October 29, 2013, Shenzhen, China - Researchers from Nanjing Normal University and BGI report their original genomic research on Baiji, also known as Yangtze River dolphin (Lipotes vexillifer). The study gives new insight into the genetic and evolutionary adaptations of Dolphin, and provides valuable resources for the conservation of mammals and cetaceans in particular. The latest study was published online in the journal Nature Communications.
Nicknamed "Goddess of the Yangtze", the baiji was regarded as the goddess of protection by local fishermen and boatmen in China. Unfortunately, this species has suffered huge losses in recent decades largely due to the extreme pressures brought by human's activities. The baiji has become one of the most famous species in aquatic conservation. There have been many great efforts made to conserve the baiji, but most of them failed.
In this study, researchers presented a high-quality draft genome and three re-sequenced genomes of the baiji using next-gen sequencing technology. Comparative genomic analysis revealed that cetaceans (baiji and the bottlenose dolphin) have a slower molecular clock than previous thought.
The further analysis reveals that the genes involved in oxidoreductase activity, ferric iron binding, metabolic processes and ATPase activity show significant expansion, whereas the genes involved in olfactory receptor activity decreased most significantly. Researchers suggested that these changes of genes maybe related with the baiqi's basic physiological activities required for underwater living, such as oxygen carrying and sensing.
Researchers found there were many factors related with the aquatic adaptations of cetaceans, such as positively selected genes (PSGs), and some functional changes. One of the noticeable findings is that PSGs in the baiji lineage were also involved in DNA repair and response to DNA damage stimulus, which have not been reported in previous studies of mammals or dolphin.
The independent origin of echolocation in toothed whales and echolocating bats is a classic model of convergent evolution. When identifying genes exhibiting convergent evolution in the baiji and bat, researchers found nine genes (including SLC26A5, TMC1, and DFNB59) have evolved under significant accelerated evolution, and 17 genes contained parallel amino acid changes in echolocating mammals.
Compared to all other mammalian genomes reported so far, researchers also found a significantly lower number of heterozygous single nucleotide polymorphisms (SNPs) in the baiji. The reconstruction of the demographic history of the baiji indicated that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.
Fengming Sun, project manager from BGI, said, "We not only found some special evolutionary characterics of baiji, but also found that the functionally extinct of this species was mainly due to human activities. The high-quality draft genome of baiji will provide a valuable resource for researchers to uncover the genetic mechanisms underlying extinct species, and will make a great contribution to the protection of endangered species."
BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.
BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 250 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, have sequenced the human Gut metagenome, and a significant proportion of the genomes for 1,000 genomes. For more information about BGI please visit http://www.genomics.cn.
Bicheng Yang, Ph.D.
Public Communication Officer
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