References (web resources and publications) used in the BIOL 497/597 - Genomics & Bioinformatics course are cited here. The citation of references supports transparency in science as well as provides opportunities for students to further their knowledge by accessing articles and books used to develop this course. The BibTex document is accessible here. Please contact the instructor (svenbuerki@boisestate.edu) to add missing references to this document.
[1] S. F. Altschul, W. Gish, W. Miller, et al. “Basic local alignment search tool”. In: Journal of Molecular Biology 215.3 (1990), pp. 403 - 410. ISSN: 0022-2836. DOI: https://doi.org/10.1016/S0022-2836(05)80360-2. http://www.sciencedirect.com/science/article/pii/S0022283605803602.
[2] S. F. Altschul, T. L. Madden, A. A. Schäffer, et al. “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”. In: Nucleic acids research 25.17 (1997), pp. 3389-3402.
[3] K. Ambrozová, T. Mandáková, P. Bures, et al. “Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies”. Eng. In: Annals of botany 107.2 (Feb. 2011). 21156758[pmid], pp. 255-268. ISSN: 1095-8290. DOI: 10.1093/aob/mcq235. https://pubmed.ncbi.nlm.nih.gov/21156758.
[4] S. Andrews. FastQC A Quality Control tool for High Throughput Sequence Data. 2012. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
[5] A. M. Aransay. Field guidelines for genetic experimental designs in high-throughput sequencing. New York, NY: Springer Science+Business Media, 2016. ISBN: 978-3-319-31348-1.
[6] S. Asaf, A. L. Khan, A. R. Khan, et al. “Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species”. In: Frontiers in Plant Science 7 (2016), p. 843. ISSN: 1664-462X. DOI: 10.3389/fpls.2016.00843. https://www.frontiersin.org/article/10.3389/fpls.2016.00843.
[7] J. Azofeifa-Bolaños, L. Gigant, M. Nicolás-García, et al. “A new vanilla species from Costa Rica closely related to V. planifolia (Orchidaceae)”. In: European Journal of Taxonomy 0.284 (2017). ISSN: 2118-9773. DOI: 10.5852/ejt.2017.284. http://www.europeanjournaloftaxonomy.eu/index.php/ejt/article/view/408.
[8] A. Bankevich, S. Nurk, D. Antipov, et al. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing”. In: J Comput Biol 19.5 (May. 2012). 22506599[pmid], pp. 455-477. ISSN: 1066-5277. DOI: 10.1089/cmb.2012.0021[PII]. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/.
[9] A. Beckerman, D. Childs, and O. Petchey. Getting Started with R: An Introduction for Biologists. Oxford University Press, 2017.
[10] D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, et al. “GenBank”. In: Nucleic Acids Research 33 (2005), pp. D34-D38.
[11] C. Bleidorn. Phylogenomics. Springer International Publishing, 2017.
[12] U. Bodenhofer, E. Bonatesta, C. Horejš-Kainrath, et al. “msa: an R package for multiple sequence alignment”. In: Bioinformatics 31.24 (2015), pp. 3997-3999. DOI: 10.1093/bioinformatics/btv494. eprint: /oup/backfile/content_public/journal/bioinformatics/31/24/10.1093/bioinformatics/btv494/2/btv494.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btv494>.
[13] R. E. Bone, J. A. C. Smith, N. Arrigo, et al. “A macro-ecological perspective on crassulacean acid metabolism (CAM) photosynthesis evolution in Afro-Madagascan drylands: Eulophiinae orchids as a case study”. In: New Phytologist 208.2 (2015). 2015-19192, pp. 469-481. ISSN: 1469-8137. DOI: 10.1111/nph.13572. http://dx.doi.org/10.1111/nph.13572.
[14] S. Bory, O. Catrice, S. Brown, et al. “Natural polyploidy in Vanilla planifolia (Orchidaceae)”. In: Genome 51.10 (2008). PMID: 18923533, pp. 816-826. DOI: 10.1139/G08-068. eprint: https://doi.org/10.1139/G08-068
. https://doi.org/10.1139/G08-068.
[15] S. Bory, M. Grisoni, M. Duval, et al. “Biodiversity and preservation of vanilla: present state of knowledge”. In: Genetic Resources and Crop Evolution 55.4 (Jun. 2008), pp. 551-571. ISSN: 1573-5109. DOI: 10.1007/s10722-007-9260-3. https://doi.org/10.1007/s10722-007-9260-3.
[16] A. Bouetard, P. Lefeuvre, R. Gigant, et al. “Evidence of transoceanic dispersion of the genus Vanilla based on plastid DNA phylogenetic analysis”. In: Molecular Phylogenetics and Evolution 55.2 (2010), pp. 621 - 630. ISSN: 1055-7903. DOI: https://doi.org/10.1016/j.ympev.2010.01.021. http://www.sciencedirect.com/science/article/pii/S1055790310000230.
[17] K. R. Bradnam, J. N. Fass, A. Alexandrov, et al. “Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species”. In: GigaScience 2.1 (2013), pp. 1-31. DOI: 10.1186/2047-217X-2-10. eprint: /oup/backfile/content_public/journal/gigascience/2/1/10.1186_2047-217x-2-10/7/13742_2013_article_29.pdf. <+%20http://dx.doi.org/10.1186/2047-217X-2-10>.
[18] T. A. Brown. Genomes 4. Garland Science, 2017.
[19] S. Buerki and W. J. Baker. “Collections-based research in the genomic era”. In: Biological Journal of the Linnean Society 117.1 (2016), pp. 5-10. DOI: 10.1111/bij.12721. eprint: /oup/backfile/content_public/journal/biolinnean/117/1/10.1111_bij.12721/1/bij12721.pdf. <+%20http://dx.doi.org/10.1111/bij.12721>.
[20] S. Buerki, F. Forest, N. Alvarez, et al. “An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae”. In: Journal of Biogeography 38.3 (2011), pp. 531-550. ISSN: 1365-2699. DOI: 10.1111/j.1365-2699.2010.02432.x. http://dx.doi.org/10.1111/j.1365-2699.2010.02432.x.
[21] S. Buerki, P. P. Lowry II, J. Munzinger, et al. “Alectryon vitiensis: A new species of Sapindaceae endemic to Fiji”. In: Novon: A Journal for Botanical Nomenclature 25.4 (2017), pp. 421-429.
[22] J. Burnier, S. Buerki, N. Arrigo, et al. “Genetic structure and evolution of Alpine polyploid complexes: Ranunculus kuepferi (Ranunculaceae) as a case study”. In: Molecular Ecology 18.17 (2009), pp. 3730-3744. ISSN: 1365-294X. DOI: 10.1111/j.1365-294X.2009.04281.x. http://dx.doi.org/10.1111/j.1365-294X.2009.04281.x.
[23] M. A. Butler and A. A. King. “Phylogenetic comparative analysis: a modeling approach for adaptive evolution”. In: American Naturalist 164 (2004), pp. 683-695. http://www.press.uchicago.edu/ucp/journals/journal/an.html.
[24] J. Cai, X. Liu, K. Vanneste, et al. “The genome sequence of the orchid Phalaenopsis equestris”. In: Nature Genetics 47.1 (2015), pp. 65-+. ISSN: 1061-4036. DOI: 10.1038/ng.3149. <%3CGo%20to%20ISI%3E://WOS:000346990400013>.
[25] CBOL. International Barcode of Life: DNA barcoding. 2021. https://ibol.org/about/dna-barcoding/.
[26] S. Chamberlain. rgbif: Interface to the Global ‘Biodiversity’ Information Facility ‘API’. 2016. https://CRAN.R-project.org/package=rgbif.
[27] D. Charif and J. Lobry. “SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis.” In: Structural approaches to sequence evolution: Molecules, networks, populations. Ed. by U. Bastolla, M. Porto, H. Roman and M. Vendruscolo. Biological and Medical Physics, Biomedical Engineering. ISBN : 978-3-540-35305-8. New York: Springer Verlag, 2007, pp. 207-232.
[28] F. Chaumont, M. Moshelion, and M. J. Daniels. “Regulation of plant aquaporin activity”. In: Biology of the Cell 97.10 (2005), pp. 749-764.
[29] T. Cheng, C. Xu, L. Lei, et al. “Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity”. In: Molecular Ecology Resources 16.1 (2016), pp. 138-149. DOI: 10.1111/1755-0998.12438. eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12438. https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12438.
[30] J. Claverie and C. Notredame. Bioinformatics For Dummies, 2nd Edition. Wiley, 2006.
[31] A. Coghlan, T. J. Fiedler, S. J. McKay, et al. “nGASP - the nematode genome annotation assessment project”. In: BMC Bioinformatics 9.1 (Dec. 2008), p. 549. ISSN: 1471-2105. DOI: 10.1186/1471-2105-9-549. https://doi.org/10.1186/1471-2105-9-549.
[32] T. G. O. Consortium. “The Gene Ontology resource: enriching a GOld mine”. In: Nucleic Acids Research 49.D1 (Dec. 2020), pp. D325-D334. ISSN: 0305-1048. DOI: 10.1093/nar/gkaa1113. eprint: https://academic.oup.com/nar/article-pdf/49/D1/D325/35364518/gkaa1113\_supplemental\_file.pdf. https://doi.org/10.1093/nar/gkaa1113.
[33] T. U. Consortium. “UniProt: a hub for protein information”. In: Nucleic Acids Research 43.D1 (Oct. 2014), pp. D204-D212. ISSN: 0305-1048. DOI: 10.1093/nar/gku989. eprint: https://academic.oup.com/nar/article-pdf/43/D1/D204/17438515/gku989.pdf. https://doi.org/10.1093/nar/gku989.
[34] M. J. Crawley. The R Book, 2nd Edition. Wiley, 2012.
[35] M. Crusoe, H. Alameldin, S. Awad, et al. “The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]”. In: F1000Research 4.900 (2015). DOI: 10.12688/f1000research.6924.1.
[36] A. Dai. “Drought under global warming: a review”. In: Wiley Interdisciplinary Reviews: Climate Change 2.1 (2011), pp. 45-65. ISSN: 1757-7799. DOI: 10.1002/wcc.81. http://dx.doi.org/10.1002/wcc.81.
[37] J. W. Dale, M. von Schantz, and N. Plant. From Genes to Genomes: Concepts and Applications of DNA Technology, 3rd Edition. Wiley, 2012.
[38] J. . Danielson and U. Johanson. “Unexpected complexity of the aquaporin gene family in the moss Physcomitrella patens”. In: BMC plant biology 8.1 (2008), pp. 1-15.
[39] B. E. Davidson, S. J. Novak, and M. D. Serpe. “Consequences of inoculation with native arbuscular mycorrhizal fungi for root colonization and survival of Artemisia tridentata ssp. wyomingensis seedlings after transplanting”. In: Mycorrhiza 26.6 (Aug. 2016), pp. 595-608. ISSN: 1432-1890. DOI: 10.1007/s00572-016-0696-1. https://doi.org/10.1007/s00572-016-0696-1.
[40] B. T. Dentinger and L. M. Suz. “What’s for dinner? Undescribed species of porcini in a commercial packet”. In: PeerJ 2 (2014), p. e570.
[41] R. DeSalle and P. Goldstein. “Review and Interpretation of Trends in DNA Barcoding”. In: Frontiers in Ecology and Evolution 7 (2019), p. 302. ISSN: 2296-701X. DOI: 10.3389/fevo.2019.00302. https://www.frontiersin.org/article/10.3389/fevo.2019.00302.
[42] R. deSalle and J. Rosenfeld. Phylogenomics: A Primer 1st Edition. Garland Science, 2013.
[43] S. Dodsworth, M. W. Chase, L. J. Kelly, et al. “Genomic Repeat Abundances Contain Phylogenetic Signal”. In: Systematic Biology 64.1 (2015), pp. 112-126. DOI: 10.1093/sysbio/syu080. eprint: /oup/backfile/content_public/journal/sysbio/64/1/10.1093_sysbio_syu080/1/syu080.pdf. <+%20http://dx.doi.org/10.1093/sysbio/syu080>.
[44] J. Doležel, J. Greilhuber, and J. Suda. “Estimation of nuclear DNA content in plants using flow cytometry”. In: Nature Protocols 2.9 (Sep. 2007), pp. 2233-2244. ISSN: 1750-2799. DOI: 10.1038/nprot.2007.310. https://doi.org/10.1038/nprot.2007.310.
[45] S. Dray and A. Dufour. “The ade4 package: implementing the duality diagram for ecologists”. In: Journal of Statistical Software 22.4 (2007), pp. 1-20.
[46] R. C. Edgar. “MUSCLE: multiple sequence alignment with high accuracy and high throughput”. In: Nucleic acids research 32.5 (2004), pp. 1792-1797.
[47] R. Ekblom and J. B. W. Wolf. “A field guide to whole-genome sequencing, assembly and annotation”. In: Evolutionary Applications 7.9 (2014), pp. 1026-1042. ISSN: 1752-4571. DOI: 10.1111/eva.12178. http://dx.doi.org/10.1111/eva.12178.
[48] P. Ellestad, M. A. P. Farrera, F. Forest, et al. “Uncovering haplotype diversity in cultivated Mexican vanilla species”. In: American Journal of Botany 109.7 (2022), pp. 1120-1138. DOI: https://doi.org/10.1002/ajb2.16024. eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/ajb2.16024. https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/ajb2.16024.
[49] P. Ellestad, F. Forest, M. Serpe, et al. “Harnessing large-scale biodiversity data to infer the current distribution of Vanilla planifolia (Orchidaceae)”. In: Botanical Journal of the Linnean Society (Feb. 2021). boab005. ISSN: 0024-4074. DOI: 10.1093/botlinnean/boab005. eprint: https://academic.oup.com/botlinnean/advance-article-pdf/doi/10.1093/botlinnean/boab005/36210432/boab005.pdf. https://doi.org/10.1093/botlinnean/boab005.
[50] P. Ellestad, M. A. Pérez-Farrera, and S. Buerki. “Genomic Insights into Cultivated Mexican Vanilla planifolia Reveal High Levels of Heterozygosity Stemming from Hybridization”. In: Plants 11.16 (2022). ISSN: 2223-7747. DOI: 10.3390/plants11162090. https://www.mdpi.com/2223-7747/11/16/2090.
[51] J. Flexas, J. M. Escalona, S. Evain, et al. “Steady-state chlorophyll fluorescence (Fs) measurements as a tool to follow variations of net CO2 assimilation and stomatal conductance during water-stress in C3 plants”. In: Physiologia Plantarum 114.2 (2002), pp. 231-240. ISSN: 1399-3054. DOI: 10.1034/j.1399-3054.2002.1140209.x. http://dx.doi.org/10.1034/j.1399-3054.2002.1140209.x.
[52] J. Gaffney, R. Tibebu, R. Bart, et al. “Open access to genetic sequence data maximizes value to scientists, farmers, and society”. In: Global Food Security 26 (2020), p. 100411. ISSN: 2211-9124. DOI: https://doi.org/10.1016/j.gfs.2020.100411. https://www.sciencedirect.com/science/article/pii/S2211912420300651.
[53] H. Gehrig, K. Faist, and M. Kluge. “Identification of phosphoenolpyruvate carboxylase isoforms in leaf, stem and roots of the obligate CAM plant Vanilla planifolia Salib. (Orchidaceae): a physiological and molecular approach”. In: Plant Molecular Biology 38.6 (Dec. 1998), pp. 1215-1223. ISSN: 1573-5028. DOI: 10.1023/A:1006006331011. https://doi.org/10.1023/A:1006006331011.
[54] S. Gnerre, I. MacCallum, D. Przybylski, et al. “High-quality draft assemblies of mammalian genomes from massively parallel sequence data”. In: Proceedings of the National Academy of Sciences 108.4 (2011), pp. 1513-1518. ISSN: 0027-8424. DOI: 10.1073/pnas.1017351108. eprint: http://www.pnas.org/content/108/4/1513.full.pdf. http://www.pnas.org/content/108/4/1513.
[55] S. Gnerre, I. MacCallum, D. Przybylski, et al. “High-quality draft assemblies of mammalian genomes from massively parallel sequence data”. In: Proceedings of the National Academy of Sciences 108.4 (2011), pp. 1513-1518. DOI: 10.1073/pnas.1017351108. eprint: http://www.pnas.org/content/108/4/1513.full.pdf. http://www.pnas.org/content/108/4/1513.abstract.
[56] P. F. Gonçalves, A. R. Oliveira-Marques, T. E. Matsumoto, et al. “DNA barcoding identifies illegal parrot trade”. In: Journal of Heredity 106.S1 (2015), pp. 560-564.
[57] M. G. Grabherr, B. J. Haas, M. Yassour, et al. “Full-length transcriptome assembly from RNA-Seq data without a reference genome”. In: Nature Biotechnology 29 (May. 2011), pp. 644 EP -. http://dx.doi.org/10.1038/nbt.1883.
[58] D. Greenberg and H. Soreq. “Alternative Splicing”. In: Brenner’s Encyclopedia of Genetics (Second Edition). Ed. by S. Maloy and K. Hughes. Second Edition. San Diego: Academic Press, 2013, pp. 97-98. ISBN: 978-0-08-096156-9. DOI: https://doi.org/10.1016/B978-0-12-374984-0.00043-7. https://www.sciencedirect.com/science/article/pii/B9780123749840000437.
[59] A. Gurevich, V. Saveliev, N. Vyahhi, et al. “QUAST: quality assessment tool for genome assemblies”. In: Bioinformatics 29.8 (2013), pp. 1072-1075. DOI: 10.1093/bioinformatics/btt086. eprint: /oup/backfile/content_public/journal/bioinformatics/29/8/10.1093_bioinformatics_btt086/2/btt086.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btt086>.
[60] C. Hahn, L. Bachmann, and B. Chevreux. “Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach”. In: Nucleic Acids Research 41.13 (2013), p. e129. DOI: 10.1093/nar/gkt371. eprint: /oup/backfile/content_public/journal/nar/41/13/10.1093_nar_gkt371/3/gkt371.pdf. <+%20http://dx.doi.org/10.1093/nar/gkt371>.
[61] D. L. Hartl. “Fly meets shotgun: shotgun wins”. In: Nature Genetics 24 (Apr. 2000), p. 327 EP. http://dx.doi.org/10.1038/74125.
[62] J. M. Heather and B. Chain. “The sequence of sequencers: The history of sequencing DNA”. In: Genomics 107.1 (2016), pp. 1-8. ISSN: 0888-7543. DOI: https://doi.org/10.1016/j.ygeno.2015.11.003. https://www.sciencedirect.com/science/article/pii/S0888754315300410.
[63] R. J. Hijmans, S. E. Cameron, J. L. Parra, et al. “Very high resolution interpolated climate surfaces for global land areas”. In: International Journal of Climatology 25.15 (2005), pp. 1965-1978. ISSN: 1097-0088. DOI: 10.1002/joc.1276. http://dx.doi.org/10.1002/joc.1276.
[64] P. M. Hollingsworth, L. L. Forrest, J. L. Spouge, et al. “A DNA barcode for land plants”. In: Proceedings of the National Academy of Sciences 106.31 (2009), pp. 12794-12797. ISSN: 0027-8424. DOI: 10.1073/pnas.0905845106. eprint: https://www.pnas.org/content/106/31/12794.full.pdf. https://www.pnas.org/content/106/31/12794.
[65] C. Holt and M. Yandell. “MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects”. In: BMC Bioinformatics 12.1 (Dec. 2011), p. 491. ISSN: 1471-2105. DOI: 10.1186/1471-2105-12-491. https://doi.org/10.1186/1471-2105-12-491.
[66] Y. Hu, V. Colantonio, B. S. F. Müller, et al. “Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn”. In: Nature Communications 12.1 (Feb. 2021), p. 1227. ISSN: 2041-1723. DOI: 10.1038/s41467-021-21380-4. https://doi.org/10.1038/s41467-021-21380-4.
[67] T. A. G. Initiative. “Analysis of the genome sequence of the flowering plant Arabidopsis thaliana”. In: Nature 408.6814 (Dec. 2000), pp. 796-815. ISSN: 1476-4687. DOI: 10.1038/35048692. https://doi.org/10.1038/35048692.
[68] K. Ishibashi. “Aquaporin subfamily with unusual NPA boxes”. In: Biochimica et Biophysica Acta (BBA)-Biomembranes 1758.8 (2006), pp. 989-993.
[69] S. D. Jackman, B. P. Vandervalk, H. Mohamadi, et al. “ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter”. In: Genome Research 27.5 (2017), pp. 768-777. DOI: 10.1101/gr.214346.116. eprint: http://genome.cshlp.org/content/27/5/768.full.pdf+html. http://genome.cshlp.org/content/27/5/768.abstract.
[70] J. Jersáková, P. Trávníček, B. Kubátová, et al. “Genome size variation in Orchidaceae subfamily Apostasioideae: filling the phylogenetic gap”. In: Botanical Journal of the Linnean Society 172.1 (2013), pp. 95-105. ISSN: 1095-8339. DOI: 10.1111/boj.12027. http://dx.doi.org/10.1111/boj.12027.
[71] M. Kanehisa, M. Furumichi, Y. Sato, et al. “KEGG for taxonomy-based analysis of pathways and genomes”. In: Nucleic Acids Research 51.D1 (Oct. 2022), pp. D587-D592. ISSN: 0305-1048. DOI: 10.1093/nar/gkac963. eprint: https://academic.oup.com/nar/article-pdf/51/D1/D587/48440889/gkac963.pdf. https://doi.org/10.1093/nar/gkac963.
[72] K. Katoh, J. Rozewicki, and K. D. Yamada. “MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization”. In: Briefings in Bioinformatics 20.4 (Sep. 2017), pp. 1160-1166. ISSN: 1477-4054. DOI: 10.1093/bib/bbx108. eprint: https://academic.oup.com/bib/article-pdf/20/4/1160/30119669/bbx108.pdf. https://doi.org/10.1093/bib/bbx108.
[73] M. Kearse, R. Moir, A. Wilson, et al. “Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data”. In: Bioinformatics 28.12 (2012), pp. 1647-1649. DOI: 10.1093/bioinformatics/bts199. eprint: /oup/backfile/content_public/journal/bioinformatics/28/12/10.1093/bioinformatics/bts199/2/bts199.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/bts199>.
[74] J. M. Keith. Bioinformatics, Volume I: Data, Sequence Analysis, and Evolution. Springer Science+Business Media New York, 2017.
[75] D. R. Kelley, M. C. Schatz, and S. L. Salzberg. “Quake: quality-aware detection and correction of sequencing errors”. In: Genome Biology 11.11 (2010), p. R116. ISSN: 1474-760X. DOI: 10.1186/gb-2010-11-11-r116. https://doi.org/10.1186/gb-2010-11-11-r116.
[76] L. A. Kelley, S. Mezulis, C. M. Yates, et al. “The Phyre2 web portal for protein modeling, prediction and analysis”. In: Nature protocols 10.6 (2015), pp. 845-858.
[77] S. Kembel, P. Cowan, M. Helmus, et al. “Picante: R tools for integrating phylogenies and ecology”. In: Bioinformatics 26 (2010), pp. 1463-1464.
[78] A. A. Kolesnikov and E. S. Gerasimov. “Diversity of mitochondrial genome organization”. English. In: BIOCHEMISTRY-MOSCOW 77.13 (), pp. 1424-1435. ISSN: 0006-2979. DOI: 10.1134/S0006297912130020.
[79] S. Koren, B. P. Walenz, K. Berlin, et al. “Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation”. In: Genome Research 27.5 (2017), pp. 722-736. DOI: 10.1101/gr.215087.116. eprint: http://genome.cshlp.org/content/27/5/722.full.pdf+html. http://genome.cshlp.org/content/27/5/722.abstract.
[80] A. M. Kozlov, D. Darriba, T. Flouri, et al. “RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference”. In: Bioinformatics 35.21 (May. 2019), pp. 4453-4455. ISSN: 1367-4803. DOI: 10.1093/bioinformatics/btz305. eprint: https://academic.oup.com/bioinformatics/article-pdf/35/21/4453/30330793/btz305.pdf. https://doi.org/10.1093/bioinformatics/btz305.
[81] A. Krogh, B. Larsson, G. Von Heijne, et al. “Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes”. In: Journal of molecular biology 305.3 (2001), pp. 567-580.
[82] S. Kumar, G. Stecher, M. Li, et al. “MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms”. In: Molecular Biology and Evolution 35.6 (May. 2018), pp. 1547-1549. ISSN: 0737-4038. DOI: 10.1093/molbev/msy096. eprint: https://academic.oup.com/mbe/article-pdf/35/6/1547/25091958/msy096.pdf. https://doi.org/10.1093/molbev/msy096.
[83] S. Kumar, G. Stecher, M. Li, et al. “MEGA X: molecular evolutionary genetics analysis across computing platforms”. In: Molecular biology and evolution 35.6 (2018), pp. 1547-1549.
[84] S. Kurtz, A. Phillippy, A. L. Delcher, et al. “Versatile and open software for comparing large genomes”. In: Genome Biology 5.2 (Jan. 2004), p. R12. ISSN: 1474-760X. DOI: 10.1186/gb-2004-5-2-r12. https://doi.org/10.1186/gb-2004-5-2-r12.
[85] B. B. Larsen, E. C. Miller, M. K. Rhodes, et al. “Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life”. In: The Quarterly Review of Biology 92.3 (2017), pp. 229-265. DOI: 10.1086/693564.
[86] A. Larsson. “AliView: a fast and lightweight alignment viewer and editor for large datasets”. In: Bioinformatics 30.22 (Aug. 2014), pp. 3276-3278. ISSN: 1367-4803. DOI: 10.1093/bioinformatics/btu531. eprint: https://academic.oup.com/bioinformatics/article-pdf/30/22/3276/17146391/btu531.pdf. https://doi.org/10.1093/bioinformatics/btu531.
[87] M. Lawrence, W. Huber, H. Pagès, et al. “Software for Computing and Annotating Genomic Ranges”. In: PLoS Computational Biology 9 (8 2013). DOI: 10.1371/journal.pcbi.1003118. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118}.
[88] P. Lemey, M. Salemi, and A. Vandamme. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Edition 2. Cambridge University Press, 2009.
[89] A. Lesk. Introduction to Genomics, Third edition. Oxford University Press, 2017.
[90] G. Li, V. Santoni, and C. Maurel. “Plant aquaporins: roles in plant physiology”. In: Biochimica et Biophysica Acta (BBA)-General Subjects 1840.5 (2014), pp. 1574-1582.
[91] H. Li and R. Durbin. “Fast and accurate short read alignment with Burrows–Wheeler transform”. In: Bioinformatics 25.14 (2009), pp. 1754-1760. DOI: 10.1093/bioinformatics/btp324. eprint: /oup/backfile/content_public/journal/bioinformatics/25/14/10.1093/bioinformatics/btp324/2/btp324.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btp324>.
[92] H. Li, B. Handsaker, A. Wysoker, et al. “The Sequence Alignment/Map format and SAMtools”. In: Bioinformatics 25.16 (2009), pp. 2078-2079. DOI: 10.1093/bioinformatics/btp352. eprint: /oup/backfile/content_public/journal/bioinformatics/25/16/10.1093/bioinformatics/btp352/2/btp352.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btp352>.
[93] R. Li, W. Fan, G. Tian, et al. “The sequence and de novo assembly of the giant panda genome”. In: Nature 463 (Dec. 2009). Article, pp. 311 EP -. http://dx.doi.org/10.1038/nature08696.
[94] X. Liao, W. Zhu, J. Zhou, et al. “Repetitive DNA sequence detection and its role in the human genome”. In: Communications Biology 6.1 (Sep. 2023), p. 954. ISSN: 2399-3642. DOI: 10.1038/s42003-023-05322-y. https://doi.org/10.1038/s42003-023-05322-y.
[95] C. Lin, J. J. W. Chen, Y. Huang, et al. “The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family”. In: Scientific Reports 5 (Mar. 2015). Article, pp. 9040 EP -. http://dx.doi.org/10.1038/srep09040.
[96] R. Luo, B. Liu, Y. Xie, et al. “SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler”. In: GigaScience 1.1 (Dec. 2012), p. 18. ISSN: 2047-217X. DOI: 10.1186/2047-217X-1-18. https://doi.org/10.1186/2047-217X-1-18.
[97] J. Males and H. Griffiths. “Stomatal biology of CAM plants”. In: Plant Physiology (2017). ISSN: 0032-0889. DOI: 10.1104/pp.17.00114. eprint: http://www.plantphysiol.org/content/early/2017/02/27/pp.17.00114.full.pdf. http://www.plantphysiol.org/content/early/2017/02/27/pp.17.00114.
[98] D. Mapleson, G. Garcia Accinelli, G. Kettleborough, et al. “KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies”. In: Bioinformatics 33.4 (2017), pp. 574-576. DOI: 10.1093/bioinformatics/btw663. eprint: /oup/backfile/content_public/journal/bioinformatics/33/4/10.1093_bioinformatics_btw663/4/btw663.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btw663>.
[99] G. Marçais and C. Kingsford. “A fast, lock-free approach for efficient parallel counting of occurrences of k-mers”. In: Bioinformatics 27.6 (2011), pp. 764-770. DOI: 10.1093/bioinformatics/btr011. eprint: /oup/backfile/content_public/journal/bioinformatics/27/6/10.1093_bioinformatics_btr011/2/btr011.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btr011>.
[100] F. Markowetz. “Five selfish reasons to work reproducibly”. In: Genome Biology 16.1 (Dec. 2015), p. 274. ISSN: 1474-760X. DOI: 10.1186/s13059-015-0850-7. https://doi.org/10.1186/s13059-015-0850-7.
[101] J. A. Martin and Z. Wang. “Next-generation transcriptome assembly”. In: Nature Reviews Genetics 12 (Sep. 2011). Review Article, pp. 671 EP -. http://dx.doi.org/10.1038/nrg3068.
[102] V. Marx. “Method of the year: long-read sequencing”. In: Nature Methods 20.1 (Jan. 2023), pp. 6-11. ISSN: 1548-7105. DOI: 10.1038/s41592-022-01730-w. https://doi.org/10.1038/s41592-022-01730-w.
[103] J. C. Masters and L. Pozzi. “Phylogenetic Inference”. In: The International Encyclopedia of Primatology. American Cancer Society, 2017, pp. 1-6. ISBN: 9781119179313. DOI: https://doi.org/10.1002/9781119179313.wbprim0419. eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119179313.wbprim0419. https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119179313.wbprim0419.
[104] N. J. Matzke. BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts. The rexpokit/cladoRcpp/BioGeoBEARS packages were first published in: Matzke, Nicholas J. (2012). Founder-event speciation in BioGeoBEARS package dramatically improves likelihoods and alters parameter inference in Dispersal-Extinction-Cladogenesis (DEC) analyses. Frontiers of Biogeography, 4(suppl. 1): 210, December 2012. Link to abstract and PDF of poster: http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster . (Poster abstract published in the Conference Program and Abstracts of the International Biogeography Society 6th Biannual Meeting, Miami, Florida. Poster Session P10: Historical and Paleo-Biogeography. Poster 129B. January 11, 2013.). University of California, Berkeley. Berkeley, CA, 2013. http://CRAN.R-project.org/package=BioGeoBEARS.
[105] K. Maxwell and G. N. Johnson. “Chlorophyll fluorescence—a practical guide”. In: Journal of Experimental Botany 51.345 (2000), pp. 659-668. DOI: 10.1093/jexbot/51.345.659. eprint: /oup/backfile/content_public/journal/jxb/51/345/10.1093_jexbot_51.345.659/1/510659.pdf. <+%20http://dx.doi.org/10.1093/jexbot/51.345.659>.
[106] A. E. Melton, J. Beck, S. J. Galla, et al. “A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change”. In: Ecology and Evolution 11.21 (2021), pp. 15417-15429. DOI: https://doi.org/10.1002/ece3.8245. eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8245. https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.8245.
[107] A. E. Melton, A. W. Child, J. Beard Richard S, et al. “A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands”. In: G3 Genes|Genomes|Genetics 12.7 (May. 2022). jkac122. ISSN: 2160-1836. DOI: 10.1093/g3journal/jkac122. eprint: https://academic.oup.com/g3journal/article-pdf/12/7/jkac122/44473065/jkac122.pdf. https://doi.org/10.1093/g3journal/jkac122.
[108] R. Ming, R. VanBuren, C. M. Wai, et al. “The pineapple genome and the evolution of CAM photosynthesis”. In: Nature Genetics 47.12 (Dec. 2015), p. 1435. ISSN: 1061-4036. DOI: 10.1038/ng.3435.
[109] H. Mizuno, Y. Kawahara, H. Sakai, et al. “Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)”. In: BMC Genomics 11.1 (Dec. 2010), p. 683. ISSN: 1471-2164. DOI: 10.1186/1471-2164-11-683. https://doi.org/10.1186/1471-2164-11-683.
[110] L. S. Mofatto, F. d. A. Carneiro, N. G. Vieira, et al. “Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars”. In: BMC Plant Biology 16.1 (Apr. 2016), p. 94. ISSN: 1471-2229. DOI: 10.1186/s12870-016-0777-5. https://doi.org/10.1186/s12870-016-0777-5.
[111] M. C. Munoz-Torres, J. T. Reese, C. P. Childers, et al. “Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera”. In: Nucleic Acids Research 39.suppl 1 (2011), pp. D658-D662. DOI: 10.1093/nar/gkq1145.
[112] Z. Niu, J. Pan, S. Zhu, et al. “Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids”. In: Frontiers in Plant Science 8 (2017), p. 1713. ISSN: 1664-462X. DOI: 10.3389/fpls.2017.01713. https://www.frontiersin.org/article/10.3389/fpls.2017.01713.
[113] S. Nurk, S. Koren, A. Rhie, et al. “The complete sequence of a human genome”. In: Science 376.6588 (2022), pp. 44-53. DOI: 10.1126/science.abj6987. eprint: https://www.science.org/doi/pdf/10.1126/science.abj6987. https://www.science.org/doi/abs/10.1126/science.abj6987.
[114] M. H. O’Leary. “Carbon Isotopes in Photosynthesis”. In: BioScience 38.5 (1988), pp. 328-336. ISSN: 00063568, 15253244. http://www.jstor.org/stable/1310735.
[115] M. Öhman and B. L. Bass. “8 - RNA Editing”. In: RNA. Ed. by D. Söll, S. Nishimura and P. Moore. Oxford: Pergamon, 2001, pp. 125-136. ISBN: 978-0-08-043408-7. DOI: https://doi.org/10.1016/B978-008043408-7/50029-0. https://www.sciencedirect.com/science/article/pii/B9780080434087500290.
[116] H. Pagès, P. Aboyoun, R. Gentleman, et al. Biostrings: Efficient manipulation of biological strings. R package version 2.54.0. 2019.
[117] E. Paradis. Analysis of Phylogenetics and Evolution with R. Springer, 2012.
[118] E. Paradis, J. Claude, and K. Strimmer. “APE: analyses of phylogenetics and evolution in R language”. In: Bioinformatics 20 (2004), pp. 289-290.
[119] E. Paradis and K. Schliep. “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R”. In: Bioinformatics 35 (2019), pp. 526-528.
[120] J. Pellicer, M. F. Fay, and I. J. Leitch. “The largest eukaryotic genome of them all?” In: Botanical Journal of the Linnean Society 164.1 (2010), pp. 10-15. DOI: 10.1111/j.1095-8339.2010.01072.x. eprint: /oup/backfile/content_public/journal/botlinnean/164/1/10.1111_j.1095-8339.2010.01072.x/2/j.1095-8339.2010.01072.x.pdf. <+%20http://dx.doi.org/10.1111/j.1095-8339.2010.01072.x>.
[121] R. Poplin, P. Chang, D. Alexander, et al. “A universal SNP and small-indel variant caller using deep neural networks”. In: Nature Biotechnology 36.10 (2018), pp. 983-987. ISSN: 1546-1696. DOI: 10.1038/nbt.4235. https://doi.org/10.1038/nbt.4235.
[122] C. A. Quinto, R. Tinoco, and R. S. Hellberg. “DNA barcoding reveals mislabeling of game meat species on the US commercial market”. In: Food Control 59 (2016), pp. 386-392.
[123] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2016. https://www.R-project.org/.
[124] A. Raj, M. Stephens, and J. K. Pritchard. “fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets”. In: Genetics 197.2 (2014), pp. 573-589. ISSN: 0016-6731. DOI: 10.1534/genetics.114.164350. eprint: http://www.genetics.org/content/197/2/573.full.pdf. http://www.genetics.org/content/197/2/573.
[125] M. G. Reese and R. Guigó. “EGASP: Introduction”. In: Genome Biology 7.1 (Aug. 2006), p. S1. ISSN: 1474-760X. DOI: 10.1186/gb-2006-7-s1-s1. https://doi.org/10.1186/gb-2006-7-s1-s1.
[126] J. A. Reuter, D. V. Spacek, and M. P. Snyder. “High-Throughput Sequencing Technologies”. In: Molecular Cell 58.4 (2015), pp. 586 - 597. ISSN: 1097-2765. DOI: https://doi.org/10.1016/j.molcel.2015.05.004. http://www.sciencedirect.com/science/article/pii/S1097276515003408.
[127] L. J. Revell. “phytools: An R package for phylogenetic comparative biology (and other things).” In: Methods in Ecology and Evolution 3 (2012), pp. 217-223.
[128] A. Rhoads and K. F. Au. “PacBio Sequencing and Its Applications”. In: Genomics, Proteomics and Bioinformatics 13.5 (2015), pp. 278 - 289.
[129] D. W. Rice, A. J. Alverson, A. O. Richardson, et al. “Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella”. In: Science 342.6165 (2013), pp. 1468-1473. ISSN: 0036-8075. DOI: 10.1126/science.1246275. eprint: https://science.sciencemag.org/content/342/6165/1468.full.pdf. https://science.sciencemag.org/content/342/6165/1468.
[130] B. A. Richardson, S. G. Kitchen, R. L. Pendleton, et al. “Adaptive responses reveal contemporary and future ecotypes in a desert shrub”. In: Ecological Applications 24.2 (2014), pp. 413-427. ISSN: 1939-5582. DOI: 10.1890/13-0587.1. http://dx.doi.org/10.1890/13-0587.1.
[131] G. Robertson, J. Schein, R. Chiu, et al. “De novo assembly and analysis of RNA-seq data”. In: Nature Methods 7 (Oct. 2010), pp. 909 EP -. http://dx.doi.org/10.1038/nmeth.1517.
[132] J. D. Robin, A. T. Ludlow, R. LaRanger, et al. “Comparison of DNA Quantification Methods for Next Generation Sequencing”. In: Scientific Reports 6 (Apr. 2016). Article, pp. 24067 EP -. http://dx.doi.org/10.1038/srep24067.
[133] J. J. Russell, J. A. Theriot, P. Sood, et al. “Non-model model organisms”. In: BMC Biology 15.1 (Jun. 2017), p. 55. ISSN: 1741-7007. DOI: 10.1186/s12915-017-0391-5. https://doi.org/10.1186/s12915-017-0391-5.
[134] N. Saitou. “Eukaryote Genomes”. In: Introduction to Evolutionary Genomics. London: Springer London, 2013, pp. 193-222. ISBN: 978-1-4471-5304-7. DOI: 10.1007/978-1-4471-5304-7_8. https://doi.org/10.1007/978-1-4471-5304-7_8.
[135] H. Satam, K. Joshi, U. Mangrolia, et al. “Next-Generation Sequencing Technology: Current Trends and Advancements”. In: Biology 12.7 (2023). ISSN: 2079-7737. DOI: 10.3390/biology12070997. https://www.mdpi.com/2079-7737/12/7/997.
[136] K. Schliep. “phangorn: phylogenetic analysis in R”. In: Bioinformatics 27.4 (2011), pp. 592-593.
[137] P. M. Schlüter, M. A. Soto Arenas, and S. A. Harris. “Genetic Variation in Vanilla planifolia (Orchidaceae)”. In: Economic Botany 61.4 (2007), pp. 328-336. DOI: 10.1663/0013-0001(2007)61[328:GVIVPO]2.0.CO;2. https://doi.org/10.1007/s10722-007-9260-3.
[138] L. Sen, M. A. Fares, B. Liang, et al. “Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns”. In: Biology Direct 6.1 (Jun. 2011), p. 29. ISSN: 1745-6150. DOI: 10.1186/1745-6150-6-29. https://doi.org/10.1186/1745-6150-6-29.
[139] K. Shinozaki and K. Yamaguchi-Shinozaki. “Gene networks involved in drought stress response and tolerance”. In: Journal of Experimental Botany 58.2 (2007), pp. 221-227. DOI: 10.1093/jxb/erl164. eprint: /oup/backfile/content_public/journal/jxb/58/2/10.1093/jxb/erl164/2/erl164.pdf. <+%20http://dx.doi.org/10.1093/jxb/erl164>.
[140] J. T. Simpson. “Exploring genome characteristics and sequence quality without a reference”. In: Bioinformatics 30.9 (2014), pp. 1228-1235. DOI: 10.1093/bioinformatics/btu023. eprint: /oup/backfile/content_public/journal/bioinformatics/30/9/10.1093_bioinformatics_btu023/3/btu023.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btu023>.
[141] J. T. Simpson and R. Durbin. “Efficient de novo assembly of large genomes using compressed data structures”. In: Genome Research 22.3 (2012), pp. 549-556. DOI: 10.1101/gr.126953.111. eprint: http://genome.cshlp.org/content/22/3/549.full.pdf+html. http://genome.cshlp.org/content/22/3/549.abstract.
[142] J. T. Simpson and M. Pop. “The Theory and Practice of Genome Sequence Assembly”. In: Annual Review of Genomics and Human Genetics 16.1 (2015). PMID: 25939056, pp. 153-172. DOI: 10.1146/annurev-genom-090314-050032. eprint: https://doi.org/10.1146/annurev-genom-090314-050032
. https://doi.org/10.1146/annurev-genom-090314-050032.
[143] A. Soorni, D. Haak, D. Zaitlin, et al. “Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data”. In: BMC Genomics 18.1 (Jan. 2017), p. 49. ISSN: 1471-2164. DOI: 10.1186/s12864-016-3412-9. https://doi.org/10.1186/s12864-016-3412-9.
[144] M. A. Soto Arenas. “Conservation of the genetic resources of Vanilla”. PhD thesis. UNAM University, 1999.
[145] M. A. Soto Arenas. Filogeografia y recursos geneticos de las vainillas de Mexico. Informe final SNIB-CONABIO proyecto No. J101. Instituto Chinoin AC, 1999.
[146] M. A. Soto Arenas and P. Cribb. “A NEW INFRAGENERIC CLASSIFICATION AND SYNOPSIS OF THE GENUS VANILLA PLUM. EX MILL. (ORCHIDACEAE: VANILLINAE)”. In: Lankesteriana International Journal on Orchidology 9 (2009), pp. 355-398.
[147] A. Srivathsan, A. Ang, A. P. Vogler, et al. “Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate”. In: Frontiers in Zoology 13.1 (Apr. 2016), p. 17. ISSN: 1742-9994. DOI: 10.1186/s12983-016-0150-4. https://doi.org/10.1186/s12983-016-0150-4.
[148] A. Stamatakis. “RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies”. Eng. In: Bioinformatics (Oxford, England) 30.9 (May. 2014). 24451623[pmid], pp. 1312-1313. ISSN: 1367-4811. DOI: 10.1093/bioinformatics/btu033. https://pubmed.ncbi.nlm.nih.gov/24451623.
[149] A. C. Telfer, M. R. Young, J. Quinn, et al. “Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve”. In: Biodiversity data journal (2015).
[150] J. N. Timmis, M. A. Ayliffe, C. Y. Huang, et al. “Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes”. In: Nature Reviews Genetics 5 (Feb. 2004). Review Article, pp. 123 EP -. http://dx.doi.org/10.1038/nrg1271.
[151] A. D. Twyford and R. W. Ness. “Strategies for complete plastid genome sequencing”. In: Molecular Ecology Resources 17.5 (2017), pp. 858-868. ISSN: 1755-0998. DOI: 10.1111/1755-0998.12626. http://dx.doi.org/10.1111/1755-0998.12626.
[152] G. W. Vurture, F. J. Sedlazeck, M. Nattestad, et al. “GenomeScope: fast reference-free genome profiling from short reads”. In: Bioinformatics 33.14 (2017), pp. 2202-2204. DOI: 10.1093/bioinformatics/btx153. eprint: /oup/backfile/content_public/journal/bioinformatics/33/14/10.1093_bioinformatics_btx153/2/btx153.pdf. <+%20http://dx.doi.org/10.1093/bioinformatics/btx153>.
[153] B. J. Walker, T. Abeel, T. Shea, et al. “Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement”. In: PLoS One 9.11 (Nov. 2014). Ed. by J. Wang. PONE-D-14-38252[PII], p. e112963. ISSN: 1932-6203. DOI: 10.1371/journal.pone.0112963. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237348/.
[154] J. D. Watson and F. H. C. Crick. “Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid”. In: Nature 171.4356 (Apr. 1953), pp. 737-738. ISSN: 1476-4687. DOI: 10.1038/171737a0. https://doi.org/10.1038/171737a0.
[155] Q. D. Wheeler. “Why the phylogenetic species concept?—Elementary”. In: Journal of nematology 31.2 (1999), p. 134.
[156] D. J. Winter. “rentrez: an R package for the NCBI eUtils API”. In: The R Journal 9 (2 2017), pp. 520-526.
[157] M. Yandell and D. Ence. “A beginner's guide to eukaryotic genome annotation”. In: Nature Reviews Genetics 13 (Apr. 2012). Review Article, pp. 329 EP -. http://dx.doi.org/10.1038/nrg3174.
[158] X. Yang, J. C. Cushman, A. M. Borland, et al. “A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world”. In: New Phytologist 207.3 (2015). 2015-19119, pp. 491-504. ISSN: 1469-8137. DOI: 10.1111/nph.13393. http://dx.doi.org/10.1111/nph.13393.
[159] Y. Yin, P. Zhong, G. Zhang, et al. “Morphological, genome-size and molecular analyses of Apostasia fogangica (Apostasioideae, Orchidaceae), a new species from China”. English. In: PHYTOTAXA 277.1 (), pp. 59-67. ISSN: 1179-3155. DOI: 10.11646/phytotaxa.277.1.5.
[160] D. R. Zerbino and E. Birney. “Velvet: Algorithms for de novo short read assembly using de Bruijn graphs”. In: Genome Res 18.5 (May. 2008). 18349386[pmid], pp. 821-829. ISSN: 1088-9051. DOI: 10.1101/gr.074492.107. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801/.
[161] G. Zhang, K. Liu, Z. Li, et al. “The Apostasia genome and the evolution of orchids”. In: Nature 549 (Sep. 2017), pp. 379 EP -. http://dx.doi.org/10.1038/nature23897.