Alan Yocca
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The evolution of pectate lyase-like genes across land plants, and their roles in haustorium formation in parasitic plant, <i>Triphysaria versicolor</i> (Orobanchaceae) Open
Parasitic plants in Orobanchaceae are noxious agricultural pests that severely impact crops worldwide. These plants acquire water and nutrients from their hosts through a specialized organ called the haustorium. A key step in haustorium de…
View article: ZW sex chromosome structure in Amborella trichopoda
ZW sex chromosome structure in Amborella trichopoda Open
Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromoso…
A haplotype-resolved, chromosome-scale genome for <i>Malus domestica</i> Borkh. ‘WA 38’ Open
Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation give breeders, researchers, and growers information about cultivar-spe…
View article: ZW sex chromosome structure in Amborella trichopoda
ZW sex chromosome structure in Amborella trichopoda Open
Sex chromosomes have evolved hundreds of times, and their recent origins in flowering plants can shed light on the early consequences of suppressed recombination. Amborella trichopoda, the sole species on a lineage that is sister to all ot…
A Haplotype-resolved, Chromosome-scale Genome for Malus domestica 'WA 38' Open
Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation gives breeders, researchers, and growers information about cultivar sp…
View article: A chromosome-scale assembly for ‘d’Anjou’ pear
A chromosome-scale assembly for ‘d’Anjou’ pear Open
Cultivated pear consists of several Pyrus species with Pyrus communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assist…
Genome of the North American wild apple species <i>Malus angustifolia</i> Open
Apple ( Malus × domestica Borkh.) production faces many challenges stemming from abiotic and biotic stresses. Abiotic stressors, such as extreme temperatures, droughts, and spring frosts, can lead to diminished yields and tree loss, while …
View article: Complementing model species with model clades
Complementing model species with model clades Open
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opport…
View article: Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts
Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts Open
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry contin…
A haplotype resolved chromosome‐scale assembly of North American wild apple <i>Malus fusca</i> and comparative genomics of the fire blight <i>Mfu10</i> locus Open
SUMMARY The Pacific crabapple ( Malus fusca ) is a wild relative of the commercial apple ( Malus × domestica ). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species repre…
dAnjou genome v1.3 Open
Genome assembly and annotations file for https://doi.org/10.1101/2023.08.22.554305
dAnjou genome v1.3 Open
Genome assembly and annotations file for https://doi.org/10.1101/2023.08.22.554305
View article: A chromosome-scale assembly for ‘d’Anjou’ pear
A chromosome-scale assembly for ‘d’Anjou’ pear Open
Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted …
View article: Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts
Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts Open
Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry contin…
<i>Vaccinium</i> as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit Open
The genus Vaccinium L. (Ericaceae) contains premium berryfruit crops, including blueberry, cranberry, bilberry, and lingonberry. Consumption of Vaccinium berries is strongly associated with various potential health benefits, many of which …
A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. Open
The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an unt…
A haplotype resolved chromosome-scale assembly of North American wild apple <i>Malus fusca</i> and comparative genomics of the fire blight <i>Mfu10</i> locus. Genome of the Pacific Crabapple <i>Malus fusca</i> Open
The Pacific crabapple ( Malus fusca ) is a wild relative of the commercial apple ( Malus × domestica ). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an…
Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory Open
The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. In this study we investigated the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) present throug…
Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species Open
Harnessing the plant microbiome has the potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses, while also relieving economic and environmental costs of crop production. While previous studies…
There and back again; historical perspective and future directions for <i>Vaccinium</i> breeding and research studies Open
The genus Vaccinium L. (Ericaceae) contains a wide diversity of culturally and economically important berry crop species. Consumer demand and scientific research in blueberry (Vaccinium spp.) and cranberry (Vaccinium macrocarpon) have incr…
<i>Linnemannia elongata</i> (Mortierellaceae) stimulates <i>Arabidopsis thaliana</i> aerial growth and responses to auxin, ethylene, and reactive oxygen species Open
Harnessing the plant microbiome has the potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses, while also relieving economic and environmental costs of crop production. While previous studies…
View article: Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry
Blueprint for Phasing and Assembling the Genomes of Heterozygous Polyploids: Application to the Octoploid Genome of Strawberry Open
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated …
Evolutionary history and pan-genome dynamics of strawberry ( <i>Fragaria</i> spp.) Open
Significance Strawberry is a very popular fruit. The strawberry genus ( Fragaria ) has emerged as a model system for various fundamental and applied research in recent years. Here, by using high-throughput sequencing technologies, we provi…
Machine learning approaches to identify core and dispensable genes in pangenomes Open
A gene in a given taxonomic group is either present in every individual (core) or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable…
Machine learning approaches to identify core and dispensable genes in pangenomes Open
A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensabl…
Evolution of Conserved Noncoding Sequences in <i>Arabidopsis thaliana</i> Open
Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence–absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation…
Disease Resistance Genetics and Genomics in Octoploid Strawberry Open
Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding p…