The sequence and de novo assembly of the giant panda genome

By Ruiqiang Li, Wei Fan, G. Tian, Hong-mei Zhu, Lin He, Jing Cai, Quanfei Huang, Q. Cai, Yinqi Bai, Zhihe Zhang and 111 more. Nature, 2009

1,210 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Nutrition and Dietetics

View Paper: https://www.semanticscholar.org/paper/054eb0a27100f38fb24d401e7485d44617e15568

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Citations in the corpus

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach (2013, positive): “The parasites’ nuclear genome size was estimated based on the k-mer frequency distributions of the entire data sets, respectively, as demonstrated in previous studies (44,45).”
Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data (2013, methodology): “More details about the voting-algorithm can be obtained from Liu et al. (2011). This voting-based refinement is employed because it”
Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum (2011, positive): “DNA libraries with 200 bp, 2 kb and 6 kb inserts were constructed and sequenced with the Illumina Genome Analyzer sequencing technique at the Beijing Genomics Institute at Shenzhen with protocols described previously for the giant panda genome [80].”
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, methodology): “The de Bruijn approach was also used by the SOAPdenovo assembler [9] in generating the first wholly de novo assembly of a large eukaryotic genome sequence (the giant panda, Ailuropoda melanoleuca [10]).”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, methodology): “Genome assembly [4,68-75], followed by whole-genome alignment [38,76,77], is the original method for variant detection between closely related bacterial genomes [78] and has been shown to perform well across multiple sequencing platforms [79].”
Limitations of next-generation genome sequence assembly (2010, background): “, and the panda genome was the first mammalian genome to be assembled using sequence data generated solely using next-generation sequencing (NGS) platform”
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, neutral): “The impact of this technology is vast, with many applications in biosciences, including genome-wide SNP 3 and copy number variation (CNV) 4 discovery, nucleosome mapping 5 and genome-wide methylation profiling 6 , genome re-sequencing 7 and de novo genome assembly 8 .”
Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, methodology): “Afterwards, within Canu, the error-corrected long reads are assembled, building on the design of the Celera Assembler 40–42 , in which the overlaps between the reads are encoded in an overlap graph containing nodes and edges to represent the relationships between the overlapping reads.”
High-quality draft assemblies of mammalian genomes from massively parallel sequence data (2010, background): “There have been some important pioneering efforts (11, 12) for large genomes, but they fall far short of the high-quality draft sequences that can be obtained with the earlier technology.”
Sequencing technologies and genome sequencing (2011, background): “It is now possible to assemble de novo a large genome, a good example can be derived from the recent genome assembly of the giant panda (Li et al. 2010b) which utilized the only short reads provided by next-generation DNA sequencing.”