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靶向捕獲測序與分析—— 助力生物系統進化和分類研究


二代測序(NGS)以高通量、可擴展和快速測序的優點,成為了生命科學領域基因組研究的 常用工具。借助NGS技術,科研人員能夠對生 物系統開展廣泛的研究和應用。然而,關于非 模式物種的研究目前還存在諸多問題(例如: 基因組數據缺失、注釋不完整、數據組裝難度大、 全基因組測序成本高等),這些問題限制了NGS 在系統發育學和群體遺傳學領域的廣泛應用。

靶向捕獲測序是一種采用靶向捕獲探針對特定 的基因組區域進行選擇性地富集,再進行測序的技術。該技術可將測序工作集中在樣品的特 定基因區域,去除冗余數據的干擾,同時降低 測序成本及基因組組裝的復雜性,進而提高 NGS數據的利用率,促進項目規模的擴大。因 此,靶向捕獲測序技術是系統發育學和群體遺 傳學研究最有前景的技術之一。 我們可為您提供靶向捕獲測序與分析全流程技術服務和個性化數據分析,及基于靶向捕獲測序技術的基因組整體解決方案。歡迎咨詢!


實驗技術流程:

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生信分析流程:

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技術優勢:

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應用領域:

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常用探針集和靶向捕獲試劑盒:

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參考文獻:

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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