A workflow of massive identification and application of intron markers using snakes as a model.
A workflow of massive identification and application of intron markers using snakes as a model.
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以蛇为模型的内含子标记大规模识别和应用的工作流程
DOI：
10.1002/ece3.3525
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发表时间：
2017-12
影响因子：
2.6
通讯作者：
Liang D
中科院分区：
文献类型：
--
作者：
Li JN;He C;Guo P;Zhang P;Liang D
相对于常用的线粒体和核蛋白编码基因，非编码内含子序列是一个有前途的信息标记来源，有可能解决困难的系统发育节点，如快速辐射和最近的分歧。然而，内含子标记在使用中存在许多问题，这阻碍了它们作为常规标记的广泛应用。我们以蛇类的多样性为例，试图为大量的内含子标记的鉴定和应用铺平道路。我们进行了一系列的生物信息学筛选，从两个蛇基因组中识别出单拷贝和保守外显子之间的适当内含子，增加了对序列长度变异性和序列变异性的特殊限制。共检索到1，273个候选内含子位点。巢式聚合酶链反应（PCR）的引物设计了超过100名候选人，并在16条蛇的代表。开发了96个内含子标记，可以在广泛的蛇类群中以高PCR成功率扩增。然后将标记物应用于49条蛇样本。对大量扩增子进行下一代测序（NGS）。开发了一种分析策略以准确地回收扩增子序列，并且回收了大约76%的标记序列。内含子标记在科间、属间、种间和种内水平上的平均p距离分别为0.168、0.052、0.015和0.004，表明它们可用于研究不同进化深度的蛇类关系。用内含子标记构建了一个蛇类遗传学模型，在科间和属内水平上都得到了一致的结果。内含子标记提供了一种方便的方法来探索非编码区的信号，以解决蛇树上的争议。我们改进的基因组筛选策略是有效的，可以应用于其他动物群体。NGS结合适当的序列处理可以极大地促进分子标记的广泛应用。
Relative to the commonly used mitochondrial and nuclear protein‐coding genes, the noncoding intron sequences are a promising source of informative markers that have the potential to resolve difficult phylogenetic nodes such as rapid radiations and recent divergences. Yet many issues exist in the use of intron markers, which prevent their extensive application as conventional markers. We used the diverse group of snakes as an example to try paving the way for massive identification and application of intron markers. We performed a series of bioinformatics screenings which identified appropriate introns between single‐copy and conserved exons from two snake genomes, adding particular constraints on sequence length variability and sequence variability. A total of 1,273 candidate intron loci were retrieved. Primers for nested polymerase chain reaction (PCR) were designed for over a hundred candidates and tested in 16 snake representatives. 96 intron markers were developed that could be amplified across a broad range of snake taxa with high PCR successful rates. The markers were then applied to 49 snake samples. The large number of amplicons was subjected to next‐generation sequencing (NGS). An analytic strategy was developed to accurately recover the amplicon sequences, and approximately, 76% of the marker sequences were recovered. The average p‐distances of the intron markers at interfamily, intergenus, interspecies, and intraspecies levels were .168, .052, .015, and .004, respectively, suggesting that they were useful to study snake relationships of different evolutionary depths. A snake phylogeny was constructed with the intron markers, which produced concordant results with robust support at both interfamily and intragenus levels. The intron markers provide a convenient way to explore the signals in the noncoding regions to address the controversies on the snake tree. Our improved strategy of genome screening is effective and can be applied to other animal groups. NGS coupled with appropriate sequence processing can greatly facilitate the extensive application of molecular markers.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
4.1
作者：
Alencar, Laura R. V.;Quental, Tiago B.;Zaher, Hussam
通讯作者：
Zaher, Hussam
影响因子：
3.5
作者：
Lee MS;Sanders KL;King B;Palci A
通讯作者：
Palci A
影响因子：
10.7
作者：
Foley NM;Thong VD;Soisook P;Goodman SM;Armstrong KN;Jacobs DS;Puechmaille SJ;Teeling EC
通讯作者：
Teeling EC
DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G