A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

. 2019 ; 10 () : 1407. [epub] 20200221

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid32153629

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.

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Aird D., Ross M. G., Chen W. S., Danielsson M., Fennell T., Russ C., et al. (2011). Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18. 10.1186/gb-2011-12-2-r18 PubMed DOI PMC

Albert T. J., Molla M. N., Muzny D. M., Nazareth L., Wheeler D., Song X., et al. (2007). Direct selection of human genomic loci by microarray hybridization. Nat. Methods 4, 903–905. 10.1038/nmeth1111 PubMed DOI

Alfaro M. E., Faircloth B. C., Harrington R. C., Sorenson L., Friedman M., Thacker C. E., et al. (2018). Explosive diversification of marine fishes at the Cretaceous–Palaeogene boundary. Nat. Ecol. Evol. 2, 688–696. 10.1038/s41559-018-0494-6 PubMed DOI

Allen J. M., Boyd B., Nguyen N. P., Vachaspati P., Warnow T., Huang D. I., et al. (2017). Phylogenomics from whole genome sequences using aTRAM. Syst. Biol. 66, 786–798. 10.1093/sysbio/syw105 PubMed DOI

Anand S., Mangano E., Barizzone N., Bordoni R., Sorosina M., Clarelli F., et al. (2016). Next generation sequencing of pooled samples: guideline for variants’ filtering. Sci. Rep. 6, 33735. 10.1038/srep33735 PubMed DOI PMC

Andermann T., Cano Á., Zizka A., Bacon C., Antonelli A. (2018). SECAPR-A bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments. PeerJ 2018, e5175. 10.7717/peerj.5175 PubMed DOI PMC

Andermann T., Fernandes A. M., Olsson U., Töpel M., Pfeil B., Oxelman B., et al. (2019). Allele phasing greatly improves the phylogenetic utility of ultraconserved elements. Syst. Biol. 68, 32–46. 10.1093/sysbio/syy039 PubMed DOI PMC

Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

Baird N. A., Etter P. D., Atwood T. S., Currey M. C., Shiver A. L., Lewis Z. A., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3, e3376. 10.1371/journal.pone.0003376 PubMed DOI PMC

Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477. 10.1089/cmb.2012.0021 PubMed DOI PMC

Bertone P., Trifonov V., Rozowsky J. S., Schubert F., Emanuelsson O., Karro J., et al. (2006). Design optimization methods for genomic DNA tiling arrays. Genome Res. 16, 271–281. 10.1101/gr.4452906 PubMed DOI PMC

Bethune K., Mariac C., Couderc M., Scarcelli N., Santoni S., Ardisson M., et al. (2019). Long-fragment targeted capture for long-read sequencing of plastomes. Appl. Plant Sci. 7, e1243. 10.1002/aps3.1243 PubMed DOI PMC

Bi K., Vanderpool D., Singhal S., Linderoth T., Moritz C., Good J. M. (2012). Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics 13, 403. 10.1186/1471-2164-13-403 PubMed DOI PMC

Blaimer B. B., Lloyd M. W., Guillory W. X., Brady S. G. (2016). Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens. PLoS One 11 (8), e0161531. 10.1371/journal.pone.0161531 PubMed DOI PMC

Bolger A. M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 PubMed DOI PMC

Bragg J. G., Potter S., Bi K., Moritz C. (2016). Exon capture phylogenomics: efficacy across scales of divergence. Mol. Ecol. Resour. 16, 1059–1068. 10.1111/1755-0998.12449 PubMed DOI

Branstetter M. G., Longino J. T., Ward P. S., Faircloth B. C. (2017). Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Methods Ecol. Evol. 8, 768–776. 10.1111/2041-210X.12742 DOI

Brewer G. E., Clarkson J. J., Maurin O., Zuntini A. R., Barber V., Bellot S., et al. (2019). Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms. Front. Plant Sci. 10, 1102. 10.3389/fpls.2019.01102 PubMed DOI PMC

Briggs A. W., Stenzel U., Meyer M., Krause J., Kircher M., Pääbo S. (2009). Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87–e87. 10.1093/nar/gkp1163 PubMed DOI PMC

Bryant D., Bouckaert R., Felsenstein J., Rosenberg N. A., Roychoudhury A. (2012). Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29, 1917–1932. 10.1093/molbev/mss086 PubMed DOI PMC

Burrell A. S., Disotell T. R., Bergey C. M. (2015). The use of museum specimens with high-throughput DNA sequencers. J. Hum. Evol. 79, 35–44. 10.1016/j.jhevol.2014.10.015 PubMed DOI PMC

Cao C. C., Sun X. (2016). Combinatorial pooled sequencing: experiment design and decoding. Quant. Biol. 4, 36–46. 10.1007/s40484-016-0064-3 DOI

Cao M. D., Ganesamoorthy D., Zhou C., Coin L. J. M. (2018). Simulating the dynamics of targeted capture sequencing with CapSim. Bioinformatics 34, 873–874. 10.1093/bioinformatics/btx691 PubMed DOI PMC

Carøe C., Gopalakrishnan S., Vinner L., Mak S. S. T., Sinding M. H. S., Samaniego J. A., et al. (2018). Single-tube library preparation for degraded DNA. Methods Ecol. Evol. 9, 410–419. 10.1111/2041-210X.12871 DOI

Cariou M., Ribière C., Morlière S., Gauthier J. P., Simon J. C., Peyret P., et al. (2018). Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis. BMC Res. Notes 11 (1), p.461. 10.1186/s13104-018-3559-3 PubMed DOI PMC

Casquet J., Thebaud C., Gillespie R. G. (2012). Chelex without boiling, a rapid and easy technique to obtain stable amplifiable DNA from small amounts of ethanol-stored spiders. Mol. Ecol. Resour. 12, 136–141. 10.1111/j.1755-0998.2011.03073.x PubMed DOI

Chafin T. K., Douglas M. R., Douglas M. E. (2018). MrBait: universal identification and design of targeted-enrichment capture probes. Bioinformatics 34, 4293–4296. 10.1093/bioinformatics/bty548 PubMed DOI

Chamala S., García N., Godden G. T., Krishnakumar V., Jordon-Thaden I. E., Smet R., et al. (2015). MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes. Appl. Plant Sci. 3, 1400115. 10.3732/apps.1400115 PubMed DOI PMC

Chen X., Ni G., He K., Ding Z. L., Li G. M., Adeola A. C., et al. (2018). “Capture hybridization of long-range DNA fragments for high-throughput sequencing,” in Methods Mol. Biol. Ed. Huang T. (New York, NY: Springer New York; ), 29–44. 10.1007/978-1-4939-7717-8_3 PubMed DOI

Coffey A. J., Kokocinski F., Calafato M. S., Scott C. E., Palta P., Drury E., et al. (2011). The GENCODE exome: sequencing the complete human exome. Eur. J. Hum. Genet 19 (7), 827. 10.1038/ejhg.2011.28 PubMed DOI PMC

Costello M., Fleharty M., Abreu J., Farjoun Y., Ferriera S., Holmes L., et al. (2018). Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms. BMC Genomics 19, 332. 10.1186/s12864-018-4703-0 PubMed DOI PMC

Couvreur T. L. P., Helmstetter A. J., Koenen E. J. M., Bethune K., Brandão R. D., Little S. A., et al. (2019). Phylogenomics of the major tropical plant family annonaceae using targeted enrichment of nuclear genes. Front. Plant Sci. 9, 1941. 10.3389/fpls.2018.01941 PubMed DOI PMC

Cruz-Dávalos D. I., Llamas B., Gaunitz C., Fages A., Gamba C., Soubrier J., et al. (2017). Experimental conditions improving in-solution target enrichment for ancient DNA. Mol. Ecol. Resour. 17, 508–522. 10.1111/1755-0998.12595 PubMed DOI

Dabney J., Meyer M. (2019). “Extraction of highly degraded DNA from ancient bones and teeth,” in Methods Mol. Biol. Eds. Shapiro B., Barlow A., Heintzman P. D., Hofreiter M., Paijmans J. L. A., Soares A. E. R. (New York, NY: Springer New York; ), 25–29. 10.1007/978-1-4939-9176-1_4 PubMed DOI

Dabney J., Knapp M., Glocke I., Gansauge M. T., Weihmann A., Nickel B., et al. (2013). Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl. Acad. Sci. U. S. A. 110, 15758–15763. 10.1073/pnas.1314445110 PubMed DOI PMC

Davey J. W., Hohenlohe P. A., Etter P. D., Boone J. Q., Catchen J. M., Blaxter M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499–510. 10.1038/nrg3012 PubMed DOI

de la Harpe M., Hess J., Loiseau O., Salamin N., Lexer C., Paris M. (2019). A dedicated target capture approach reveals variable genetic markers across micro-and macro-evolutionary time scales in palms. Mol. Ecol. Resour. 19 (1), 221–234. 10.1111/1755-0998.12945 PubMed DOI

De Sousa F., Bertrand Y. J. K., Nylinder S., Oxelman B., Eriksson J. S., Pfeil B. E. (2014). Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next-generation sequencing. PLoS One 9, e109704. 10.1371/journal.pone.0109704 PubMed DOI PMC

Dodsworth S., Pokorny L., Johnson M. G., Kim J. T., Maurin O., Wickett N. J., et al. (2019). Hyb-Seq for flowering plant systematics. Trends Plant Sci. 24 (10), 887–891. 10.1016/j.tplants.2019.07.011 PubMed DOI

Doyle J. J. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15.

Dugat-Bony E., Missaoui M., Peyretaillade E., Biderre-Petit C., Bouzid O., Gouinaud C., et al. (2011). HiSpOD: probe design for functional DNA microarrays. Bioinformatics 27 (5), 641–648. 10.1093/bioinformatics/btq712 PubMed DOI

Elshire R. J., Glaubitz J. C., Sun Q., Poland J. A., Kawamoto K., Buckler E. S., et al. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6, e19379. 10.1371/journal.pone.0019379 PubMed DOI PMC

Espeland M., Breinholt J., Willmott K. R., Warren A. D., Vila R., Toussaint E. F., et al. (2018). A comprehensive and dated phylogenomic analysis of butterflies. Curr. Biol. 28 (5), 770–778. 10.1016/j.cub.2018.01.061 PubMed DOI

Faircloth B. C., McCormack J. E., Crawford N. G., Harvey M. G., Brumfield R. T., Glenn T. C. (2012). Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61, 717–726. 10.1093/sysbio/sys004 PubMed DOI

Faircloth B. C., Sorenson L., Santini F., Alfaro M. E. (2013). A phylogenomic perspective on the radiation of Ray-Finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 8, e65923. 10.1371/journal.pone.0065923 PubMed DOI PMC

Faircloth B. C., Branstetter M. G., White N. D., Brady S. G. (2015). Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among hymenoptera. Mol. Ecol. Resour. 15, 489–501. 10.1111/1755-0998.12328 PubMed DOI PMC

Faircloth B. C. (2016). PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786–788. 10.1093/bioinformatics/btv646 PubMed DOI

Faircloth B. C. (2017). Identifying conserved genomic elements and designing universal bait sets to enrich them. Methods Ecol. Evol. 8, 1103–1112. 10.1111/2041-210X.12754 DOI

Folk R. A., Mandel J. R., Freudenstein J. V. (2015). A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae). Appl. Plant Sci. 3, 1500039. 10.3732/apps.1500039 PubMed DOI PMC

Forrest L. L., Hart M. L., Hughes M., Wilson H. P., Chung K.-F., Tseng Y.-H., et al. (2019). The limits of Hyb-Seq for Herbarium specimens: impact of preservation techniques. Front. Ecol. Evol. 7, 439. 10.3389/fevo.2019.00439 DOI

Gamba C., Hanghøj K., Gaunitz C., Alfarhan A. H., Alquraishi S. A., Al-Rasheid K. A. S., et al. (2016). Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol. Ecol. Resour. 16, 459–469. 10.1111/1755-0998.12470 PubMed DOI

Garrigos Y. E., Hugueny B., Koerner K., Ibañez C., Bonillo C., Pruvost P., et al. (2013). Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae). Zootaxa 3640, 373–394. 10.11646/zootaxa.3640.3.3 PubMed DOI

Gasc C., Peyret P. (2018). Hybridization capture reveals microbial diversity missed using current profiling methods. Microbiome 6 (1), p.61. 10.1186/s40168-018-0442-3 PubMed DOI PMC

Gasc C., Ribière C., Parisot N., Beugnot R., Defois C., Petit-Biderre C., et al. (2015). Capturing prokaryotic dark matter genomes. Res. Microbiol. 166 (10), 814–830. 10.1016/j.resmic.2015.06.001 PubMed DOI

Gasc C., Peyretaillade E., Peyret P. (2016). Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res. 44, 4504–4518. 10.1093/nar/gkw309 PubMed DOI PMC

Gevers D., Cohan F. M., Lawrence J. G., Spratt B. G., Coenye T., Feil E. J., et al. (2005). Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3 (9), 733. 10.1038/nrmicro1236 PubMed DOI

Glenn T. C., Nilsen R. A., Kieran T. J., Sanders J. G., Bayona-Vásquez N. J., Finger J. W., et al. (2019). Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext). PeerJ 7, e7755. 10.7717/peerj.7755 PubMed DOI PMC

Gnirke A., Melnikov A., Maguire J., Rogov P., LeProust E. M., Brockman W., et al. (2009). Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189. 10.1038/nbt.1523 PubMed DOI PMC

Grabherr M. G., Haas B. J., Yassour M., Levin J. Z., Thompson D. A., Amit I., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652. 10.1038/nbt.1883 PubMed DOI PMC

Green R. E., Krause J., Briggs A. W., Maricic T., Stenzel U., Kircher M., et al. (2010). A draft sequence of the neandertal genome. Science 328 (5979), 710–722. 10.1126/science.1188021 PubMed DOI PMC

Grover C. E., Salmon A., Wendel J. F. (2012). Targeted sequence capture as a powerful tool for evolutionary analysis. Am. J. Bot. 99, 312–319. 10.3732/ajb.1100323 PubMed DOI

Gutaker R. M., Reiter E., Furtwängler A., Schuenemann V. J., Burbano H. A. (2017). Extraction of ultrashort DNA molecules from herbarium specimens. Biotechniques 62, 76–79. 10.2144/000114517 PubMed DOI

Hajibabaei M., dewaard J. R., Ivanova N. V., Ratnasingham S., Dooh R. T., Kirk S. L., et al. (2005). Critical factors for assembling a high volume of DNA barcodes. Philos. T. R. Soc. B. 360 (1462), 1959–1967. 10.1098/rstb.2005.1727 PubMed DOI PMC

Hart M. L., Forrest L. L., Nicholls J. A., Kidner C. A. (2016). Retrieval of hundreds of nuclear loci from herbarium specimens. Taxon 65, 1081–1092. 10.12705/655.9 DOI

Harvey M. G., Smith B. T., Glenn T. C., Faircloth B. C., Brumfield R. T. (2016). Sequence capture versus restriction site associated DNA sequencing for shallow systematics. Syst. Biol. 65 (5), 910–924. 10.1093/sysbio/syw036 PubMed DOI

He D., Choi A., Pipatsrisawat K., Darwiche A., Eskin E. (2010). Optimal algorithms for haplotype assembly from whole-genome sequence data. Bioinformatics 26, i183–i190. 10.1093/bioinformatics/btq215 PubMed DOI PMC

Head S. R., Kiyomi Komori H., LaMere S. A., Whisenant T., Van Nieuwerburgh F., Salomon D. R., et al. (2014). Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56, 61–77. 10.2144/000114133 PubMed DOI PMC

Healey A., Furtado A., Cooper T., Henry R. J. (2014). Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods 10, 21. 10.1186/1746-4811-10-21 PubMed DOI PMC

Hedtke S. M., Morgan M. J., Cannatella D. C., Hillis D. M. (2013). Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time. PLoS One 8, e67908. 10.1371/journal.pone.0067908 PubMed DOI PMC

Heyduk K., Trapnell D. W., Barrett C. F., Leebens-Mack J. (2016). Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture. Biol. J. Linn. Soc. 117, 106–120. 10.1111/bij.12551 DOI

Himmelbach A., Knauft M., Stein N. (2014). Plant sequence capture optimised for Illumina sequencing. Bio-Protocol 4, 1–23. 10.21769/BioProtoc.1166 DOI

Hoffberg S. L., Kieran T. J., Catchen J. M., Devault A., Faircloth B. C., Mauricio R., et al. (2016). RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data. Mol. Ecol. Resour. 16, 1264–1278. 10.1111/1755-0998.12566 PubMed DOI

Hug L. A., Baker B. J., Anantharaman K., Brown C. T., Probst A. J., Castelle C. J., et al. (2016). A new view of the tree of life. Nat. Microbiol. 1, 16048. 10.1038/nmicrobiol.2016.48 PubMed DOI

Hutter C. R., Cobb K. A., Portik D., Travers S. L., Wood P. L., Brown R. M. (2019). FrogCap: a modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. bioRxiv, 825307. 10.1101/825307 PubMed DOI

Illumina coverage calculator Estimating sequencing coverage. Tech. Note Seq. Available at: https://emea.support.illumina.com/downloads/sequencing_coverage_calculator.html. (Accessed January, 2020).

Ilves K. L., López-Fernández H. (2014). A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. Mol. Ecol. Resour. 14, 802–811. 10.1111/1755-0998.12222 PubMed DOI

Ivanova N. V., Dewaard J. R., Hebert P. D. N. (2006). An inexpensive, automation-friendly protocol for recovering high-quality DNA. Mol. Ecol. Notes 6, 998–1002. 10.1111/j.1471-8286.2006.01428.x DOI

Johnson M. G., Gardner E. M., Liu Y., Medina R., Goffinet B., Shaw A. J., et al. (2016). HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl. Plant Sci. 4, 1600016. 10.3732/apps.1600016 PubMed DOI PMC

Johnson M. G., Pokorny L., Dodsworth S., Botigué L. R., Cowan R. S., Devault A., et al. (2019). A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Syst. Biol. 68, 594–606. 10.1093/sysbio/syy086 PubMed DOI PMC

Jones M. R., Good J. M. (2016). Targeted capture in evolutionary and ecological genomics. Mol. Ecol. 25, 185–202. 10.1111/mec.13304 PubMed DOI PMC

Karamitros T., Magiorkinis G. (2018). “Multiplexed targeted sequencing for oxford nanopore MinION: A detailed library preparation procedure,” in Methods Mol. Biol. Eds. Head S. R., Ordoukhanian P., Salomon D. R. (New York, NY: Springer New York; ), 43–51. 10.1007/978-1-4939-7514-3_4 PubMed DOI

Kawahara A. Y., Breinholt J. W., Espeland M., Storer C., Plotkin D., Dexter K. M., et al. (2018). Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set. Mol. Phylogenet. Evol. 127, 600–605. 10.1016/j.ympev.2018.06.002 PubMed DOI

Kircher M., Sawyer S., Meyer M. (2012). Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3–e3. 10.1093/nar/gkr771 PubMed DOI PMC

Kistler L., Ware R., Smith O., Collins M., Allaby R. G. (2017). A new model for ancient DNA decay based on paleogenomic meta-analysis. Nucleic Acids Res. 45, 6310–6320. 10.1093/nar/gkx361 PubMed DOI PMC

Korneliussen T. S., Albrechtsen A., Nielsen R. (2014). ANGSD: analysis of next generation sequencing data. BMC Bioinf. 15, 356. 10.1186/s12859-014-0356-4 PubMed DOI PMC

Kushwaha S. K., Manoharan L., Meerupati T., Hedlund K., Ahrén D. (2015). MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. BMC Bioinf. 16 (1), 65. 10.1186/s12859-015-0501-8 PubMed DOI PMC

Lagarde J., Uszczynska-Ratajczak B., Carbonell S., Pérez-Lluch S., Abad A., Davis C., et al. (2017). High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat. Genet. 49, 1731–1740. 10.1038/ng.3988 PubMed DOI PMC

Langmead B., Trapnell C., Pop M., Salzberg S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. 10.1186/gb-2009-10-3-r25 PubMed DOI PMC

Leinonen R., Akhtar R., Birney E., Bower L., Cerdeno-Tarraga A., Cheng Y., et al. (2011. a). The European nucleotide archive. Nucleic Acids Res. 39, D28–D31. 10.1093/nar/gkq967 PubMed DOI PMC

Leinonen R., Sugawara H., Shumway M. (2011. b). The sequence read archive. Nucleic Acids Res. 39, D19–D21. 10.1093/nar/gkq1019 PubMed DOI PMC

Lemmon A. R., Emme S. A., Lemmon E. M. (2012). Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol. 61, 727–744. 10.1093/sysbio/sys049 PubMed DOI

Lessard J. C. (2013). Molecular cloning. Methods Enzymol. 529, 85–98. 10.1016/B978-0-12-418687-3.00007-0 PubMed DOI

Li H., Durbin R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595. 10.1093/bioinformatics/btp698 PubMed DOI PMC

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079. 10.1093/bioinformatics/btp352 PubMed DOI PMC

Li C., Hofreiter M., Straube N., Corrigan S., Naylor G. J. P. (2013). Capturing protein-coding genes across highly divergent species. Biotechniques 54, 321–326. 10.2144/000114039 PubMed DOI

Li H. (2016). Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32 (14), 2103–2110. 10.1093/bioinformatics/btw152 PubMed DOI PMC

Lienhard A., Schäffer S. (2019). Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods. PeerJ 7, e6753. 10.7717/peerj.6753 PubMed DOI PMC

Loiseau O., Olivares I., Paris M., de La Harpe M., Weigand A., Koubínová D., et al. (2019). Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse neotropical palm tribe geonomateae. Front. Plant Sci. 10, 864. 10.3389/fpls.2019.00864 PubMed DOI PMC

Loman N. J., Quick J., Simpson J. T. (2015). A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12, 733–735. 10.1038/nmeth.3444 PubMed DOI

Mamanova L., Coffey A. J., Scott C. E., Kozarewa I., Turner E. H., Kumar A., et al. (2010). Target-enrichment strategies for next-generation sequencing. Nat. Methods 7, 111. 10.1038/nmeth.1419 PubMed DOI

Martin M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10. 10.14806/ej.17.1.200 DOI

Matos-Maraví P., Duarte Ritter C., Barnes C. J., Nielsen M., Olsson U., Wahlberg N., et al. (2019). Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 7, e6727. 10.7717/peerj.6727 PubMed DOI PMC

Mayer C., Sann M., Donath A., Meixner M., Podsiadlowski L., Peters R. S., et al. (2016). BaitFisher: a software package for multispecies target DNA enrichment probe design. Mol. Biol. Evol. 33 (7), 1875–1886. 10.1093/molbev/msw056 PubMed DOI

McCartney-Melstad E., Mount G. G., Shaffer H. B. (2016). Exon capture optimization in amphibians with large genomes. Mol. Ecol. Resour. 16, 1084–1094. 10.1111/1755-0998.12538 PubMed DOI

McCormack J. E., Tsai W. L. E., Faircloth B. C. (2016). Sequence capture of ultraconserved elements from bird museum specimens. Mol. Ecol. Resour. 16, 1189–1203. 10.1111/1755-0998.12466 PubMed DOI

Meyer M., Kircher M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 5, pdb.prot5448–pdb.prot5448. 10.1101/pdb.prot5448 PubMed DOI

Meyer M., Kircher M., Gansauge M. T., Li H., Racimo F., Mallick S., et al. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science 338 (6104), .222–226. 10.1126/science.1224344 PubMed DOI PMC

Miller M. R., Dunham J. P., Amores A., Cresko W. A., Johnson E. A. (2007). Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17 (2), 240–248. 10.1101/gr.5681207 PubMed DOI PMC

Murat F., Armero A., Pont C., Klopp C., Salse J. (2017). Reconstructing the genome of the most recent common ancestor of flowering plants. Nat. Genet. 49, 490–496. 10.1038/ng.3813 PubMed DOI

Neethiraj R., Hornett E. A., Hill J. A., Wheat C. W. (2017). Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa. Mol. Ecol. 26, 4990–5002. 10.1111/mec.14205 PubMed DOI

Noyes N. R., Weinroth M. E., Parker J. K., Dean C. J., Lakin S. M., Raymond R. A., et al. (2017). Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. Microbiome 5 (1), 142. 10.1186/s40168-017-0361-8 PubMed DOI PMC

Okou D. T., Steinberg K. M., Middle C., Cutler D. J., Albert T. J., Zwick M. E. (2007). Microarray-based genomic selection for high-throughput resequencing. Nat. Methods 4, 907. 10.1038/nmeth1109 PubMed DOI

Paijmans J. L. A., Fickel J., Courtiol A., Hofreiter M., Förster D. W. (2016). Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Mol. Ecol. Resour. 16, 42–55. 10.1111/1755-0998.12420 PubMed DOI

Parisot N., Denonfoux J., Dugat-Bony E., Peyret P., Peyretaillade E. (2012). KASpOD—a web service for highly specific and explorative oligonucleotide design. Bioinformatics 28 (23), 3161–3162. 10.1093/bioinformatics/bts597 PubMed DOI

Perry G. H., Marioni J. C., Melsted P., Gilad Y. (2010). Genomic-scale capture and sequencing of endogenous DNA from feces. Mol. Ecol. 19, 5332–5344. 10.1111/j.1365-294X.2010.04888.x PubMed DOI PMC

Philippe H. (2011). “Une décroissance de la recherche scientifique pour rendre la science durable?” in Décroissance versus Développement Durable: Débats Pour la Suite du Monde. (Montreal: Écosociété; ), 166–186.

Portik D. M., Smith L. L., Bi K. (2016). An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura). Mol. Ecol. Resour. 16, 1069–1083. 10.1111/1755-0998.12541 PubMed DOI

Quattrini A. M., Faircloth B. C., Dueñas L. F., Bridge T. C. L., Brugler M. R., Calixto-Botía I. F., et al. (2018). Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems. Mol. Ecol. Resour. 18, 281–295. 10.1111/1755-0998.12736 PubMed DOI

Robin J. D., Ludlow A. T., La Ranger R., Wright W. E., Shay J. W. (2016). Comparison of DNA quantification methods for next generation sequencing. Sci. Rep. 6, 24067. 10.1038/srep24067 PubMed DOI PMC

Rohland N., Reich D. (2012). Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939–946. 10.1101/gr.128124.111 PubMed DOI PMC

Rohland N., Siedel H., Hofreiter M. (2010). A rapid column-based ancient DNA extraction method for increased sample throughput. Mol. Ecol. Resour. 10, 677–683. 10.1111/j.1755-0998.2009.02824.x PubMed DOI

Rothfels C. J., Pryer K. M., Li F. W. (2017). Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytol. 213, 413–429. 10.1111/nph.14111 PubMed DOI

Rubin B. E. R., Ree R. H., Moreau C. S. (2012). Inferring phylogenies from RAD sequence data. PLoS One 7, 1–12. 10.1371/journal.pone.0033394 PubMed DOI PMC

Sánchez Barreiro F., Vieira F. G., Martin M. D., Haile J., Gilbert M. T. P., Wales N. (2017). Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNA probes. Mol. Ecol. Resour. 17, 209–220. 10.1111/1755-0998.12610 PubMed DOI

Saeidi S., McKain M. R., Kellogg E. A. (2018). Robust DNA isolation and high-throughput sequencing library construction for herbarium specimens. J. Vis. Exp. 2018, e56837–e56837. 10.3791/56837 PubMed DOI PMC

Schiebelhut L. M., Abboud S. S., Gómez Daglio L. E., Swift H. F., Dawson M. N. (2017). A comparison of DNA extraction methods for high-throughput DNA analyses. Mol. Ecol. Resour. 17, 721–729. 10.1111/1755-0998.12620 PubMed DOI

Schildkraut C., Lifson S. (1965). Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3, 195–208. 10.1002/bip.360030207 PubMed DOI

Schlötterer C., Tobler R., Kofler R., Nolte V. (2014). Sequencing pools of individuals-mining genome-wide polymorphism data without big funding. Nat. Rev. Genet. 15, 749–763. 10.1038/nrg3803 PubMed DOI

Schott R. K., Panesar B., Card D. C., Preston M., Castoe T. A., Chang B. S. (2017). Targeted capture of complete coding regions across divergent species. Genome Biol. Evol. 9, evx005. 10.1093/gbe/evx005 PubMed DOI PMC

Seguin-Orlando A., Schubert M., Clary J., Stagegaard J., Alberdi M. T., Prado J. L., et al. (2013). Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS One 8, 1–11. 10.1371/journal.pone.0078575 PubMed DOI PMC

Simpson J. T., Wong K., Jackman S. D., Schein J. E., Jones S. J. M., Birol I. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123. 10.1101/gr.089532.108 PubMed DOI PMC

Singhal S., Grundler M., Colli G., Rabosky D. L. (2017). Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles. Mol. Ecol. Resour. 17, e12–e24. 10.1111/1755-0998.12681 PubMed DOI

Slater G., Birney E. (2005). Automated generation of heuristics for biological sequence comparison. BMC Bioinf. 6, 31. 10.1186/1471-2105-6-31 PubMed DOI PMC

Smith B. T., Harvey M. G., Faircloth B. C., Glenn T. C., Brumfield R. T. (2014). Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst. Biol. 63, 83–95. 10.1093/sysbio/syt061 PubMed DOI

Sonnhammer E. L. L., Koonin E. V. (2002). Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18, 619–620. 10.1016/S0168-9525(02)02793-2 PubMed DOI

Suchan T., Pitteloud C., Gerasimova N. S., Kostikova A., Schmid S., Arrigo N., et al. (2016). Hybridization capture using RAD probes (hyRAD), a new tool for performing genomic analyses on collection specimens. PLoS One 11, e0151651. 10.1371/journal.pone.0151651 PubMed DOI PMC

Targeted Sequencing & Phasing on the PacBio RS II (2015). Available at: https://www.pacb.com/wp-content/uploads/2015/09/Application-Note-Targeted-Sequencing-on-the-PacBio-RS-II-Using-the-Roche-NimbleGen-SeqCap-EZ-System.pdf. (Accessed October 2019).

Tarver J. E., Dos Reis M., Mirarab S., Moran R. J., Parker S., O’Reilly J. E., et al. (2016). The interrelationships of placental mammals and the limits of phylogenetic Inference. Genome Biol. Evol. 8, evv261–. 10.1093/gbe/evv261 PubMed DOI PMC

Teasdale L. C., Köhler F., Murray K. D., O’Hara T., Moussalli A. (2016). Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture. Mol. Ecol. Resour. 16, 1107–1123. 10.1111/1755-0998.12552 PubMed DOI

Templeton J. E., Brotherton P. M., Llamas B., Soubrier J., Haak W., Cooper A., et al. (2013). DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification. Investig. Genet. 4 (1), p.26. 10.1186/2041-2223-4-26 PubMed DOI PMC

Terrat S., Peyretaillade E., Gonçalves O., Dugat-Bony E., Gravelat F., Moné A., et al. (2010). Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. BMC Bioinf. 11 (1), 478. 10.1186/1471-2105-11-478 PubMed DOI PMC

Thermes C. (2014). Ten years of next-generation sequencing technology. Trends Genet. 30, 418–426. 10.1016/j.tig.2014.07.001 PubMed DOI

Thilliez G. J., Armstrong M. R., Lim T. Y., Baker K., Jouet A., Ward B., et al. (2019). Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. New Phytol. 221 (3), 1634–1648. 10.1111/nph.15441 PubMed DOI PMC

Thompson M. J., Timmermans M. J., Jiggins C. D., Vogler A. P. (2014). The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus. BMC Evol. Biol. 14, 140. 10.1186/1471-2148-14-140 PubMed DOI PMC

Vestheim H., Deagle B. E., Jarman S. N. (2011). Application of blocking oligonucleotides to improve signal-to-noise ratio in a PCR. In: PCR Protocols. Methods in Molecular Biology (Methods and Protocols). Ed Park D. , (Humana Press; ). vol. 687 PubMed

Wales N., Kistler L. (2019). “Extraction of ancient DNA from plant remains,” in Ancient DNA (Humana Press: New York, NY: ), 45–55. 10.1007/978-1-4939-9176-1_6 PubMed DOI

Wandeler P., Hoeck P. E. A., Keller L. F. (2007). Back to the future: museum specimens in population genetics. Trends Ecol. Evol. 22, 634–642. 10.1016/j.tree.2007.08.017 PubMed DOI

Wang M., Beck C. R., English A. C., Meng Q., Buhay C., Han Y., et al. (2015). PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics 16, 214. 10.1186/s12864-015-1370-2 PubMed DOI PMC

Wylie T. N., Wylie K. M., Herter B. N., Storch G. A. (2015). Enhanced virome sequencing using targeted sequence capture. Genome Res. 25, 1910–1920. 10.1101/gr.191049.115 PubMed DOI PMC

Yu S., Wang Y., Li X., Yu F., Li W. (2017). The factors affecting the reproducibility of micro-volume DNA mass quantification in Nanodrop 2000 spectrophotometer. Optik (Stuttg). 145, 555–560. 10.1016/j.ijleo.2017.08.031 DOI

Yuan H., Jiang J., Jiménez F. A., Hoberg E. P., Cook J. A., Galbreath K. E., et al. (2016). Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms. Mol. Ecol. Resour. 16, 1095–1106. 10.1111/1755-0998.12532 PubMed DOI

Zerbino D. R., Birney E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829. 10.1101/gr.074492.107 PubMed DOI PMC

Zhang T. H., Wu N. C., Sun R. (2016). A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing. BMC Genomics 17, 108. 10.1186/s12864-016-2388-9 PubMed DOI PMC

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