GT4SP Project Ipomoea Genome Pseudomolecules and Annotation - Version 3

The International Sweetpotato Genome Initiative (ISPGI) is pleased to make available I. trifida and I. triloba genome sequences for use by public and private research communities as a resource to facilitate plant biology discoveries and plant breeding programs.

The paper "Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement" describing the sequencing and analysis of the I. trifida and I. triloba genome sequences was published in Nature Communications. ( https://doi.org/10.1038/s41467-018-06983-8 ). The data below is also archived at the Dryad Digital Repository ( https://doi.org/10.5061/dryad.b9m61cg ).

The I. trifida and I. triloba genome sequencing is primarily supported by Bill & Melinda Gates Foundation through the GT4SP (Genomic Tools for Sweetpotato Improvement) project.


Zhangjun Fei (Boyce Thompson Institute/Cornell) has sequenced and assembled two diploid Ipomoea species: Ipomoea trifida (NSP306) and Ipomoea triloba (NSP323). The genome assemblies have been annotated by Robin Buell and her group at Michigan State University.

The version 3 pseudomolecules, annotation, and RNA-seq gene expression data are available to download below. The genome annotation can also be viewed in the JBrowse genome browser. The browser also provides tracks displaying evidence alignments, RNA-seq coverage, putative repeats, and SNP calls. A BLAST server is also available for searching your sequences against the version 3 annotation and assemblies.

The annotation files and JBrowse links below are the v3 annotations based the pseudomolecules (assembly v3).

Release Date: April 17, 2017:

JBrowse Genome Browser

BLAST Server

Genome Assemblies

Genome Annotation

The genome annotation is based on the version 2 Ipomoea trifida (NSP306) and Ipomoea triloba (NSP323) assemblies. The annotation was transferred to the v3 pseudomolecules and final locus names assigned.

RNA-seq Gene Expression Data

I. trifida and I. triloba RNA-seq libraries were mapped in paired-end read and single-stranded library mode to their respective version 3 genome assemblies using Tophat (v2.1.0). Gene expression for the version 3 high confidence gene models was calculated as FPKM using Cufflinks (v2.2.1).

Contact:

Dr. C. Robin Buell, Michigan State University - buell@msu.edu