Wan Q.-H.,Zhejiang University |
Pan S.-K.,BGI Shenzhen |
Hu L.,BGI Shenzhen |
Zhu Y.,Zhejiang University |
And 20 more authors.
Cell Research | Year: 2013
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. © 2013 IBCB, SIBS, CAS All rights reserved.
Zhao L.,Zhejiang University |
Yang H.-Q.,Zhejiang University |
Fang L.-M.,Changxing Yinjiabian Chinese Alligator Nature Reserve |
Pan G.-L.,Changxing Yinjiabian Chinese Alligator Nature Reserve |
And 4 more authors.
Current Zoology | Year: 2013
The Chinese alligator Alligator sinensis is one of the most endangered crocodilian species, and typically exhibits temperature-dependent sex determination. It is extremely important to clarify the sex structure of Chinese alligators to implement recovery projects successfully. However, the sex ratio of wild Chinese alligators remains unknown. In this study, we collected 28 years of sex ratio data from Chinese alligators residing in the natural and artificial habitats of Changxing Nature Reserve, China, and examined the differences in the sex ratio dynamics between these two populations. We observed that the sex ratio of wild Chinese alligators is 1 male to 4.507 females, which was significantly lower compared to that of the captive population (1 to 2.040; P < 0.001), and is significantly different to previously documented sex ratios for this species (all P < 0.01). Furthermore, we documented an annually stable (P = 1.000) female-biased sex ratio for wild alligators at hatching [1 male to 4.747 females; 0.174 (0.167-0.182)], in contrast to a dramatically fluctuating sex ratio (P < 0.001) in captivity [1 male to 1.674 females; 0.374 (0.246-0.593)], showing a potential mechanism for adjusting the sex structure. Finally, we found that the hatchling sex ratios were similar to that of the population sex ratio (P = 0.748), with little correlation to air temperature values in the 60-70 day incubation period during the breeding season (July and August; both P > 0.05). Overall, this study indicates that the stabilized female-biased sex ratio of Changxing Chinese alligators might result from selection pressure caused by local mate competition and major inbreeding. © 2013 Current Zoology.