NEW YORK (GenomeWeb News) – In a paper appearing in the advance, online edition of Nature yesterday, researchers from the Beijing Genomics Institute and elsewhere reported on their sequencing and initial analyses of a draft version of the giant panda genome.
The sequencing effort makes the giant panda, Ailuropoda melanoleura, the second carnivore and first member of the bear family to have its full genome sequenced and reported. The team sequenced the genome using the Illumina Genome Analyzer and their analyses are providing insights into everything from the animal's bamboo diet to its genetic diversity. Those involved say the genome sequence may also aid in panda conservation in the future.
Past studies suggest just 2,500 to 3,000 giant pandas remain in a mountainous region of western China. And, researchers explained, the animal is facing extinction threats due to habitat destruction and other factors.
Such conservation issues, coupled with a long-standing debate over the animal's phylogenetic relationship to other mammals, have spurred interest in the panda genome. The BGI team announced that they had sequenced a draft panda genome last October, but the current paper marks the first publication of this work.
The researchers used the Illumina Genome Analyzer to tackle the 2.4 billion base giant panda genome, which is housed on 20 autosomal chromosome pairs and one pair of sex chromosomes.
Using a whole genome shotgun approach, the team sequenced paired-end libraries constructed from a three-year-old female panda at China's Chengdu breeding center. They also used Sanger sequencing of nine bacterial artificial chromosomes to verify their sequence assembly.
Overall, contigs generated so far cover contain 2.25 billion bases of DNA covering roughly 94 percent of the giant panda genome. Although they were able to fill many small sequence gaps, the team noted, some remain — likely corresponding to repeats, including tandem repeats and carnivore-specific transposable elements.
During their analyses of the panda sequence, the researchers detected 26 of the 27 panda genes already found in GenBank. As expected, the remaining gene, found on the Y chromosome, was absent in the female panda.
Similar to the dog genome, the researchers found that more than 36 percent the panda genome is comprised of transposable elements. In contrast, about 46 percent of the human genome is thought to consist of such transposable elements.
Overall, the team found fairly high genomic synteny when they did whole genome alignments of the panda, dog, and human genomes, though the dog genome contained far more rearrangements than the panda genome, and the panda genome appears to have evolved relatively slowly.
So far the team has identified 2.7 million heterozygous SNPs, 267,958 small insertions and deletions, and nearly 4,400 larger insertions and deletions in the panda genome. Even so, they noted, the current assembly has likely led to underestimates of the structural variation in the panda genome.
Based on comparisons of panda sequence with sequence from other mammals, the researchers estimate that the panda genome contains 21,001 genes, including 18,643 gene clusters orthologous to dog, mouse, or human genes.
Among the genes detected were 626 genes that apparently function in processes such as defense, immunity, and cell signaling as well as more than 2,500 panda-specific genes.
The researchers also began investigating the genetic bases of panda characteristics affecting the animal's diet, reproductive patterns, and so on.
For example, they identified frameshift mutations in a gene called T1R1, a member of the gene family involved in sensing savory flavors, which has rendered T1R1 a pseudogene. But while that might explain the panda's preference for bamboo over meat, they explained, the team could not find genes expected to contribute to bamboo digestion, suggesting the animal's gut microbiome might assist in this process.
Those involved say the study underscores the value of short read sequencing for looking at other mammalian genomes. At the Genomic Tools and Technologies Summit this spring, BGI associate director Jun Wang noted that the use of the SOAPdenovo short read algorithm to assemble the panda genome served as proof-of-concept that the algorithm could also be used to assemble the human genome.
"Our ability to generate and assemble a draft sequence for an entire mammalian genome using only next-generation Illumina Genome Analyzer short-read sequencing technology indicates that such technology can be used to generate many more mammalian genome draft sequences in a rapid and cost-effective manner," the paper's authors concluded.