An Enhanced Method for the Use of Reptile Skin Sheds as a High-Quality DNA Source for Genome Sequencing.
An Enhanced Method for the Use of Reptile Skin Sheds as a High-Quality DNA Source for Genome Sequencing.
复制标题
DOI：
10.3390/genes14091678
复制
发表时间：
2023-08-25
期刊：
影响因子：
3.5
通讯作者：
Xu, Xiao
中科院分区：
文献类型：
--
作者：
Fu, Yeyizhou;Zhuang, Yan;Luo, Shu-Jin;Xu, Xiao
随着高通量测序技术的出现，许多非鸟类爬行动物物种的基因组规模测序，揭示了与爬行动物生态学和进化有关的各种科学问题。然而，常规的组织或血液样本的基因组测序的要求往往构成了挑战，在许多难以捉摸的爬行动物，从而限制了高通量测序技术的应用，爬行动物的研究。目前迫切需要一种适合基因组测序的替代爬行动物DNA资源。在这里，我们使用玉米蛇（Pantherophis guttatus）作为爬行动物模式物种，以证明脱落的皮肤是基因组测序的高质量DNA来源。皮棚提供了一种非侵入性的样本，可以很容易地收集，而不会限制或伤害动物。我们的研究结果表明，玉米蛇的蜕皮产生的DNA的数量和质量足以与组织DNA提取物相媲美。基因组测序数据分析显示，脱落皮肤DNA受到不同水平的细菌污染，这是与脱落皮肤DNA相关的主要问题，并且可以通过引入30分钟预消化步骤的改良DNA提取方法来解决。这项研究提供了一个增强的方法，使用爬行动物脱落的皮肤作为高质量的DNA来源的全基因组测序。利用脱落的皮肤DNA使研究人员能够克服通常与获得传统组织或血液样本相关的限制，并有望促进基因组测序在爬行动物研究中的应用。
With the emergence of high-throughput sequencing technology, a number of non-avian reptile species have been sequenced at the genome scale, shedding light on various scientific inquiries related to reptile ecology and evolution. However, the routine requirement of tissue or blood samples for genome sequencing often poses challenges in many elusive reptiles, hence limiting the application of high-throughput sequencing technologies to reptile studies. An alternative reptilian DNA resource suitable for genome sequencing is in urgent need. Here, we used the corn snake (Pantherophis guttatus) as a reptile model species to demonstrate that the shed skin is a high-quality DNA source for genome sequencing. Skin sheds provide a noninvasive type of sample that can be easily collected without restraining or harming the animal. Our findings suggest that shed skin from corn snakes yields DNA of sufficient quantity and quality that are comparable to tissue DNA extracts. Genome sequencing data analysis revealed that shed skin DNA is subject to bacteria contamination at variable levels, which is a major issue related to shed skin DNA and may be addressed by a modified DNA extraction method through introduction of a 30 min pre-digestion step. This study provides an enhanced method for the use of reptile shed skins as a high-quality DNA source for whole genome sequencing. Utilizing shed skin DNA enables researchers to overcome the limitations generally associated with obtaining traditional tissue or blood samples and promises to facilitate the application of genome sequencing in reptilian research.
登录
查看更多内容
DOI：
10.1073/pnas.2003724117
发表时间：
2020-10-20
影响因子：
11.1
作者：
Ullate-Agote A;Burgelin I;Debry A;Langrez C;Montange F;Peraldi R;Daraspe J;Kaessmann H;Milinkovitch MC;Tzika AC
通讯作者：
Tzika AC
影响因子：
14.9
作者：
Federhen S
通讯作者：
Federhen S
DOI：
10.1126/science.1254449
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Green RE;Braun EL;Armstrong J;Earl D;Nguyen N;Hickey G;Vandewege MW;St John JA;Capella-Gutiérrez S;Castoe TA;Kern C;Fujita MK;Opazo JC;Jurka J;Kojima KK;Caballero J;Hubley RM;Smit AF;Platt RN;Lavoie CA;Ramakodi MP;Finger JW Jr;Suh A;Isberg SR;Miles L;Chong AY;Jaratlerdsiri W;Gongora J;Moran C;Iriarte A;McCormack J;Burgess SC;Edwards SV;Lyons E;Williams C;Breen M;Howard JT;Gresham CR;Peterson DG;Schmitz J;Pollock DD;Haussler D;Triplett EW;Zhang G;Irie N;Jarvis ED;Brochu CA;Schmidt CJ;McCarthy FM;Faircloth BC;Hoffmann FG;Glenn TC;Gabaldón T;Paten B;Ray DA
通讯作者：
Ray DA
影响因子：
1.1
作者：
Xu, Yuan;Guan, Tianming;Bai, Xiujuan
通讯作者：
Bai, Xiujuan
SeqKit：用于 FASTA/Q 文件操作的跨平台超快工具包
影响因子：
3.7
作者：
Shen W;Le S;Li Y;Hu F
通讯作者：
Hu F