- Award ID(s):
- 1741627
- NSF-PAR ID:
- 10404512
- Date Published:
- Journal Name:
- Scientific Data
- Volume:
- 9
- Issue:
- 1
- ISSN:
- 2052-4463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Vitis riparia , a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence ofV. riparia Michx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated usingV. riparia ESTs, BACs, and three de novo transcriptome assemblies of three differentV. riparia genotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of theV. riparia assembly and predicted CDS with the latestV. vinifera ‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with theV. vinifera transcription factors. QTL mapping toV. riparia ‘Manitoba 37’ andV. vinifera PN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understandingV. riparia ’s genetic contributions in grape breeding and research. -
Abstract It remains a major challenge to identify the genes and mutations that lead to plant sexual differentiation. Here, we study the structure and evolution of the sex-determining region (SDR) in
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Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.
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