靶向捕獲測(cè)序服務(wù)
捕獲效率高，覆蓋范圍廣，對(duì)被子植物的353個(gè)單拷貝核基因進(jìn)行定向捕獲測(cè)序
適用多種樣本類型，節(jié)約時(shí)間成本和經(jīng)費(fèi)成本
- 技術(shù)簡(jiǎn)介
- 實(shí)驗(yàn)數(shù)據(jù)
- 發(fā)表文獻(xiàn)
藍(lán)景科信將探針雜交捕獲技術(shù)和NGS技術(shù)結(jié)合，提供被子植物353個(gè)單拷貝核基因靶向捕獲測(cè)序服務(wù)。為研究被子植物的系統(tǒng)進(jìn)化和分類、植物適應(yīng)性機(jī)制、種群進(jìn)化歷史、種群的結(jié)構(gòu)、基因滲透和漂移提供高效的整體解決方案。靶向捕獲測(cè)序技術(shù)服務(wù)，使用生物素化的探針，捕獲被子植物353個(gè)單拷貝核基因。您可以提供新鮮植物樣本，臘葉標(biāo)本或者古老的博物館標(biāo)本，我們負(fù)責(zé)DNA提取、文庫(kù)構(gòu)建、靶向捕獲、測(cè)序和數(shù)據(jù)分析。
技術(shù)流程
Fig 1. Heatmap of Gene Recovery Efficiency. Each row is one sample, and each column is one gene. Colors indicate the percentage of the target length (calculated by the mean length of all k-medoid transcripts for each gene) recovered.
Fig 2. Total Length of Sequence Recovery for Both Coding and Non-coding Regions Across 353 Loci for 42 Angiosperm Species. Reads were mapped back to either coding sequence (yellow) or coding sequence plus flanking non-coding (i.e. intron) sequence (purple)… The total length of coding sequence targeted was 260,802 bp. The median recovery of coding sequence was 137,046 bp and the median amount of non-coding sequence recovered was 216,816 bp (with at least 8x depth of coverage).
參考文獻(xiàn)：
Johnson MG, Pokorny L, Dodsworth S, Botigué LR, Cowan RS, Devault A, Eiserhardt WL, Epitawalage N, Forest F, Kim JT, Leebens-Mack JH, Leitch IJ, Maurin O, Soltis DE, Soltis PS, Wong GK, Baker WJ, Wickett NJ. 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. doi: 10.1093/sysbio/syy086.
使用被子植物353個(gè)單拷貝核基因捕獲探針進(jìn)行靶向捕獲測(cè)序，發(fā)表的部分文獻(xiàn)：
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Baker, W.J., Bailey, P., Barber, V., Barker, A., Bellot, S., Bishop, D., … Forest, F. (2021). A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Systematic Biology.
Brewer, G.E., Clarkson, J.J., Maurin, O., Zuntini, A.R., Barber, V., Bellot, S., … Baker, W.J. (2019). Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms. Front. Plant Sci. 0.
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Johnson, M., Pokorny, L., Dodsworth, S., Botigue, L.R., Cowan, R.S., Devault, A., … Wickett, N. (2019). A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering. Systematic Biology 68(4): 594-606.
Larridon, I., Villaverde, T., Zuntini, A.R., Pokorny, L., Brewer, G.E., Epitawalage, N., … Baker, W.J. (2020). Tackling Rapid Radiations With Targeted Sequencing. Frontiers in Plant Science 10: 1.
Larridon, I., Zuntini, A.R., Barrett, R.L., Wilson, K.L., Bruhl, J.J., Goetghebeur, P., … Roalson, E.H. (2021). Resolving generic limits in Cyperaceae tribe Abildgaardieae using targeted sequencing. Botanical Journal of the Linnean Society 196, 163–187.
Larridon, I., Zuntini, A.R., Léveillé-Bourret, é., Barrett, R.L., Starr, J.R., Muasya, A.M., … Baker, W.J. (2021). A new classification of Cyperaceae (Poales) supported by phylogenomic data. Journal of Systematics and Evolution 59, 852–895.
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Pérez-Escobar, O.A., Dodsworth, S., Bogarín, D., Bellot, S., Balbuena, J.A., Schley, R.J., … Baker, W.J. (2021). Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American Journal of Botany 108, 1166–1180.
Pillon, Y., Hopkins, H.C.F., Maurin, O., Epitawalage, N., Bradford, J., Rogers, Z.S., … Forest, F. (2021). Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments. American Journal of Botany 108, 1181–1200.
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