Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca)

BGI has carried out deep sequence exploration on nine BACs of giant panda with traditional sanger sequencing methods. Sequences and structure information of new genes and repeats were predicted, which greatly fills the gaps of genomics study on giant panda. In addition, the nine sequences assembled based on traditional phrap methods provided as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda generated by the Illumina GA sequencing technology. This study is reported in Volumn 53 (Januray, 2010) of SCIENCE CHINA Life Sciences because of its significant research value.

Giant panda (Ailuropoda melanoleuca), known as the “Chinese treasure”, is one of the most endangered species in the world. A survey revealed that only about 2500~3000 individuals remain in the wild. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an “evolutionary dead end”. In recent years, strenuous efforts have been made to study and protect this animal. Considerable knowledge of its physiology, biochemistry, genetic diversity and ecology has been gathered.

MHC II genomic region and mitochondrial sequence of giant panda were sequenced and annotated. Phylogenic tree was generated with mitochondrial sequences of giant panda and other bear speices, suggesting that giant panda belongs to the species of Usrides. Genome diversities of giant panda were also explored, suggesting that giant panda is not a species at an evolutionary “dead end”. Conservation strategies should focus on the restoration and protection of wild habitat and the maintenance of the substantial regional genetic diversity.

In this work, we sequenced and assembled nine BACs of giant panda, about a genomic region of 878 kb, which greatly fills the gaps of genomic study on giant panda. Twelve protein coding genes were predicted, seven of which could be functionally annotated. About 27 percent of the BAC sequence was predicted to be composed of repeats. A phylogenetic tree was constructed across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panada.

With the detailed sequence information provided, further studies should be carried out on interested genes of giant panda to get deeper understanding of this species. Our data is a preview of the giant panda genome. The whole genome sequence of giant panda has been released and the research article has been published on Nature recently. The assembled sequences of these nine BACs were used as a validation resource for accuracy assessment of the assembly of the whole genome sequencing reads based on new Illumina GA sequencing technology.

All these studies greatly accelerate the genomics studies on giant panda which supports the discovery of fundamental molecular biology knowledge to guide the protection of the endangered animal giant panda.

Most authors are affiliated at BGI, which is a forerunner in the field of genomics and is a influential sequencing and bioinformatics center in the world.

Funding from the Shenzhen Municipal Government and the Yantian District Government supported this research.

Reference: ZHENG Y, CAI J, LI J W, et al. Sequencing, annotation and comparative analysis of nine BACs of giant panda (Ailuropoda melanoleuca). Sci China Life Sci, 2010, 53:107-111
http://www.scichina.com:8082/sciCe/EN/abstract/abstract416116.shtml

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