The sequence and de novo assembly of the giant panda genome

Abstract

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Figure 1. Assessment of assembly quality

a, Distribution of sequencing depth of the assembled genome. b, Comparison of the assembled genome with a BAC sequence. Read depth on the BAC was calculated by mapping the Illumina Genome Analyser short reads onto the BAC sequence. The predicted gene and annotated transposable elements (TEs) on the BAC sequence are shown in green and red, respectively. The remaining unclosed gaps on the scaffolds are marked as white blocks.

Figure 2. Conserved sequences among the panda, dog and human genomes

a, The total lengths of aligned and unaligned non-repetitive sequences. Each of the three genomes contains 1.4Gb of non-repetitive sequences. Pairwise whole-genome alignment was performed using Blastz. The lengths shown are in Mb. b, Syntenic view of the dog chromosome 37, 35 panda scaffolds (>10 kb), and the human chromosome 2. Note that the 3Mb region at the end of dog chromosome 37 was unanchored.

Figure 3. Dynamic evolution of orthologous gene clusters

The estimated numbers of orthologue groups in the common ancestral species are shown on the internal nodes. The numbers of orthologous groups that expanded or contracted in each lineage after speciation are shown on the corresponding branch, with ‘+’ referring to expansion and ‘−’ referring to contraction.

Figure 4. Structure of the umami receptor T1R1 gene

Two frameshift mutations occurred in the third and sixth exons (red) of the panda T1R1 gene. The third exon contained a 2-bp (‘GG’) insertion; the sixth exon contained a 4-bp (‘GTGT’) deletion.

Figure 5. Panda heterozygous SNP density

a, Statistics of identified heterozygous SNPs. Analysed regions are the genomic regions with proper unique read coverage that were used for heterozygote detection. The panda X-chromosome-derived scaffolds were identified by Blastz alignment to the dog X chromosome. b, Distribution of heterozygosity density in the panda diploid genome. Heterozygous SNPs between the two sets of chromosomes of the panda diploid genome were annotated, then non-overlapping 50-kb windows were chosen and heterozygosity density in each window was calculated.