Video tip of the week: Yak Genome Database


For this week’s video tip of the week we’ll explore the Yak Genome Database. Honestly I wouldn’t have predicted a week where I talk about the Sasquatch genome, the abominable snowman (really, it was a Nature paper), and yaks. But genomics is pretty wild these days.

Some folks are getting jaded about the new genome every day we seem to be getting–Carl Zimmer called it YAGS: “yet another genome syndrome” a couple of years ago already. But I’m delighted every time I see a new genome. Certainly the press releases are overselling the results in many cases. However, as Carl also points out:

What remains truly exciting is the kind of research starts after the genomes are sequenced: discovering what genes do, mapping out the networks in which genes cooperate, and reconstructing the deep history of life.

And I completely agree with this. However, I think the research teams deserve a bit of horn-tooting when they roll out their sequencing paper. The foundation for the future work needs to be done, and it needs to become available with some initial analysis. Then it becomes available for others to take that work further and for that team to continue to learn more.

The other great thing about the price reduction in sequencing and the access of new research groups is the range of species we now see coming along. Mushrooms. Birch trees. Puerto Rican parrots. Watermelon. Bananas (with the best Venn diagram in genome papers so far). Some of these are species that only small research groups have focused on before. But the sequence data leads to so many potential novelties in our understanding of their biological niche. Such is the case with yak.

Yaks are probably not on the radar of a lot of American researchers. But this is an important agricultural species for Tibet. It also has climate adaptations that are useful to understand. If we continue to face potentially rapid climate alterations, there are a lot of things we are going to want to know about how species adapt to different scenarios. We may need to help protect them from emerging pathogens. We may need to help coax some to different breeding cycles. And the more data we have about those species, the better.

However, the “big” genome data centers are not always able to absorb new and less supported species quickly. They have funding focus issues and limited resources too. So these species groups are often the ones who have to deliver genome access themselves. Most often I’m seeing these groups are setting up an installation of GBrowse. So understanding how to interact with that software can be really helpful as you look for new insights from new genomes.

So I offer you the Yak Genome Database:

We used the Generic Genome Browser (GBrowse) developed as part of the Generic Model Organism Database project (GMOD; http://gmod.org/wiki/GMOD) to visualize the genome of the yak [7]. In addition, predicted genes, single nucleotide variants (SNVs), multiple types of RNA sets and repeats contained within the YGD can be visualized using Gbrowse.

Have a browse around the yak genome. In the browser paper they highlight the ARG2 gene page in Figure 1, and the region of the GPR125 G-protein coupled receptor in Figure 2. I’ll show that in the video as well.

 

Quick link:

Yak Genome Database: http://me.lzu.edu.cn/yak/

References:

Hu, Q., Ma, T., Wang, K., Xu, T., Liu, J., & Qiu, Q. (2012). The Yak genome database: an integrative database for studying yak biology and high-altitude adaption BMC Genomics, 13 (1) DOI: 10.1186/1471-2164-13-600

Qiu, Q., Zhang, G., Ma, T., Qian, W., Wang, J., Ye, Z., Cao, C., Hu, Q., Kim, J., Larkin, D., Auvil, L., Capitanu, B., Ma, J., Lewin, H., Qian, X., Lang, Y., Zhou, R., Wang, L., Wang, K., Xia, J., Liao, S., Pan, S., Lu, X., Hou, H., Wang, Y., Zang, X., Yin, Y., Ma, H., Zhang, J., Wang, Z., Zhang, Y., Zhang, D., Yonezawa, T., Hasegawa, M., Zhong, Y., Liu, W., Zhang, Y., Huang, Z., Zhang, S., Long, R., Yang, H., Wang, J., Lenstra, J., Cooper, D., Wu, Y., Wang, J., Shi, P., Wang, J., & Liu, J. (2012). The yak genome and adaptation to life at high altitude Nature Genetics, 44 (8), 946-949 DOI: 10.1038/ng.2343

Stein, L. (2002). The Generic Genome Browser: A Building Block for a Model Organism System Database Genome Research, 12 (10), 1599-1610 DOI: 10.1101/gr.403602