Sweetpotato Genomic Tools

BLAST Search I. trifida JBrowse I. triloba JBrowse Annotation Search Tool
Ipomoea e-PCR Tool Download

Sweetpotato Genomics Resource

Sweetpotato (Ipomoea batatas) is an important food crop throughout the world and especially in developing countries due to its caloric and nutritional benefits. Efforts to improve breeding of sweetpotato for traits important to small farmers can be accelerated through the use of genomics-assisted (genomics-guided) breeding. The sweetpotato genome is large and complex due to its ploidy (hexaploid) and heterozygosity. Thus, to facilitate genome-enabled breeding in hexaploid sweetpotato, participants in the Bill & Melinda Gates Foundation-funded Genomic Tools for Sweetpotato Improvement project have generated the sequence for two diploid, highly inbred Ipomoea species: Ipomoea trifida (NSP306) and Ipomoea triloba (NSP323) to serve as a reference sequence for the hexaploid sweetpotato genome.

The two genomes were first repeat masked then annotated for protein-coding genes using a set of transcript and protein evidence. The Ipomoea trifida (NSP306) assembly is 462 Mb with 32,301 annotated high confidence gene models whereas the Ipomoea triloba (NSP323) assembly is 458 Mb with 31,426 annotated high confidence gene models. The Sweetpotato Genomics Resource contains a set of search and query tools including a BLAST server, genome browsers for these two reference genomes, and gene report pages for all annotated genes in the two species. Also included on both the genome browsers and in the gene report pages are sequence polymorphisms identified by aligning whole genome shotgun and RNA-sequencing reads from hexaploid sweetpotato to both Ipomoea reference genomes.

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What's New

November 2, 2018: The paper "Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement" by Wu et al. was published in Nature Communications. (https://doi.org/10.1038/s41467-018-06983-8).

October 11, 2018: The paper "Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance" by Lau et al. was published in Plant Direct. (https://doi.org/10.1002/pld3.92).

April 18, 2018: The Ipomoea e-PCR tool has been released. The Ipomoea e-PCR tool performs an in-silico PCR simulation (e-PCR) using the diploid Ipomoea pseudomolecules.

August 11, 2017: The FPKM matrix for 15 abiotic and biotic stress RNA-seq libraries is available on the GT4SP Project Download Page. RNA-seq coverage tracks for these libraries are also available on the I. trifida and I. triloba genome browsers. Tracks for putative SSRs and alignments of the DM potato, Arabidopsis, morning glory (I. nil), and tomato proteins have also been added to the genome browsers.

April 17, 2017: The I. trifida and I. triloba pseudomolecules and annotation were released. The SPGR web tools, BLAST server, genome browser, and GT4SP download page were updated.

August 1, 2016: The Sweetpotato Genomics Resource was released.

July 4, 2016: Four researchers including two from the GT4SP project were awarded the World Food Prize for work on developing orange-fleshed sweetpotato.

Maintenance Notice

Web pages may be unavailable or only partially functional during server maintenance, which is planned for the first Wednesday of every month.