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.

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

“…In total, we generated 237.2 Gb data of paired-ends ranging from 50 to 100 bp. To reduce the effect of sequencing error to the assembly, we have taken a series of checking and filtering steps on reads generated 10 . Using stringent criteria, only 130.7 Gb data were considered for de novo genome assembly.…”

“…This increased N50 to 516.06 kb (longest scaffold in chromosome level of 48.97 Mb) ( Table 1). Our draft genome assembly has <5.69% (~34 Mb) unclosed gaps 10 . These analyses showed that mapped genetic loci provide additional information for assembling superscaffolds, especially in regions in which scaffolds were not large enough to cross the repeat rich regions (Supplementary Fig.…”

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

“…The libraries were prepared following the manufacturer's standard instructions and sequenced on Illumina HiSeq (2000) platform. Whole genome sequencing was done as described previously 22 . A total of 178.98 Gb data and 198.39 Gb data were generated from these libraries for the CR macaque and CE macaque, respectively.…”

Genetics of Taste and Smell

“…The giant panda, which eats only plant food, has lost the umami receptor during evolution. 101 The recent observation that obese women prefer higher concentrations of MSG in soup suggests that this taste quality may be of importance in determining food intake and body weight. 102 …”