A total of 80 Gb of Oxford Nanopore Technologies reads was used to assemble the ‘Munstead’ genome using the Canu genome assembler software. Following multiple rounds of error correction and scaffolding using Hi-C data, the final chromosome-scale assembly represents 795,075,733 bp across 25 chromosomes with an N50 scaffold length of 31,371,815 bp. Benchmarking Universal Single Copy Orthologs analysis revealed 98.0% complete orthologs, indicative of a high-quality assembly representative of genic space. Annotation of protein-coding sequences revealed 58,702 high-confidence genes encoding 88,528 gene models. Access to the ‘Munstead’ genome will permit comparative analyses within and among lavender accessions and provides a pivotal species for comparative analyses within Lamiaceae.
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Abstract Objectives Lavandula angustifolia (English lavender) is commercially important not only as an ornamental species but also as a major source of fragrances. To better understand the genomic basis of chemical diversity in lavender, we sequenced, assembled, and annotated the ‘Munstead’ cultivar ofL. angustifolia .Data description -
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Abstract Objectives Petrea volubilis , a member of the Order Lamiales and the Verbenaceae family, is an important horticultural species that has been used in traditional folk medicine. To provide a genome sequence for comparative studies within the Order Lamiales that includes important families such as Lamiaceae (mints), we generated a long-read, chromosome-scale genome assembly of this species.Data description Using a total of 45.5 Gb of Pacific Biosciences long read sequence, we generated a 480.2 Mb assembly of
P. volubilis, of which, 93% is chromosome anchored. Representation of genic regions was robust with 96.6% of the Benchmarking of Universal Single Copy Orthologs present in the genome assembly. A total of 57.8% of the genome was annotated as a repetitive sequence. Using a gene annotation pipeline that included refinement of gene models using transcript evidence, 30,982 high confidence genes were annotated. Access to theP. volubilis genome will facilitate evolutionary studies in the Lamiales, a key order of Asterids that includes significant crop and medicinal plant species. -
Udall, J (Ed.)Abstract Availability of readily transformable germplasm, as well as efficient pipelines for gene discovery are notable bottlenecks in the application of genome editing in potato. To study and introduce traits such as resistance against biotic and abiotic factors, tuber quality traits and self-fertility, model germplasm that is amenable to gene editing and regeneration is needed. Cultivated potato is a heterozygous autotetraploid and its genetic redundancy and complexity makes studying gene function challenging. Genome editing is simpler at the diploid level, with fewer allelic variants to consider. A readily transformable diploid potato would be further complemented by genomic resources that could aid in high throughput functional analysis. The heterozygous Solanum tuberosum Group Phureja clone 1S1 has a high regeneration rate, self-fertility, desirable tuber traits and is amenable to Agrobacterium-mediated transformation. We leveraged its amenability to Agrobacterium-mediated transformation to create a Cas9 constitutively expressing line for use in viral vector-based gene editing. To create a contiguous genome assembly, a homozygous doubled monoploid of 1S1 (DM1S1) was sequenced using 44 Gbp of long reads generated from Oxford Nanopore Technologies (ONT), yielding a 736 Mb assembly that encoded 31,145 protein-coding genes. The final assembly for DM1S1 represents a nearly complete genic space, shown by the presence of 99.6% of the genes in the Benchmarking Universal Single Copy Orthologs (BUSCO) set. Variant analysis with Illumina reads from 1S1 was used to deduce its alternate haplotype. These genetic and genomic resources provide a toolkit for applications of genome editing in both basic and applied research of potato.more » « less
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Abstract Sweet corn (
Zea mays L.) is consistently one of the most highly consumed vegetables in the United States, providing a valuable opportunity to increase nutrient intake through biofortification. Significant variation for carotenoid (provitamin A, lutein, zeaxanthin) and tocochromanol (vitamin E, antioxidants) levels is present in temperate sweet corn germplasm, yet previous genome‐wide association studies (GWAS) of these traits have been limited by low statistical power and mapping resolution. Here, we employed a high‐quality transcriptomic dataset collected from fresh sweet corn kernels to conduct transcriptome‐wide association studies (TWAS) and transcriptome prediction studies for 39 carotenoid and tocochromanol traits. In agreement with previous GWAS findings, TWAS detected significant associations for four causal genes,β‐carotene hydroxylase (crtRB1 ),lycopene epsilon cyclase (lcyE ),γ‐tocopherol methyltransferase (vte4 ), andhomogentisate geranylgeranyltransferase (hggt1 ) on a transcriptome‐wide level. Pathway‐level analysis revealed additional associations fordeoxy‐xylulose synthase2 (dxs2 ),diphosphocytidyl methyl erythritol synthase2 (dmes2 ),cytidine methyl kinase1 (cmk1 ), andgeranylgeranyl hydrogenase1 (ggh1 ), of which,dmes2 ,cmk1 , andggh1 have not previously been identified through maize association studies. Evaluation of prediction models incorporating genome‐wide markers and transcriptome‐wide abundances revealed a trait‐dependent benefit to the inclusion of both genomic and transcriptomic data over solely genomic data, but both transcriptome‐ and genome‐wide datasets outperformed a priori candidate gene‐targeted prediction models for most traits. Altogether, this study represents an important step toward understanding the role of regulatory variation in the accumulation of vitamins in fresh sweet corn kernels.
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