP gene family diversity Open
Background Amaranthus tuberculatus (waterhemp) is a troublesome agronomic weed species that is dioecious with an XY sex-determination system. The evolution of the sex-determining region (SDR), the contiguity of the region, genomic landscap…
View article: A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism
A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism Open
Making sense of whole-genome polymorphism data is challenging, but it is essential for overcoming the biases in SNP data. Here we analyze 27 genomes of Arabidopsis thaliana to illustrate these issues. Genome size variation is mostly due to…
View article: The Genome of <i>Apera spica-venti</i>: A Major Grass Weed
The Genome of <i>Apera spica-venti</i>: A Major Grass Weed Open
Apera spica-venti (loose silky bent, or common windgrass) is a diploid grass-weed endemic to Europe and north Asia that has spread to the United States and Canada. This species has become a major grass weed in winter cereals, especially in…
View article: Oryza genome evolution through a tetraploid lens
Oryza genome evolution through a tetraploid lens Open
Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present…
View article: Chromosome-Level Assemblies of the Allohexaploid Genomes of <i>Conyza sumatrensis</i> and <i>Conyza bonariensis</i>
Chromosome-Level Assemblies of the Allohexaploid Genomes of <i>Conyza sumatrensis</i> and <i>Conyza bonariensis</i> Open
Conyza sumatrensis and Conyza bonariensis are two important hexaploid weed species that impact crop production systems across the globe. Here, we report reference genome assemblies for both species. The sequenced accession of C. sumatrensi…
View article: Chromosome‐level assemblies of <i>Amaranthus palmeri</i>, <i>Amaranthus retroflexus</i>, and <i>Amaranthus hybridus</i> allow for genomic comparisons and identification of a sex‐determining region
Chromosome‐level assemblies of <i>Amaranthus palmeri</i>, <i>Amaranthus retroflexus</i>, and <i>Amaranthus hybridus</i> allow for genomic comparisons and identification of a sex‐determining region Open
SUMMARY Amaranthus palmeri (Palmer amaranth), Amaranthus retroflexus (redroot pigweed), and Amaranthus hybridus (smooth pigweed) are troublesome weeds that are economically damaging to several cropping systems. Collectively referred to as …
View article: Assembly and Annotation of the Tetraploid <i>Salsola tragus</i> (Russian Thistle) Genome
Assembly and Annotation of the Tetraploid <i>Salsola tragus</i> (Russian Thistle) Genome Open
This report presents two phased chromosome-scale genome assemblies of allotetraploid Salsola tragus (2n = 4x = 36) and fills the current genomics resource gap for this species. Flow cytometry estimated 1C genome size was 1.319 Gb. PacBio H…
View article: Extensive genome evolution distinguishes maize within a stable tribe of grasses
Extensive genome evolution distinguishes maize within a stable tribe of grasses Open
Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, …
View article: Saltgrass genomes reveal unique features of a dioecious, perennial, halophytic grass
Saltgrass genomes reveal unique features of a dioecious, perennial, halophytic grass Open
For agriculture, the climate crisis will center on the key resource of fresh water. Understanding of halophytic adaptations for productivity without fresh water will open possibilities for crop production through neodomestication. Saltgras…
View article: High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436
High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436 Open
Sorghum bicolor (L.) Moench is a significant grass crop globally, known for its genetic diversity. High quality genome sequences are needed to capture the diversity. We constructed high-quality, chromosome-level genome assemblies for two v…
View article: A phased chromosome-level genome assembly provides insights into the evolution of sex chromosomes in<i>Amaranthus tuberculatus</i>
A phased chromosome-level genome assembly provides insights into the evolution of sex chromosomes in<i>Amaranthus tuberculatus</i> Open
Summary Amaranthus tuberculatus (waterhemp) is a troublesome weed species of agronomic importance that is dioecious with an XY sex-determination system. The evolution of sex chromosomes, the contiguity of sex-determining region (SDR) and t…
View article: Oryza genome evolution through a tetraploid lens
Oryza genome evolution through a tetraploid lens Open
Oryza is remarkable genus - with two domesticated (i.e. Asian and African rice) and 25 diploid and tetraploid wild species, 11 extant genome types, and a ~3.4-fold genome size variation - that possesses a virtually untapped reservoir of ge…
View article: Towards an unbiased characterization of genetic polymorphism: a comparison of 27<i>A. thaliana</i> genomes
Towards an unbiased characterization of genetic polymorphism: a comparison of 27<i>A. thaliana</i> genomes Open
Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to provide nearly complete genome sequences for population samples, should sol…
View article: Current status of community resources and priorities for weed genomics research
Current status of community resources and priorities for weed genomics research Open
View article: The complex polyploid genome architecture of sugarcane
The complex polyploid genome architecture of sugarcane Open
View article: The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes
The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes Open
View article: Author Correction: A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology
Author Correction: A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology Open
View article: Author Correction: Mapping the genomic landscape of CRISPR–Cas9 cleavage
Author Correction: Mapping the genomic landscape of CRISPR–Cas9 cleavage Open
View article: Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research
Near‐gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research Open
Complete, gapless telomere‐to‐telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orie…
View article: Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications
Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications Open
High-quality reference genome assemblies, representative of global heterotic patterns, offer an ideal platform to accurately characterize and utilize genetic variation in the primary gene pool of hybrid crops. Here we report three platinum…
View article: A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology
A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology Open
Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled …
View article: The International Weed Genomics Consortium: Community Resources for Weed Genomics Research
The International Weed Genomics Consortium: Community Resources for Weed Genomics Research Open
The International Weed Genomics Consortium is a collaborative group of researchers focused on developing genomic resources for the study of weedy plants. Weeds are attractive systems for basic and applied research due to their impacts on a…
View article: A happy accident: a novel turfgrass reference genome
A happy accident: a novel turfgrass reference genome Open
Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled d…
View article: Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice Open
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice ( Oryza sativa ), plus the g…
View article: The <scp>NLRomes</scp> of <i>Zea mays</i> <scp>NAM</scp> founder lines and <i>Zea luxurians</i> display presence–absence variation, integrated domain diversity, and mobility
The <span>NLRomes</span> of <i>Zea mays</i> <span>NAM</span> founder lines and <i>Zea luxurians</i> display presence–absence variation, integrated domain diversity, and mobility Open
Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, i…
View article: The gyrfalcon (<i>Falco rusticolus</i>) genome
The gyrfalcon (<i>Falco rusticolus</i>) genome Open
High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and popula…
View article: A multi-omic<i>Nicotiana benthamiana</i>resource for fundamental research and biotechnology
A multi-omic<i>Nicotiana benthamiana</i>resource for fundamental research and biotechnology Open
Nicotiana benthamiana is an invaluable model plant and biotechnology platform. To further improve its usefulness and versatility, we have produced high quality chromosome level genome assemblies and multi-omic datasets for both the ubiquit…
View article: Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes"
Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes" Open
This dataset contains supporting files referenced by the following publication: • Rabanal FA, Gräff M, Lanz C, Fritschi K, Llaca V, Lang M, Carbonell-Bejerano P, Henderson I, Weigel D. Pushing the limits of HiFi assemblies reveals …
View article: Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes"
Supporting Data for "Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes" Open
This dataset contains supporting files referenced by the following publication: • Rabanal FA, Gräff M, Lanz C, Fritschi K, Llaca V, Lang M, Carbonell-Bejerano P, Henderson I, Weigel D. Pushing the limits of HiFi assemblies reveals …
View article: Pushing the limits of HiFi assemblies reveals centromere diversity between two <i>Arabidopsis thaliana</i> genomes
Pushing the limits of HiFi assemblies reveals centromere diversity between two <i>Arabidopsis thaliana</i> genomes Open
Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col…