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Dioscorea alata genome version 2.1

A new version of the Dioscorea alata genomes has been released.

The reference genome is from accession TDa9500328.

Data Usage Policy: Dioscorea alata v2.1

Restrictions on dataset usage

I would like to use this data to help clone a gene, analyse a gene family, etc.
Please use this data to advance your studies. Please cite "Dioscorea alata v2.1 DOE-JGI, http://phytozome.jgi.doe.gov/".

I would like to do a large-scale comparison of Dioscorea alatato other genomes, and/or a global analysis of its gene content.
We are committed to early data release and, as a service to the yam research and breeding community, we are therefore making the chromosome-scale D. alata genome assembly version 2 available prior to publication. Please note that gene names are provisional and subject to change over time.

We (the data producers) encourage the pre-publication use of these data in accordance with the Toronto data sharing principles described at https://www.nature.com/articles/461168a. We anticipate publishing a description of the genome and genetic linkage maps in 2020. Questions about data use should be directed to Dr. Jessica Lyons (see below).

By accessing these resources, data users agree that the following analyses are reserved for first description by the data producers:

  • Genomic landscape and higher-order chromatin structure
  • Chromosome structure comparison with D. rotundata
  • Gene and repeat content analyses
  • Analyses of genome-wide intra-species variation
  • Genome-wide inter-species comparisons

Contacts

  • Jessica Lyons (UC Berkeley) (email: jblyons AT berkeley DOT edu)
  • Ranjana Bhattacharjee (IITA) (email: r.bhattacharjee AT cgiar DOT org)
  • Jude Obidiegwu (NRCRI) (email: ejikeobi AT yahoo DOT com)

Available Tools:

BLAST

FTP Site

ftp://ftp.yambase.org

Genome browser

Dioscorea alata Genome Browser at JGI

Publication

Chromosome evolution and the genetic basis of agronomically important traits in greater yam (2021). Jessen V. Bredeson*, Jessica B. Lyons*, Ibukun O. Oniyinde, Nneka R. Okereke, Olufisayo Kolade, Ikenna Nnabue, Christian O. Nwadili, Eva Hřibová, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey J. Barton, Anna V. Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie N. Egesi, Jonathan Featherston, Asrat Asfaw, Gordon G. Simpson, Jaroslav Doležel, Prasad S. Hendre, Allen Van Deynze, Pullikanti Lava Kumar, Jude E. Obidiegwu, Ranjana Bhattacharjee, Daniel S. Rokhsar. https://doi.org/10.1101/2021.04.14.439117