CANLILIĞI BARKODLAMA VE BİLİMSEL UYGULAMA ALANLARI

Wilson, E.O. (2016): Half Earth: Our Planet’s Fight for Life; WW Norton and Company: New York, NY, USA.

Hebert, P. D. N., Cywinska, A., Ball, S. L., deWaard, J. R. (2003): Biological Identifications through DNA barcodes. Proceedings Of The Royal Society B: Biological Sciences, 270:313–321.

Arnot, D. E., Roper, C., Bayoumi, R. A. (1993): Digital Codes from Hypervariable Tandemly Repeated DNA Sequences in the Plasmodium falciparum circumsporozoite Gene can Genetically Barcode Isolates. Molecular and Biochemical Parasitology, 61:15–24.

Olive, D. M., Bean, P. (1999): Principles and Applications of methods for DNA-based Typing of Microbial Organisms. Journal of Clinical Microbiology, 37: 1661–1669. https://doi.org/10.1128/JCM.37.6.1661-1669.1999.

Tautz, D., Arctander, P., Minelli, A., Thomas, R. H., Vogler, A. P. (2003): A plea for DNA Taxonomy. Trends Ecology in Evolution, 18 (2): 70–74.

Kress, W. J., Erickson, D. L. (2008): DNA Barcodes: Genes, Genomics, and Bioinformatics. Proceedings of the National Academy of Sciences, 105: 2761–2762.

Kang, Y., Deng, Z., Zang, R. (2017): DNA Barcoding Analysis and Phylogenetic Relationships of Tree Species in Tropical Cloud Forests. Scientific Reports, 7: 12564.

Keskin, E., Atar, H. H. (2013): DNA Barkodlama: Mitokondriyal COI Geni Kullanılarak Moleküler Tanımlama. Türk Bilimsel Derlemeler Dergisi, 2: 1–8.

Kress, W. J., Erickson, D. L. (2012): DNA Barcodes: Methods and Protocols; Humana Press: Totowa, NJ, USA, 858: 3–8.

Kress, W. J., Erickson, D. L. (2007): A two-locus Global DNA Barcode for Land plants: The Coding rbcL Gene Complements the Non-coding trnH-psbA Spacer Region. PLoS ONE, 2:e508.

Pennisi, E. (2007): Taxonomy. Wanted: A Barcode for Plants. Science, 318:190 –191.

Erickson, D.L., Spouge, J., Resch, A., Weigt, L. A., Kress. J. W. (2008): DNA Barcoding in Land Plants: Developing Standards to Quantify and Maximize Success. Taxon, 57: 1304 –1316.

Fazekas, A.J. (2008): Multiple Multilocus DNA Barcodes from the Plastid genome discriminate plant species equally well. PLoS ONE, 3:e2802.

Lahaye, R., Van Der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, O., Duthoit, S., Barraclough, T.G., Savolainen, V. (2008): DNA Barcoding the Floras of Biodiversity Hotspots. Proceedings of the National Academy of Sciences, 105: 2923–2928.

Ledford, H. (2008): Botanical Identities: DNA Barcoding for Plants Comes a Step Closer. Nature, 451: 616.

Hollingsworth, M. L. (2009): Selecting Barcoding Loci for Plants: Evaluation of Seven Candidate Loci with Species-level Sampling in Three Divergent Groups of Land Plants. Molecular Ecology Resources 9: 439 – 457.

CBOL Plant Working Group. (2009): A DNA barcode for land plants. Proceedings of the National Academy of Sciences, 106(31):12794-7. doi: 10.1073/pnas.0905845106.

Saunders, G. W., McDevit, D.C. (2013): DNA Barcoding Unmasks Overlooked Diversity Improving Knowledge on the Composition and Origins of the Churchill Algal Flora. BMC Ecology, 13: 9.

Peters, A.F., Couceiro, L., Tsiamis, K., Küpper F.C., Valero, M. (2015): Barcoding of Cryptic Stages of Marine Brown Algae Isolated from Incubated Substratum Reveals High Diversity in Acinetosporaceae (Ectocarpales, Phaeophyceae). Cryptogamie Algology, 36: 3–29.

Bittner, L., Payri, C. E., Couloux, A., Cruaud, C., de Reviers B., Rousseau, F. (2008): Molecular Phylogeny of the Dictyotales and Their Position within the Phaeophyceae, Based on Nuclear, Plastid and Mitochondrial DNA Sequence Data. Molecular Phylogenetic and Evolution, 49: 211–226.

Manghisi, A., Gall, L. L., Ribera, M.A., Bonillo, C., Gargiulo G.M., Morabito, M. (2014): The Mediterranean Endemic New Genus Felicinia (Halymeniales, Rhodophyta) Recognized by a Morphological and Phylogenetic Integrative Approach. Cryptogamie Algology, 35: 221–243.

Pombert, J., Otis, C., Lemieux C., Turmel, M: (2004). The Complete Mitochondrial DNA Sequence of the Green Alga Pseudendoclonium akinetum (Ulvophyceae) Highlights Distinctive Evolutionary Trends in the Chlorophyta and Suggests a Sister-group Relationship Between the Ulvophyceae and Chlorophyceae. Molecular Biology and Evolution, 21: 922–935.

Pombert, J., Beauchamp, P., Otis, C., Lemieux C., Turmel, M. (2006): The Complete Mitochondrial DNA Sequence of the Green Alga Oltmannsiellopsis viridis: Evolutionary Trends of the Mitochondrial Genome in the Ulvophyceae. Current Genetics, 50: 137–147.

Saunders, G. W., Kucera, H. (2010): An Evaluation of rbcL, tufA, UPA, LSU and ITS as DNA Barcode Markers for the Marine Green Macroalgae. Cryptogamie Algology, 31: 487–528.

Zou, S., Fei, C., Wang, C., Gao, Z., Bao, Y., He, M., Wang. C. (2016): How DNA Barcoding can be More Effective in Microalgae Identification: a Case of Cryptic Diversity Revelation in Scenedesmus (Chlorophyceae). Scientific Reports, 6: 36822. doi: 10.1038/srep36822. PMID: 27827440;

Seifert, K. A. (2009): Progress towards DNA Barcoding of Fungi. Molecular Ecology Resources, 9: 83–89.

Kress, W. J. García-Robledo, C., Uriarte, M., Erickson, D. L. (2015): DNA Barcodes for Ecology, Evolution, and Conservation. Trends in Ecology & Evolution, 30(1): 25–35.

O’Brien, H. E., Parrent, J. L., Jackson, J. A., Moncalvo, J.-M., Vilgalys, R. (2005): Fungal Community Analysis by Large-scale Sequencing of Environmental Samples. Applied and Environmental Microbiology, 71: 5544–5550. doi:10.1128/AEM.71.9.5544-5550.2005.

Schmit, J., Mueller, G. (2007): An Estimate of the Lower Limit of Global Fungal Diversity. Biodiversity and Conservation, 16: 99–111. doi: 10.1007/s10531-006-9129-3.

Blackwell, M. (2011): The Fungi: 1, 2, 3…5.1 million species? American Journal of Botany, 98: 426–438. doi:10.3732/ajb.1000298.

Taylor, D. L., Hollingsworth, T. N., McFarland, J. W., Lennon, N. J., Nusbaum, C., Ruess, R. W. (2014): A first Comprehensive Census of Fungi in Soil Reveals Both Hyperdiversity and Finescale Niche Partitioning. Ecological Monographs, 84(1): 3–20. doi:10.1890/ 12-1693.1.

Hoang, M. T. V., Irinyi, L., Chen, S. C. A., Sorrell, T. C. (2019): the ISHAM Barcoding of Medical Fungi Working Group and Meyer, W. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections. Frontiers Microbiology, 10:1647. doi: 10.3389/fmicb.2019.01647

Wilkinson, M. J. Szabo, C., Ford, C. S., Yarom, Y., Croxford, A. E., Camp, A., Gooding, P. (2017): Replacing Sanger with Next Generation Sequencing to Improve Coverage and Quality of Reference DNA Barcodes for Plants. Scientific Reports, 7: 46040.

Gostel, M. R., Kress, W. J. (2022): The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation. Diversity, 14: 213. https://doi.org/10.3390/d14030213

Kane, N., Cronk, M. (2008): Botany without Borders: Barcoding in Focus. Molecular Ecology, 17: 5175–5176.

Li, X., Yang, Y., Henry, R. J., Rossetto, M., Wang, Y., Chen, S. (2015): Plant DNA Barcoding: From Gene to Genome. Biological Reviews, 90: 157–166.

Kane, N., Sveinsson, S., Dempewolf, H., Yang, J. Y., Zhang, D., Engels, J. M. M., Cronk, Q. (2012): Ultra-Barcoding in Cacao (Theobroma Spp.; Malvaceae) Using Whole Chloroplast Genomes and Nuclear Ribosomal DNA. American Journal of Botany, 99: 320–329.

Young, R. G., Yu, J., Cote, M. J., Hanner, R. H. (2020): The Molecular Data Organization for Publication (MDOP) R Package to Aid the Upload of Data to Shared Databases. Biodiversity Data Journal, 8: e50630.

Fontes, J. T., Vieira, P. E., Ekrem, T., Soares, P., Costa, F. O. (2021). BAGS: An Automated Barcode, Audit & Grade System for DNA Barcode Reference Libraries. Molecular Ecology Resource, 21: 573–583.

Young, R., Gill, R., Gillis, D., Hanner, R. (2021): Molecular Acquisition, Cleaning and Evaluation in R (MACER)—A Tool to Assemble Molecular Marker Datasets from BOLD and GenBank. Biodiversity Data Journal: 9.

Oliveira, R. R. M., Nunes, G. L., de Lima, T. G. L., Oliveira, G., Alves, R. (2018): PIPEBAR and OverlapPER: Tools for a Fast and Accurate DNA Barcoding Analysis and Paired-End Assembly. BMC Bioinformatics, 19: 297.

Sahlin, K., Lim, M. C. W., Prost, S. (2021): NGSpeciesID: DNA Barcode and Amplicon Consensus Generation from Long-Read Sequencing Data. Ecology and Evolution, 11: 1392–1398.

Wood, D. E., Salzberg, S. L. (2014): Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments. Genome Biology, 15: R46.

Somervuo, P., Koskela, S., Pennanen, J., Nilsson, R. H., Ovaskainen, O. (2016): Unbiased Probabilistic Taxonomic Classification for DNA Barcoding. Bioinformatics, 32: 2920–2927.

Altschul, S. F., Gish, W., Miller, E. W., Lipman, D. J. (1990): Basic Local Alignment Search Tool. Journal of Molecular Biology, 215: 403–410.

Bokulich, N. A., Kaehler, B. D., Rideout, J. R., Dillon, M., Bolyen, E., Knight, R., Huttley, G. A., Gregory Caporaso, J. (2018): Optimizing Taxonomic Classification of Marker-Gene Amplicon Sequences with QIIME 2’s Q2-Feature-Classifier Plugin. Microbiome, 6: 90.

Murali, A., Bhargava, A., Wright, E. S. (2018): IDTAXA: A Novel Approach for Accurate Taxonomic Classification of Microbiome Sequences. Microbiome, 6: 140.

Bengtsson-Palme, J., Richardson, R. T., Meola, M., Wurzbacher, C., Tremblay, É.D., Thorell, K., Kanger, K., Eriksson, K. M., Bilodeau, G. J., Johnson, R. M. (2018): MetaxA2 Database Builder: Enabling Taxonomic Identification from Metagenomic or Metabarcoding Data Using Any Genetic Marker. Bioinformatics, 34: 4027–4033.

Kahlke, T., Ralph, P. (2018): BASTA–Taxonomic Classification of Sequences and Sequence Bins Using Last Common Ancestor Estimations. Methods Ecology and Evolution, 10: 100–103.

Hleap, J. S., Littlefair, J. E., Steinke, D., Hebert, P. D. N., Cristescu, M. E. (2021): Assessment of Current Taxonomic Assignment Strategies for Metabarcoding Eukaryotes. Molecular Ecology and Resource, 21: 2190–2203.

Miller, K. B., Alarie, Y., Wolfe, G. W., Whiting, M.F. (2005): Association of Insect Life Stages Using DNA Sequences: the Larvae of Philodytes umbrinus (Motschulsky) (Coleoptera: Dytiscidae). Systematic Entomology, 30: 499–509.

Machin-Sanchez, M. (2014): A Combined Barcode and Morphological Approach to the Systematics and Biogeography of Laurencia pyramidalis and Laurenciella marilzae (Rhodophyta). European Journal of Phycology, 49: 115–127.

Dauphin, B. (2014): Molecular Phylogenetics Supports Widespread Cryptic Species in Moonworts (Botrychium ss, Ophioglossaceae). American Journal of Botany, 101: 128–140

Uğurlu Aydın, Z., Kaya Y., Dönmez A. A. (2022): DNA Barcoding evaluation of Geophytes: Comparative Efficiency of Three Barcode loci for Anemone (Ranunculaceae) and Gladiolus (Iridaceae). Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, 156: 926–937. doi: 10.1080/11263504.2021.1979678

Yap, H. Y. Y. (2014): DNA Barcode Markers for Two New species of Tiger Milk Mushroom: Lignosus tigris and L. cameronensis. International Journal of Agricultural Biology, 16: 841–844.

Felix, M. A. (2014): A Streamlined System for Species Diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with Name Designations for 15 distinct Biological Species. PLoS ONE, 9: e94723

Pillai, P. M. (2014): Description, DNA barcode and phylogeny of a new species, Macrobrachium abrahami (Decapoda: Palaemonidae) from Kerala, India. Zootaxa, 3768: 546–556

Layton, K. K. S. (2014): Patterns of DNA Barcode Variation in Canadian marine molluscs. PLoS ONE 9: e9500

Winterbottom, R. (2014): A Cornucopia of Cryptic species: a DNA Barcode Analysis of the Gobiid Fish Genus Trimma (Percomorpha, Gobiiformes). Zookeys 381: 79–111.

Saitoh, T., Sugita, N., Someya, S., Iwami, Y., Kobayashi, S., Kamigaichi, H., Higuchi, A., Asai, S., Yamamoto, Y., Nishiumi, I. (2015): DNA Barcoding Reveals 24 Distinct Lineages as Cryptic Bird Species Candidates in and Around the Japanese Archipelago. Molecular Ecology Resource, 15: 177-186. https://doi.org/10.1111/1755-0998.12282

Wilson, J. J. (2014): Utility of DNA Barcoding for Rapid and Accurate Assessment of Bat Diversity in Malaysia in the Absence of Formally Described Species. Genetics and Molecular Resource, 13: 920–925.

Smith, M. A. (2008): Extreme Diversity of Tropical Parasitoid Wasps Exposed by Iterative Integration of Natural History, DNA Barcoding, Morphology, and Collections. Proceedings of the National Academy of Sciences, 105: 12359–12364.

Smith, M. A. (2012): DNA Barcoding and the Taxonomy of Microgastrinae wasps (Hymenoptera, Braconidae): Impacts after 8 years and nearly 20 000 Sequences. Molecular Ecology Resource, 13: 168–176.

Silva, E. D. (2014): Alona iheringula Sinev & Kotov, 2004 (Crustacea, Anomopoda, Chydoridae, Aloninae): Life cycle and DNA Barcode with Implications for the Taxonomy of the Aloninae subfamily. PLoS ONE, 9: e97050.

Hamsher, S. E., Saunders, G. W. (2014): A Foristic Survey of Marine Tube-forming Diatoms Reveals Unexpected Diversity and Extensive Cohabitation among Genetic Lines of the Berkeleya rutilans complex (Bacillariophyceae). Eurepean Journal of Phycology, 49: 47–59.

Kress, W. J. (2009): Plant DNA Barcodes and a Community Phylogeny of a Tropical Forest Dynamics Plot in Panama. Proceedings of the National Academy of Sciences, 106: 18621–18626.

Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H., Hallwachs, W. (2004): Ten Species in One: DNA Barcoding Reveals Cryptic Species in the Neotropical Skipper Butterfly Astraptes Fulgerator. Proceedings of the National Academy of Sciences, 104: 41.

Hebert, P. D. N., Barrett, R. D. H. (2005): Reply to the Comment by L. Prendini on ‘Identifying spiders through DNA barcodes’. Canadian Journal of Zoology 83: 505–506.

Madden, M. J. L., Young, R. G., Brown, J. W., Miller, S. E., Frewin, A. J., Hanner, R. H. (2019): Using DNA Barcoding to Improve Invasive Pest Identification at U.S. Ports-of-Entry. PLoS ONE, 2019, 14: e0222291.

Krishnamurthy, P. K., Francis, R. A. (2012): A Critical Review on the Utility of DNA Barcoding in Biodiversity Conservation. Springer, 21: 1901–1919.

Funk, V. A., Gostel, M., Devine, A., Kelloff, C. L., Wurdack, K., Tuccinardi, C., Radosavljevic, A., Peters, M., Coddington, J. (2017): Guidelines for Collecting Vouchers and Tissues Intended for Genomic Work (Smithsonian Institution): Botany Best Practices. Biodiversity Data Journal, 5: e11625.

Purvis, A., Hector, A. (2000): Getting the measure of biodiversity. Nature 405: 212–219.

Nithaniyal, S., Newmaster, S. G., Ragupathy, S., Krishnamoorthy, D., Vassou, S.L., Parani, M. (2014): DNA Barcode Authentication of Wood Samples of Threatened and Commercial Timber Trees within the Tropical Dry Evergreen Forest of India. PLoS ONE 9: e107669.

Bell, K. L., Burgess, K. S., Okamoto, K. C., Aranda, R., Brosi, B. J. (2016): Review and Future Prospects for DNA Barcoding Methods in Forensic Palynology. Forensic Science International Genetic, 21: 110–116.

Liu, J., Milne, R. I., Möller, M., Zhu, G. F., Ye, L. J., Luo, Y. H., Yang, J. B., Wambulwa, M. C., Wang, C. N., Li, D. Z. (2018): Integrating a Comprehensive DNA Barcode Reference Library with a Global Map of Yews (Taxus L.) for Forensic Identification. Molecular Ecology Resource, 18: 1115–1131.

Sickel, W., Ankenbrand, M. J., Grimmer, G., Holzschuh, A., Härtel, S., Lanzen, J., Steffan-Dewenter, I., Keller, A. (2015): Increased Efficiency in Identifying Mixed Pollen Samples by Meta-Barcoding with a Dual-Indexing Approach. BMC Ecology, 15: 20.

Lowe, A., Jones, L., Witter, L., Creer, S., de Vere, N. (2022): Using DNA Metabarcoding to Identify Floral Visitation by Pollinators. Diversity, 14.

Webb, C. O. (2000): Exploring the Phylogenetic Structure of Ecological Communities: an Example for Rain Forest Trees. American Naturalist, 156: 145–155.

Jones, F. A. (2011): The Roots of Diversity: Below Ground Species Richness and Rooting Distributions in a Tropical Forest Revealed by DNA Barcodes and Inverse Modeling. PLoS ONE, 6: e24506.

Kesanakurti, P. R. (2011): Spatial Patterns of Plant Diversity Below-Ground as Revealed by DNA Barcoding. Molecular Ecology, 20: 1289–1302.

Gonzalez-Varo, J. P. (2014): Who dispersed the seeds? The Use of DNA Barcoding in Frugivory and Seed Dispersal Studies. Methods Ecology and Evolution, 5: 806–814.

Garcia-Robledo, C. (2013): Tropical Plant–Herbivore Networks: Reconstructing Species Interactions using DNA Barcodes. PLoS ONE, 8: e52967.

Young, M. R., Proctor, H. C., Dewaard, J. R., Hebert, P. D. N. (2019): DNA Barcodes Expose Unexpected Diversity in Canadian Mites. Molecular Ecology, 28: 5347–5359.

Bonato, K. O., Silva, P. C., Malabarba, L. R. (2018): Unrevealing Parasitic Trophic Interactions-A Molecular Approach for Fluid-Feeding Fishes. Frontiers Ecology and Evolution, 6: 1–8.

Keet, J.-H., Ellis, A. G., Hui, C., Roux, J. J. L. (2017): Legume–Rhizobium Symbiotic Promiscuity and Effectiveness Do Not Affect Plant Invasiveness. Annals of Botany, 119: 1319–1331.

Lücking, R., Aime, M. C., Robbertse, B., Miller, A. N., Ariyawansa, H. A., Aoki, T., Cardinali, G., Crous, P. W., Druzhinina, I. S., Geiser, D. M. (2020): Unambiguous Identification of Fungi: Where Do We Stand and How Accurate and Precise Is Fungal DNA Barcoding?. IMA Fungus, 11: 14.

Smith, H. B., Dal Grande, F., Muggia, L., Keuler, R., Divakar, P. K., Grewe, F., Schmitt, I., Lumbsch, H. T., Leavitt, S. D. (2020): Metagenomic Data Reveal Diverse Fungal and Algal Communities Associated with the Lichen Symbiosis. Symbiosis, 82: 133–147.

Taberlet, P., Coissac, E., Pompanon, F. (2012): Towards Next-generation Biodiversity Assessment Using DNA Metabarcoding. Molecular, 21: 2045–2050.

Ogram, A., Sayler, G. S., Barkay, T. (1987): The Extraction and Purification of Microbial DNA from Sediments. Journal of Microbiology Methods, 7: 57–66. doi:10.1016/0167-7012(87) 90025-x

Clare, E. L., Economou, C. K., Chris, G. F., Gilbert, J. D., Bennet, F., Drinkwater, R. (2021): eDNAir: Proof of Concept that Animal DNA can be Collected from Air Sampling. Peerj 9: e11030. doi:10.7717/peerj.11030

Kyle, K. E., Allen, M. C., Dragon, J., Bunnell, J. F., Reinert, H. K., Zappalorti, R. (2022): Combining Surface and Soil Environmental DNA with Artificial Cover Objects to Improve Terrestrial Reptile Survey Detection. Conservation Biology 9: e13939. doi:10.1111/cobi. 13939

Yu, D. W., Ji, Y. Q., Emerson, B. C., Wang, X. Y., Ye, C. X., Yang, C. Y. (2012): Biodiversity soup: Metabarcoding of Arthropods for Rapid Biodiversity Assessment and Biomonitoring. Methods Ecology and Evolution 3: 613–623. doi:10.1111/j.2041-210X.2012. 00198.x

Pompanon, F., Coissac, E., Taberlet, P. (2011): Metabarcoding a New Way to Analyze Biodiversity. Biofuture 319: 30–32.