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

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.

We are indebted to Stuart A. West, Jacqui A. Shykoff, Stephen Compton, Douglas W. Yu, JIA AiQun, ZHANG ZhaoYang, LI YaoTang and Edward A. Herre for their discussions and comments during the preparation and revision of this manuscript. SUN BaoFa and ZHENG Qi provided the empirical data analysis. This work was supported by the National Basic Research Program of China (Grant No. 2007CB411600), the National Natural Science Foundation of China (Grant Nos. 30670272, 30770500 and 10761010), the Yunnan Natural Science Foundation (Grant No. 2009CD104), the West Light Foundation of the Chinese Academy of Sciences and the National Social Science Foundation of China (Grant No. 08XTJ001).