They are the cuddly, roly-poly giants that are the face of the wildlife conservation movement. Unfortunately, giant pandas have earned the honor. They are one of the most endangered species on earth. They are also something of an enigma. They are carnivores who subsist almost entirely on a diet of plants. They have opposable thumb-like appendages on their front paws. They look like a bear that wants to be a raccoon (or a raccoon that wants to be a bear?). Their unique characteristics kept scientists debating their classification for years. Did they belong with the bears (Ursidae), raccoons (Procyonidae) or did they belong in a family of their own?
Molecular studies seem to have resolved the classification debate; giant pandas (Ailuropoda melanoleuca) are most closely related to bears. Their ancestors split from the ursid lineage just before the radiation that led to modern bears, and thus have their own subfamily Ailuropodinae. But what of the other puzzling characteristics? Why on earth do they eat bamboo?
In a paper published in the January 21, 2010 issue of Nature, we begin to find answers. The authors have generated and assembled a draft sequence of the giant panda genome (Li, R. et al.;1). Using next-generation massively parallel sequencing technology allowed the giant panda genome to be sequenced and assembled in a fraction of the time that it would take to sequence a large eukaryotic genome using traditional sequencing methods. The technology the authors employed uses randomly fragmented genomic DNA, which can be amplified to create dense clusters of DNA copies that can be sequenced. These sequences can be overlapped to generate a contiguous sequence. The authors used 134Gb of high-quality sequence reads (equivalent to 56-fold coverage of the whole panda genome) to do the de novo assembly.
The whole-genome sequencing of one of the most endangered creatures on earth is an accomplishment all on its own. It is the first fully sequenced genome from the bear (Ursudae) family and only the second (behind the dog; 2) from the order Carnivora.
It is also the sequence of a carnivore that doesn’t eat meat. And now, thanks to the work of Li et al., we are beginning to understand why. Pandas, they found, have the genes that encode the digestive enzymes you would expect in a carnivore (protease, amylase, lipase, cellulose, lactase, invertase and maltase). At the same time, they do not have the digestive enzymes expected in an herbivore (endoglucanase, exoglucanase and beta-glucosidase). So they eat plants, but don’t have the genetic means to digest them. Most likely they are depending upon some sort of microbial break down of the plant material in their digestive tract.
Why, exactly, would a carnivore almost exclusively eat plants? Li et al. may have found the answer to that as well. They looked at the receptors implicated in the sense of taste. In particular they focused on the T1R gene family, that encodes the receptors for savoriness (or umami, as it is termed in the paper). Savoriness is sensed by detecting the carboxylate anion of glutamic acid, the naturally occurring amino acid in things like meat, cheese and other high-protein foods. In the panda genome, two of the genes (T1R2 and T1R3) in this family are intact, but the third (T1R1) has become a pseudogene. The T1R1/T1R3 heterodimer is the known receptor for savoriness, and it appears that the pandas don’t have a functioning one thanks to that T1R1 pseudogene. Genetically speaking, giant pandas are carnivores. However, dietary habits are greatly influenced by the sense of taste, and the giant panda is a carnivore that can’t taste meat.
Luckily for the giant panda, Li et al. also found a high heterozygosity rate. This suggests that the genetic variability may still exist in the giant panda population to offer a good hope of long-term survivability despite the species’ depressingly small population numbers.
So there you have it. Li et al has offered potential answers to some of the mysteries surrounding the giant pandas, and hope for their future as well.
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., Zhang, Z., Zhang, Y., Wang, W., Li, J., Wei, F., Li, H., Jian, M., Li, J., Zhang, Z., Nielsen, R., Li, D., Gu, W., Yang, Z., Xuan, Z., Ryder, O., Leung, F., Zhou, Y., Cao, J., Sun, X., Fu, Y., Fang, X., Guo, X., Wang, B., Hou, R., Shen, F., Mu, B., Ni, P., Lin, R., Qian, W., Wang, G., Yu, C., Nie, W., Wang, J., Wu, Z., Liang, H., Min, J., Wu, Q., Cheng, S., Ruan, J., Wang, M., Shi, Z., Wen, M., Liu, B., Ren, X., Zheng, H., Dong, D., Cook, K., Shan, G., Zhang, H., Kosiol, C., Xie, X., Lu, Z., Zheng, H., Li, Y., Steiner, C., Lam, T., Lin, S., Zhang, Q., Li, G., Tian, J., Gong, T., Liu, H., Zhang, D., Fang, L., Ye, C., Zhang, J., Hu, W., Xu, A., Ren, Y., Zhang, G., Bruford, M., Li, Q., Ma, L., Guo, Y., An, N., Hu, Y., Zheng, Y., Shi, Y., Li, Z., Liu, Q., Chen, Y., Zhao, J., Qu, N., Zhao, S., Tian, F., Wang, X., Wang, H., Xu, L., Liu, X., Vinar, T., Wang, Y., Lam, T., Yiu, S., Liu, S., Zhang, H., Li, D., Huang, Y., Wang, X., Yang, G., Jiang, Z., Wang, J., Qin, N., Li, L., Li, J., Bolund, L., Kristiansen, K., Wong, G., Olson, M., Zhang, X., Li, S., Yang, H., Wang, J., & Wang, J. (2009). The sequence and de novo assembly of the giant panda genome Nature, 463 (7279), 311-317 DOI: 10.1038/nature08696
- Li, R. et al.. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317
- Lindblad-Toh, K. et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803–819
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