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靶向捕获测序与分析

简要描述:基于被子植物353个单拷贝核基因探针集、超保守元件(UCEs)探针集、线粒体(Mito)探针集、全基因组富集(WGE)试剂盒、基因组SNPs富集试剂盒,以及各种即用型和定制型探针Panels和NGS杂交捕获试剂盒的靶向捕获测序技术,为研究生物系统进化和分类、生物适应性机制、种群进化历史、种群的结构、基因渗透和漂移提供高效的整体解决方案。我们可为您提供靶向捕获测序与分析服务,欢迎咨询!

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  • 更新时间:2023-06-02
  • 访  问  量:499

详细介绍

靶向捕获测序与分析—— 助力生物系统进化和分类研究

二代测序(NGS)以高通量、可扩展和快速测序的优点,成为了生命科学领域基因组研究的 常用工具。借助NGS技术,科研人员能够对生 物系统开展广泛的研究和应用。然而,关于非 模式物种的研究目前还存在诸多问题(例如: 基因组数据缺失、注释不完整、数据组装难度大、 全基因组测序成本高等),这些问题限制了NGS 在系统发育学和群体遗传学领域的广泛应用。 

靶向捕获测序是一种采用靶向捕获探针对特定 的基因组区域进行选择性地富集,再进行测序的技术。该技术可将测序工作集中在样品的特 定基因区域,去除冗余数据的干扰,同时降低 测序成本及基因组组装的复杂性,进而提高 NGS数据的利用率,促进项目规模的扩大。因 此,靶向捕获测序技术是系统发育学和群体遗 传学研究最有前景的技术之一。 我们可为您提供靶向捕获测序与分析全流程技术服务和个性化数据分析,及基于靶向捕获测序技术的基因组整体解决方案。欢迎咨询!


实验技术流程:

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生信分析流程:

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技术优势:

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应用领域:

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常用探针集和靶向捕获试剂盒:

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参考文献:

Johnson MG, Pokorny L, Dodsworth S, et al. A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering. Syst Biol. 2019;68(4):594-606.

Singhal S, Grundler M, Colli G, et al. Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Mol Ecol Resour. 2017;17(6):e12-e24.

Shaffer HB, McCartney-Melstad E, Near TJ, et al. Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines). Mol Phylogenet Evol. 2017;115:7-15.

Dodsworth S, Pokorny L, Johnson MG, et al. Hyb-Seq for Flowering Plant Systematics. Trends Plant Sci. 2019;24(10):887-891.

Hale H, Gardner EM, Viruel J, et al. Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants. Appl Plant Sci. 2020;8(4):e11337.

Slimp M, Williams LD, Hale H, et al. On the potential of Angiosperms353 for population genomic studies. Appl Plant Sci. 2021;9(7):10.1002/aps3.11419.

McLay TGB, Birch JL, Gunn BF, et al. New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Appl Plant Sci. 2021;9(7):10.1002/aps3.11420.

Nauheimer L, Weigner N, Joyce E, et al. HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets. Appl Plant Sci. 2021;9(7):10.1002/aps3.11441.

McDonnell AJ, Baker WJ, Dodsworth S, et al. Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics. Appl Plant Sci. 2021;9(7):10.1002/aps3.11443.

Baker WJ, Dodsworth S, Forest F, et al. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. Am J Bot. 2021;108(7):1059-1065.

Faircloth BC, Branstetter MG, White ND, et al. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Mol Ecol Resour. 2015;15(3):489-501.

McCormack JE, Tsai WL, Faircloth BC. Sequence capture of ultraconserved elements from bird museum specimens. Mol Ecol Resour. 2016;16(5):1189-203.

Starrett J, Derkarabetian S, Hedin M, et al. High phylogenetic utility of an ultraconserved element probe set designed for Arachnida. Mol Ecol Resour. 2017;17(4):812-823.

Bejerano G,  Pheasant M,  Makunin I, et al. Ultra-conserved elements in the human genome. Science. 2004;304(5675):1321-1325. doi:10.1126/science.1098119.

Miller W, Rosenbloom K, Hardison RC, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007;17(12):1797-808.

Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15(8):1034-50.

Faircloth BC, McCormack JE, Crawford NG, et al. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol. 2012;61(5):717-26.

Faircloth BC, Sorenson L, Santini F, et al. A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs). PLoS One. 2013;8(6):e65923.

McCormack JE, Faircloth BC, Crawford NG, et al. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 2012;22(4):746-54.

Smith BT, Harvey MG, Faircloth BC, et al. Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst Biol. 2014;63(1):83-95.

Crawford NG, Faircloth BC, McCormack JE, et al. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biol Lett. 2012;8(5):783-6.

McCormack JE, Harvey MG, Faircloth BC, et al. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS One. 2013;8(1):e54848.

Hutter CR, Cobb KA, Portik DM, et al. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Molecular Ecology Resources. 2022;22:1100-1119. 

Murchie TJ, Kuch M, Duggan AT, et al. Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set.Quaternary Research. 2021;99:305-328.

Eserman LA, Thomas SK, Coffey EED, et al. Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci. Applications in Plant Sciences. 2021;9(7):e11416.

Guitor AK, Raphenya AR, Klunk J, et al. Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrobial Agents and Chemotherapy. 2019;64(1):e01324-19.

Forth JH, Forth LF, King J, et al. A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses. 2019;11(9):846. 

Tillmar A, Sturk-Andreaggi K, Daniels-Higginbotham J, et al. The FORCE Panel: An All-in-One SNP Marker Set for Confirming Investigative Genetic Genealogy Leads and for General Forensic Applications. Genes. 2021;12(12):1968.

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