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- Avian-specific conserved genomic elements play important regulatory roles in the macroevolution of avian-specific features
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- BGI involved in publication of the first seahorse genome in Nature
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December 15, 2016, Whole genome of the tiger tail seahorse (Hippocampus comes) was sequenced for the first time and the latest study was published as a cover story in Nature.
The study was an international collaboration including researchers from South China Sea Institute of Oceanology of Chinese Academy of Sciences (China), University of Konstanz (Germany), BGI (China) and A*STAR (Singapore).
Seahorses (Family Syngnathidae) exhibit certain highly specialized phenotypes, such as a toothless tubular mouth, a body covered with bony plates, absence of caudal and pelvic fins, and a prehensile tail. They are also unique among vertebrates due to their ‘male pregnancy’ and an unusual sex-role reversal whereby males nourish developing embryos in a brood pouch until hatching and parturition occur.
In order to understand the genetic bases of their unique morphology and reproductive system, the research team sequenced the genome of the tiger tail seahorse and performed comparative analyses with genomes of other ray-finned fishes.
In this study, the researchers found that the seahorse genome is the fastest evolving one among the sequenced fishes so far, although the exact reasons still unknown. However, the higher evolutionary rate could have facilitated the emergence of proteins with more efficient or new functions, contributing to the unique body plan. In addition, compared to other teleosts the seahorse genome has lost a substantially higher number of potential cis-regulatory elements, which may play a major role in the evolutionary innovations of seahorses.
Male pregnancy is a unique evolutionary innovation of seahorses and pipefishes. In teleost fishes, the C6AST subfamily of astacin metalloproteases, including high choriolytic enzyme (HCE) and low choriolytic enzyme (LCE), are involved in lysing the chorion surrounding the eggs and leading to hatching of embryos. Another important member of this subfamily, patristacin (pastn), has undergone expansion in the seahorse; meanwhile, five pastn genes are highly expressed in the brood pouch during mid- and late-pregnancy, suggesting a possible common role of this gene for the male pregnancy of syngnathids.
T-box 4 (Tbx4) is a master control gene for limb development. The researchers observed that tbx4 has been lost in the assembled seahorse genome and hypothesized its association with disappearance of pelvic fins. Further knockout of tbx4 in zebrafish recapitulated the ‘pelvic fin-loss’ phenotype of seahorses. The result is a critical highlight of this study.
Meng Xu and Yulan Yang, two of the first authors from BGI, are in charge of genome assembly, annotation and comparative analysis. Prof. Qiong Shi, the vice president and the Chief Scientist of BGI Fisheries, is one of the corresponding authors. He has had co-launched the seahorse genome project with Prof. Qiang Lin from South China Sea Institute of Oceanology and Prof. Byrappa Venkatesh from A*STAR five years ago.
Since seahorses have been widely used for Chinese medicine and treated as vulnerable or endangered animal, the researchers also sequenced the lined seahorse (Hippocampus erectus), an important aquaculture species in China. These datasets will definitely be helpful for improvement of the artificial/molecular breeding and ecological protection of seahorses in the world.