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Chinese alligator genome sequenced (free pdf)



From: Ben Creisler
bcreisler@gmail.com

A new online paper in open access that may be of interest:


Qiu-Hong Wan, Sheng-Kai Pan, Li Hu, Ying Zhu, Peng-Wei Xu, Jin-Quan
Xia, Hui Chen, Gen-Yun He, Jing He, Xiao-Wei Ni, Hao-Long Hou,
Sheng-Guang Liao, Hai-Qiong Yang, Ying Chen, Shu-Kun Gao, Yun-Fa Ge,
Chang-Chang Cao, Peng-Fei Li, Li-Ming Fang, Li Liao, Shu Zhang,
Meng-Zhen Wang, Wei Dong and Sheng-Guo Fang.
Genome analysis and signature discovery for diving and sensory
properties of the endangered Chinese alligator.
Cell Research (advance online publication)
doi: 10.1038/cr.2013.104
http://www.nature.com/cr/journal/vaop/ncurrent/full/cr2013104a.html


Crocodilians are diving reptiles that can hold their breath under
water for long periods of time and are crepuscular animals with
excellent sensory abilities. They comprise a sister lineage of birds
and have no sex chromosome. Here we report the genome sequence of the
endangered Chinese alligator (Alligator sinensis) and describe its
unique features. The next-generation sequencing generated 314 Gb of
raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200
genes were predicted in Alligator sinensis using a de novo, homology-
and RNA-based combined model. The genetic basis of long-diving
behavior includes duplication of the bicarbonate-binding hemoglobin
gene, co-functioning of routine phosphate-binding and special
bicarbonate-binding oxygen transport, and positively selected energy
metabolism, ammonium bicarbonate excretion and cardiac muscle
contraction. Further, we elucidated the robust Alligator sinensis
sensory system, including a significantly expanded olfactory receptor
repertoire, rapidly evolving nerve-related cellular components and
visual perception, and positive selection of the night vision-related
opsin and sound detection-associated otopetrin. We also discovered a
well-developed immune system with a considerable number of
lineage-specific antigen-presentation genes for adaptive immunity as
well as expansion of the tripartite motif-containing C-type lectin and
butyrophilin genes for innate immunity and expression of antibacterial
peptides. Multifluorescence in situ hybridization showed that
alligator chromosome 3, which encodes DMRT1, exhibits significant
synteny with chicken chromosome Z. Finally, population history
analysis indicated population admixture 0.60-1.05 million years ago,
when the Qinghai-Tibetan Plateau was uplifted.


Also a news release:

http://phys.org/news/2013-08-whole-genome-sequencing-uncovers-mysteries-endangered.html