Development and characterization of SNP markers in many-lined sun skink (Eutropis multifasciata) from transcriptomic sequences

被引：0

作者：

Lin, Youfu ^{[1
]}

Qian, Zijin ^{[2
]}

Shen, Shiyu ^{[3
]}

Huang, Yicheng ^{[3
]}

Du, Yu ^{[4
]}

Li, Hong ^{[2
]}

Chen, Lian ^{[1
]}

机构：

[1] Nanjing Forestry Univ, Coll Biol & Environm, Coinnovat Ctr Sustainable Forestry Southern China, Nanjing 210037, Peoples R China

[2] Nanjing Normal Univ, Coll Life Sci, Jiangsu Key Lab Biodivers & Biotechnol, Nanjing 210023, Peoples R China

[3] Nanjing Forestry Univ, Coll Forestry, Nanjing 210037, Peoples R China

[4] Hainan Trop Ocean Univ, Coll Fisheries & Life Sci, Sanya 572022, Peoples R China

来源：

CONSERVATION GENETICS RESOURCES | 2021年 / 13卷 / 04期

基金：

中国国家自然科学基金;

关键词：

Single nucleotide polymorphism (SNP); Many-lined sun skink; Next generation sequencing; Transcriptome;

D O I：

10.1007/s12686-021-01224-5

中图分类号：

X176 [生物多样性保护];

学科分类号：

090705 ;

摘要：

Many-lined sun skink (Eutropis multifasciata) is a medium sized viviparous scincid lizard. Insufficient molecular markers have limited the effective conservation and management of E. multifasciata. In the present study, 28 novel single nucleotide polymorphism (SNP) markers were developed from the transcriptome dataset of E. multifasciata using SNaPshot method. The minor allele frequency ranged from 0.117 to 0.483. The observed heterozygosity and expected heterozygosity ranged from 0.167 to 0.567 and from 0.210 to 0.508, respectively. Polymorphic information content ranged from 0.185 to 0.375. None of the loci deviated significantly from Hardy-Weinberg equilibrium and no significant linkage disequilibrium was found. Those polymorphic SNP markers will be helpful for the further studies on population structure and conservation genetics in E. multifasciata.

引用

页码：405 / 408

页数：4

共 15 条

[1] Allopatric divergence drives the genetic structuring of an endangered alpine endemic lizard with a sky-island distribution [J].

Atkins, Z. S. ;

Amor, M. D. ;

Clemann, N. ;

Chapple, D. G. ;

While, G. M. ;

Gardner, M. G. ;

Haines, M. L. ;

Harrisson, K. A. ;

Schroder, M. ;

Robert, K. A. .

ANIMAL CONSERVATION, 2020, 23 (01) :104-118

[2] Full-length transcriptome assembly from RNA-Seq data without a reference genome [J].

Grabherr, Manfred G. ;

Haas, Brian J. ;

Yassour, Moran ;

Levin, Joshua Z. ;

Thompson, Dawn A. ;

Amit, Ido ;

Adiconis, Xian ;

Fan, Lin ;

Raychowdhury, Raktima ;

Zeng, Qiandong ;

Chen, Zehua ;

Mauceli, Evan ;

Hacohen, Nir ;

Gnirke, Andreas ;

Rhind, Nicholas ;

di Palma, Federica ;

Birren, Bruce W. ;

Nusbaum, Chad ;

Lindblad-Toh, Kerstin ;

Friedman, Nir ;

Regev, Aviv .

NATURE BIOTECHNOLOGY, 2011, 29 (07) :644-U130

[3] Population genomics for wildlife conservation and management [J].

Hohenlohe, Paul A. ;

Funk, W. Chris ;

Rajora, Om P. .

MOLECULAR ECOLOGY, 2021, 30 (01) :62-82

[4] Evolution of viviparity in warm-climate lizards: an experimental test of the maternal manipulation hypothesis [J].

Ji, X. ;

Lin, C.-X. ;

Lin, L.-H. ;

Qiu, Q.-B. ;

Du, Y. .

JOURNAL OF EVOLUTIONARY BIOLOGY, 2007, 20 (03) :1037-1045

[5]

Ji X, 2006, J HERPETOL, V40, P351, DOI 10.1670/0022-1511(2006)40[351:SDAFRI]2.0.CO

[6]

[7] Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment [J].

Kalinowski, Steven T. ;

Taper, Mark L. ;

Marshall, Tristan C. .

MOLECULAR ECOLOGY, 2007, 16 (05) :1099-1106

[8] Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana (Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes [J].

Koomgun, Tassika ;

Laopichienpong, Nararat ;

Singchat, Worapong ;

Panthum, Thitipong ;

Phatcharakullawarawat, Rattanin ;

Kraichak, Ekaphan ;

Sillapaprayoon, Siwapech ;

Ahmad, Syed Farhan ;

Muangmai, Narongrit ;

Peyachoknagul, Surin ;

Duengkae, Prateep ;

Ezaz, Tariq ;

Srikulnath, Kornsorn .

FRONTIERS IN GENETICS, 2020, 11

[9] Tail loss compromises immunity in the many-lined skink, Eutropis multifasciata [J].

Kuo, Chi-Chien ;

Yao, Chiou-Ju ;

Lin, Te-En ;

Liu, Hsu-Che ;

Hsu, Yu-Cheng ;

Hsieh, Ming-Kun ;

Huang, Wen-San .

NATURWISSENSCHAFTEN, 2013, 100 (04) :379-384

[10]

Li H, 2009, BIOINFORMATICS, V25, P1094, DOI [10.1093/bioinformatics/btp324, 10.1093/bioinformatics/btp100]

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