Next Generation Sequencing De Novo Assembly of Vulnerable Species
Reference genomes are valuable tools for understanding the unique biology of any organism, especially for species considered vulnerable or at risk of extinction. Knowing the genetic basis behind an organism’s activities for survival – namely obtaining food and reproducing – can guide conservation efforts, which have no resources to waste.
NGS methods, which lowered the cost of the human genome by orders of magnitude, made it possible to sequence many more genomes. However, NGS strategies came with new computational challenges for assembling the sequences DNA polymers, which span eight orders of magnitude, from short reads of 50-300 bp. BGI developed SOAPdenovo, a suite of open-source computational tools specifically for de novo assembly with NGS reads, that enabled many first-time genome assemblies of diverse and interesting species.
The 2.25 Gb genome of the giant panda, Ailuropoda melanoleura, was the first genome assembled de novo entirely through NGS methods alone in 2009. With fewer than 2,000 animals living in the wild, a famously restricted diet of mostly bamboo, and a very low rate of reproduction, efforts were urgent but assembling this large and highly heterozygous (high variation between homologous chromosomes) genome would have been prohibitively costly with pre-NGS methods.
This genome, the first from an animal in the Ursidae, i.e. bears, family, and the second ever carnivore sequenced gave first-time insights into the panda’s diet and reproduction. Interestingly, pandas retain the genes that make bears carnivores and lack genes for digesting bamboo, prompting questions about its relationship with gut microbes that allow it to digest bamboo. The BGI-led team also identified genes critical to reproduction, paving the way for further investigation that could help conservation efforts.
In 2016, a global collaboration including BGI assembled the genome of another vulnerable animal with features unlike any other - the seahorse. Their bony bodies lack caudal fins - the basic means for locomotion for most fish, and pelvic fins - which are analogous to the hindlimbs of four-limbed animals, they feed through a tubular mouth, and they are one of two species where males - not females - have a brood pouch, i.e. they become ‘pregnant’ and carry the fertilized eggs until they hatch. The team identified key genes for these features using NGS, SOAPdenovo, and complementary gene knockout experiments, providing us with the genetic basis to understand their livelihood.
BGI has now enabled big leaps in the conservation of over a dozen vulnerable plant and animal species by spearheading or contributing to their de novo genomes. They include the polar bear, the sperm whale, the salt-tolerant desert poplar, and a ‘living fossil’ known as the dove tree.
