title: Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator.
abstract: 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.
authors.affiliation: The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
authors.forename: Qiu-Hong
authors.initials: QH
authors.lastname: Wan
authors.forename: Sheng-Kai
authors.initials: SK
authors.lastname: Pan
authors.forename: Li
authors.initials: L
authors.lastname: Hu
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhu
authors.forename: Peng-Wei
authors.initials: PW
authors.lastname: Xu
authors.forename: Jin-Quan
authors.initials: JQ
authors.lastname: Xia
authors.forename: Hui
authors.initials: H
authors.lastname: Chen
authors.forename: Gen-Yun
authors.initials: GY
authors.lastname: He
authors.forename: Jing
authors.initials: J
authors.lastname: He
authors.forename: Xiao-Wei
authors.initials: XW
authors.lastname: Ni
authors.forename: Hao-Long
authors.initials: HL
authors.lastname: Hou
authors.forename: Sheng-Guang
authors.initials: SG
authors.lastname: Liao
authors.forename: Hai-Qiong
authors.initials: HQ
authors.lastname: Yang
authors.forename: Ying
authors.initials: Y
authors.lastname: Chen
authors.forename: Shu-Kun
authors.initials: SK
authors.lastname: Gao
authors.forename: Yun-Fa
authors.initials: YF
authors.lastname: Ge
authors.forename: Chang-Chang
authors.initials: CC
authors.lastname: Cao
authors.forename: Peng-Fei
authors.initials: PF
authors.lastname: Li
authors.forename: Li-Ming
authors.initials: LM
authors.lastname: Fang
authors.forename: Li
authors.initials: L
authors.lastname: Liao
authors.forename: Shu
authors.initials: S
authors.lastname: Zhang
authors.forename: Meng-Zhen
authors.initials: MZ
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Dong
authors.forename: Sheng-Guo
authors.initials: SG
authors.lastname: Fang
mesh_terms: D000489:Alligators and Crocodiles / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D001639:Bicarbonates / Q000378:metabolism; D001692:Biological Transport / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D016678:Genome / Q000235:genetics*; D006454:Hemoglobins / Q000235:genetics; D007107:Immune System; D009119:Muscle Contraction / Q000235:genetics; D055254:Night Vision / Q000235:genetics; D009833:Olfactory Pathways / Q000166:cytology; D055355:Opsins / Q000235:genetics; D010100:Oxygen / Q000378:metabolism; D017422:Sequence Analysis, DNA; D019849:Sex Determination Processes / Q000235:genetics; D012903:Smell / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014796:Visual Perception / Q000235:genetics
chemical_list: D001639:Bicarbonates; C110547:DMRT1 protein; D004251:DNA Transposable Elements; D006454:Hemoglobins; D055355:Opsins; D014157:Transcription Factors; C027043:ammonium bicarbonate; D010100:Oxygen
references.citation: Eur J Clin Invest. 2001;31 Suppl 2:1-4
references.pmid: 11525232
references.citation: Q Rev Biol. 1991 Jun;66(2):149-79
references.pmid: 1891591
references.citation: Trends Immunol. 2012 Jan;33(1):34-41
references.pmid: 22030238
references.citation: J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2002 Apr;188(3):217-23
references.pmid: 11976890
references.citation: Nat Genet. 2012 Jul 01;44(8):946-9
references.pmid: 22751099
references.citation: Circulation. 2007 Jul 10;116(2):134-42
references.pmid: 17592081
references.citation: Genomics. 2003 May;81(5):443-56
references.pmid: 12706103
references.citation: Behav Brain Funct. 2011 May 14;7:13
references.pmid: 21569590
references.citation: Proc Natl Acad Sci U S A. 1990 Oct;87(19):7457-61
references.pmid: 2120700
references.citation: Vet Immunol Immunopathol. 2006 Apr 15;110(3-4):221-8
references.pmid: 16298430
references.citation: PLoS Biol. 2010 Sep 07;8(9):
references.pmid: 20838655
references.citation: J Biol Chem. 2004 Apr 16;279(16):15975-83
references.pmid: 14761968
references.citation: Cytogenetics. 1970;9(2):81-105
references.pmid: 5461083
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8655-60
references.pmid: 17494744
references.citation: Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12235-40
references.pmid: 14507991
references.citation: Reprod Biol Endocrinol. 2006 Nov 13;4:59
references.pmid: 17101057
references.citation: Chromosome Res. 2009;17(5):687-97
references.pmid: 19802708
references.citation: J Exp Biol. 2000 Jun;203(Pt 11):1671-8
references.pmid: 10804157
references.citation: Nature. 2002 May 30;417(6888):559-63
references.pmid: 12037570
references.citation: Nature. 2010 Apr 1;464(7289):757-62
references.pmid: 20360741
references.citation: Dev Biol. 2004 Dec 15;276(2):391-402
references.pmid: 15581873
references.citation: Am J Physiol. 1998 Mar;274(3):R661-71
references.pmid: 9530231
references.citation: Bioessays. 2004 Feb;26(2):120-32
references.pmid: 14745830
references.citation: Genome Biol. 2005;6(3):213
references.pmid: 15774036
references.citation: FEBS J. 2011 Oct;278(20):3942-51
references.pmid: 21848912
references.citation: Nature. 2011 Aug 31;477(7366):587-91
references.pmid: 21881562
references.citation: Trends Genet. 2004 May;20(5):242-7
references.pmid: 15109778
references.citation: Trends Biochem Sci. 2008 Mar;33(3):101-3
references.pmid: 18276143
references.citation: Nature. 1995 Jan 19;373(6511):244-6
references.pmid: 7816138
references.citation: Nature. 2004 Dec 9;432(7018):695-716
references.pmid: 15592404
references.citation: Traffic. 2013 Feb;14(2):135-52
references.pmid: 23127154
references.citation: J Med Assoc Thai. 2010 Dec;93 Suppl 7:S58-64
references.pmid: 21294399
references.citation: Mol Biol Evol. 2005 Oct;22(10):1992-9
references.pmid: 15972846
references.citation: Proc Natl Acad Sci U S A. 1971 Jul;68(7):1498-500
references.pmid: 5283940
references.citation: Gene. 2008 Dec 1;425(1-2):56-63
references.pmid: 18775479
references.citation: Neuron. 2001 Mar;29(3):749-55
references.pmid: 11301033
references.citation: Semin Immunol. 2008 Dec;20(6):361-8
references.pmid: 18640056
references.citation: Acta Physiol Scand. 1961 Sep;53:23-45
references.pmid: 13861173
references.citation: Comp Biochem Physiol B Biochem Mol Biol. 2006 Feb;143(2):133-7
references.pmid: 16376129
references.citation: Europace. 2012 Oct;14(10):1428-32
references.pmid: 22562657
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Hear Res. 1989 Feb;37(3):255-67
references.pmid: 2468635
references.citation: Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2869-74
references.pmid: 10077603
references.citation: Nat Genet. 2008 Jul;40(7):909-14
references.pmid: 18500340
references.citation: Trends Genet. 2004 Dec;20(12):611-6
references.pmid: 15522456
references.citation: Nat Methods. 2011 Jan;8(1):61-5
references.pmid: 21102452
references.citation: Physiol Behav. 2011 May 3;103(2):240-7
references.pmid: 21316378
references.citation: Pflugers Arch. 2004 Feb;447(5):495-509
references.pmid: 14722772
references.citation: Mol Phylogenet Evol. 2007 Jun;43(3):787-94
references.pmid: 17433721
references.citation: Dev Genes Evol. 2007 Feb;217(2):119-26
references.pmid: 17120025
references.citation: Am J Med Genet B Neuropsychiatr Genet. 2007 Apr 5;144B(3):332-40
references.pmid: 17192956
references.citation: Nature. 2011 Jul 10;475(7355):189-95
references.pmid: 21743474
references.citation: Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2469-74
references.pmid: 18268317
references.citation: Nature. 2011 Jul 13;475(7357):493-6
references.pmid: 21753753
references.citation: Nat Rev Immunol. 2008 Nov;8(11):849-60
references.pmid: 18836477
references.citation: BMC Genomics. 2009 Apr 03;10:146
references.pmid: 19344507