title: A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus.
abstract: Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ∼50 GB making it extremely difficult to be assembled.
  
  
  
  We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog.
  
  
  
  These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.
authors.affiliation: State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.|Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China.
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Geng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Wanshun
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China.
authors.forename: Haitao
authors.initials: H
authors.lastname: Shang
authors.affiliation: Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Gou
authors.affiliation: Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China.
authors.forename: Fuchun
authors.initials: F
authors.lastname: Zhang
authors.affiliation: State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.
authors.forename: Xiayan
authors.initials: X
authors.lastname: Zang
authors.affiliation: Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China.
authors.forename: Benhua
authors.initials: B
authors.lastname: Zeng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Li
authors.affiliation: Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Ma
authors.affiliation: State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.
authors.forename: Jianlin
authors.initials: J
authors.lastname: Guo
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Jian
authors.affiliation: Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Chen
authors.affiliation: State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Qiao
authors.affiliation: Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China.
authors.forename: Minghui
authors.initials: M
authors.lastname: Zhou
authors.affiliation: Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Wei
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.
authors.forename: Cunshuan
authors.initials: C
authors.lastname: Xu
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D016366:Open Reading Frames; D009928:Organ Specificity; D059467:Transcriptome; D014562:Caudata / Q000235:genetics*
keywords: Andrias davidianus; Assembly; Chinese giant salamander; De novo transcriptome