De novo transcriptome analysis and the phylogenetic position of glass lizards

Abstract

Abstract: Glass lizards are a group of reptiles that resemble snake
and possess many lizard's characteristics that contributed to its
ambiguous taxonomy. Meanwhile, glass lizards were recorded to have
many therapeutic applications in TCM. Hence, we present the
sequencing, de novo assembly and annotation of transcriptome from
\textit{Ophisaurus}\textit{ harti}'s gastrointestinal tract. A total
4.6~Gbp of high quality data was generated, 58~959 unigenes were
assembled and 35~708 (60.56{\%}) unigenes were annotated to the
public databases. To understand the evolutionary relationship among
glass lizard, snake and lizard, ortholog gene families and
phylogenic tree were performed, and the results all showed that
\textit{Ophisaurus}\textit{harti} is more closely related to the
snakes than to the lizard. A total of 10~613 cSSR markers from the
\textit{Ophisaurus}\textit{harti} transcriptome were identified and
1~644 markers were obtained using at least one primer with a strict
criterion. This is the first time to give insight into the
transcriptome and phylogenetic evolution in \textit{Ophisaurus
harti}. These sequences and markers will provide valuable sources
for \textit{Ophisaurus harti} studies.

Key words: glass lizard, Ophisaurus harti, phylogenetic evolution, transcriptome, cSSR

CLC Number:

Q111

References

{1} SECOR S M. Digestive physiology of the Burmese python: broad regulation of integrated performance [J]. J Exp Biol, 2008, 211(24): 3767-3774.
{2} WIENS J J, SLINGLUFF J L. How lizards turn into snakes: a phylogenetic analysis of body-form evolution in anguid lizards [J]. Evolution, 2001, 55(11): 2303-2318.
{3} BRANDLEY M C, HUELSENBECK J P, WIENS J J. Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms [J]. Evolution, 2008, 62(8): 2042-2064.
{4} CASTOE T A, de KONING J A, HALL K T, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes [J]. Genome Biol, 2011, 12(7): 406.
{5} VIDAL N, HEDGES S B. The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes [J]. C R Biol, 2005, 328(10-11): 1000-1008.
{6} LI S Z. Compendium of Materia Medica (Bencao Gangmu) [M]. LUO X W translator. Beijing: Foreign Languages Press, 2004.
{7} NENE V, WORTMAN J R, LAWSON D, et al. Genome sequence of Aedes aegypti, a major arbovirus vector [J]. Science, 2007, 316(5832): 1718-1723.
{8} FARKAS S L, BENKO M, ELO P, et al. Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus [J]. J Gen Virol, 2002, 83(Pt 10): 2403-2410.
{9} ALFOLDI J, DI PALMA F, Grabherr M, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals [J]. Nature, 2011, 477(7366): 587-591.
{10} MARDIS E R. Next-generation DNA sequencing methods [J]. Annu Rev Genomics Hum Genet, 2008(9): 387-402.
{11} GRABHERR M G, HAAS B J, YASSOUR M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome [J]. Nat Biotechnol, 2011, 29(7): 644-652.
{12} PERTEA G, HUANG X, LIANG F, et al. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets [J]. Bioinformatics, 2003, 19(5): 651-652.
{13} KANEHISA M, GOTO S, KAWASHIMA S, et al. The KEGG resource for deciphering the genome [J]. Nucleic Acids Res, 2004, 32(Database issue): D277-280.
{14} ISELI C, JONGENEEL C V, BUCHER P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences [J]. Proc Int Conf Intell Syst Mol Biol, 1999, : 138-148.
{15} CONESA A, GOTZ S, GARCIA-GOMEZ J M, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research [J]. Bioinformatics, 2005, 21(18): 3674-3676.
{16} MORTAZAVI A, WILLIAMS B A, MCCUE K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq [J]. Nat Methods, 2008, 5(7): 621-628.
{17} YU X J, ZHENG H K, WANG J, et al. Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup [J]. Genomics, 2006, 88(6): 745-751.
{18} HUELSENBECK J P, RONQUIST F. MRBAYES: Bayesian inference of phylogenetic trees [J]. Bioinformatics, 2001, 17(8): 754-755.
{19} POSADA D, CRANDALL K A. MODELTEST: testing the model of DNA substitution [J]. Bioinformatics, 1998, 14(9): 817-818.
{20} UNTERGASSER A, CUTCUTACHE I, KORESSAAR T, et al. FAIRCLOTH B C, REMM M, ROZEN S G. Primer3--new capabilities and interfaces [J]. Nucleic Acids Res, 2012, 40(15): e115.
{21} CASTOE T A, FOX S E, JASON de KONING A, et al. A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus) [J]. BMC Res Notes, 2011(4): 310.
{22} SCHWARTZ T S, TAE H, YANG Y, et al. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences [J]. BMC Genomics, 2010(11): 694.
{23} Consortium ICGS. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution [J]. Nature, 2004, 432(7018): 695-716.
{24} HELLSTEN U, HARLAND R M, GILCHRIST M J, et al. The genome of the Western clawed frog Xenopus tropicalis [J]. Science, 2010, 328(5978): 633-636.
{25} DU H, BAO Z, HOU R, et al. Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867) [J]. PLoS One, 2012, 7(3): e33311.
{26} GARG R, PATEL R K, TYAGI A K, et al. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification [J]. DNA Res, 2011, 18(1): 53-63.
{27} CASTOE T A, GU W, de KONING A P, et al. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes [J]. Cytogenet Genome Res, 2009, 127(2-4): 112-127.
{28} DUBEY S, SHINE R. Evolutionary diversification of the lizard genus Bassiana (Scincidae) across Southern Australia [J]. PLoS One, 2010, 5(9): e12982.
{29} KOCOT K M, CANNON J T, TODT C, et al. Phylogenomics reveals deep molluscan relationships [J]. Nature, 2011, 477(7365): 452-456.
{30} LI H, COGHLAN A, RUAN J, et al. TreeFam: a curated database of phylogenetic trees of animal gene families [J]. Nucleic Acids Res, 2006, 34(Database issue): D572-580.
{31} Carroll R L. Patterns and processes of vertebrate evolution. Cambridge Univ. New York1997.
{32} NISHYAMA T, FUJITA T, SHIN T, et al. Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution [J]. Proc Natl Acad Sci U S A, 2003, 100, 13: 8007-8012.
{33} BOURDON V, NAEF F, RAO P H, et al. Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes [J]. Cancer Res, 2002, 62(21): 6218-6223.
{34} PARCHMAN T L, GEIST K S, GRAHNEN J A, et al. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery [J]. BMC Genomics, 2010(11): 180.
{35} TEMNYKH S, DECLERCK G, LUKASHOVA A, et al. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential [J]. Genome Res, 2001, 11(8): 1441-1452.