A genome draft of the legless anguid lizard, Ophisaurus gracilis

Oxford University Press (OUP) - Tập 4 - Trang 1-3 - 2015
Bo Song1, Shifeng Cheng1,2, Yanbo Sun3, Xiao Zhong1, Jieqiong Jin3, Rui Guan4, Robert W Murphy3,5, Jing Che3, Yaping Zhang3,6, Xin Liu4
1BGI- Shenzhen, Shenzhen, China
2HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The Computer Science Department, The University of Hong Kong, Hong Kong, China
3State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
4BGI-Shenzhen, Shenzhen, China
5Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
6Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China

Tóm tắt

Transition from a lizard-like to a snake-like body form is one of the most important transformations in reptilian evolution. The increasing number of sequenced reptilian genomes is enabling a deeper understanding of vertebrate evolution, although the genetic basis of the loss of limbs in reptiles remains enigmatic. Here we report genome sequencing, assembly, and annotation for the Asian glass lizard Ophisaurus gracilis, a limbless lizard species with an elongated snake-like body form. Addition of this species to the genome repository will provide an excellent resource for studying the genetic basis of limb loss and trunk elongation. O. gracilis genome sequencing using the Illumina HiSeq2000 platform resulted in 274.20 Gbp of raw data that was filtered and assembled to a final size of 1.78 Gbp, comprising 6,717 scaffolds with N50 = 1.27 Mbp. Based on the k-mer estimated genome size of 1.71 Gbp, the assembly appears to be nearly 100% complete. A total of 19,513 protein-coding genes were predicted, and 884.06 Mbp of repeat sequences (approximately half of the genome) were annotated. The draft genome of O. gracilis has similar characteristics to both lizard and snake genomes. We report the first genome of a lizard from the family Anguidae, O. gracilis. This supplements currently available genetic and genomic resources for amniote vertebrates, representing a major increase in comparative genome data available for squamate reptiles in particular.

Tài liệu tham khảo

Li R, Fan W, Tian G, Zhu H, He L, Cai J, et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010;463:311–7. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1:36–41. Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003;19(2):ii215–25. Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protocol Bioinform. 2009;4:11–4. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nuc Acid Res. 1999;27:573–80. Smit A, Hubley R. RepeatModeler-1.0.5. Institute for Systems Biology. 2012. http://www.repeatmasker.org/RepeatModeler.html. [Accessed] Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 2011;477:587–91. Castoe TA, De Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A. 2013;110:20645–50. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, et al. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A. 2013;110:20651–6. Pyron RA, Burbrink FT, Wiens JJ. A phylogeny and revised classification of squamata, including 4161 species of lizards and snakes. BMC Evol Biol. 2013;13:93. Song, B; Cheng, S; Sun, Y; Zhong, X; Jin, J; Guan, R; Murphy, RW; Che, J; Zhang, Y; Liu, X. (2015): Anguidae lizard (Ophisaurus gracilis) genome assembly data. GigaScience Database. http://doi.org/10.5524/100119