Staats M, Erkens RH, van de Vossenberg B, Wieringa JJ, Kraaijeveld K, Stielow B, Geml J, Richardson JE, Bakker FT. Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens. PLoS ONE. 2013;8(7):e69189.
Article
CAS
Google Scholar
Dormontt E, Van Dijk KJ, Bell K, Biffin E, Breed M, Byrne M, Caddy-Retalic S, Encinas-Viso F, Nevill P, Shapcott A, Young J. Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective. Front Ecol Evol. 2018. https://doi.org/10.3389/fevo.2018.00134.
Article
Google Scholar
Martin MD, Quiroz-Claros E, Brush GS, Zimmer EA. Herbarium collection-based phylogenetics of the ragweeds (Ambrosia, Asteraceae). Mol Phylogenet Evol. 2018;120:335–41.
Article
Google Scholar
Williams AV, Miller JT, Small I, Nevill PG, Boykin LM. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia. Mol Phylogenet Evol. 2016;31(96):1–8.
Article
Google Scholar
Straub SCK, Parks M, Weithmier K, Fishbein M, Cronn RC, Liston A. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am J Bot. 2012;99:349–64.
Article
CAS
Google Scholar
Bakker FT, Lei D, Yu JY, Mohammadin S, Wei Z, van de Kerke S, Gravendeel B, Nieuwenhuis M, Staats M, Alquezar-Planas DE, Holmer R. Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline. Biol J Lin Soc. 2016;117(1):33–43.
Article
Google Scholar
Zeng CX, Hollingsworth PM, Yang J, He ZS, Zhang ZR, Li DZ, Yang JB. Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods. 2018;14(1):43.
Article
Google Scholar
McKenzie NL, van Leeuwen S, Pinder AM. Introduction to the Pilbara biodiversity survey, 2002–2007. Rec West Aust Mus. 2009;78:3–89.
Article
Google Scholar
Australia's 15 National Biodiversity Hotspots. https://www.environment.gov.au/biodiversity/conservation/hotspots/national-biodiversity-hotspots. Accessed 29 Jan 2019.
Comtois C, Slack B. Dynamic determinants in global iron ore supply chain. CIRRELT. 2016;06.
AusPlots. https://www.tern.org.au/AusPlots-pg26979.html. Accessed 29 Jan 2019.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12.
Article
Google Scholar
Gardner SN, Slezak T. Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes. BMC Bioinformatics. 2014;15:237.
Article
Google Scholar
Särkinen T, Staats M, Richardson JE, Cowan RS, Bakker FT. How to open the treasure chest? Optimising DNA extraction from herbarium specimens. PLoS ONE. 2012;7:e43808.
Article
Google Scholar
Staats M, Cuenca A, Richardson JE, Vrielink-van Ginkel R, Petersen G, Seberg O, Bakker FT. DNA damage in plant herbarium tissue. PLoS ONE. 2011;6:e28448.
Article
CAS
Google Scholar
Heather JM, Chain B. The sequence of sequencers: the history of sequencing DNA. Genomics. 2016;107:1–8.
Article
CAS
Google Scholar
Ruhsam M, Rai HS, Mathews S, Ross TG, Graham SW, Raubeson LA, Mei W, Thomas PI, Gardner MF, Ennos RA, Hollingsworth PM. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria? Mol Ecol Resour. 2015;15(5):1067–78.
Article
CAS
Google Scholar
Hammer TA, Zhong X, Colas des Francs-Small, Nevill PG, Small ID, Thiele KR. Resolving intergeneric relationships in the aervoid clade and the backbone of Ptilotus (Amaranthaceae): evidence from whole plastid genomes and morphology. Taxon. In press.
Anderson B, Thiele K, Grierson P, Krauss S, Nevill PG, Small I, Zhong X, Barrett M. Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing. AoB Plants. 2019. https://doi.org/10.1093/aobpla/plz017.
Article
PubMed
PubMed Central
Google Scholar
Boyer S, Wratten SD, Holyoake A, Abdelkrim J, Cruickshank RH. Correction: Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms. PLoS ONE. 2013;8(e10):1371.
Google Scholar
Nevill PG, Wallace MJ, Miller JT, Krauss SL. DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia. Mol Ecol Resour. 2013;13:1033–42.
CAS
PubMed
Google Scholar
Tonti-Filippini J, Nevill PG, Dixon K, Small I. What can we do with 1000 plastid genomes? Plant J. 2017;90:808–18.
Article
CAS
Google Scholar
Nevill PG, Howell KA, Cross AT, Williams AV, Zhong X, Tonti-Filippini J, Boykin LM, Small I. Plastome-wide rearrangements and gene losses in carnivorous Droseraceae. Gen Biol Evol. 2019;11:472–85.
Article
Google Scholar
Silva SR, Diaz YCA, Penha HA, Pinheiro DG, Fernandes CC, Miranda VFO, Michael TP, Varani AM. The chloroplast genome of Utricularia reniformis sheds light on the evolution of the ndh gene complex of terrestrial carnivorous plants from the Lentibulariaceae family. PLoS ONE. 2016;11:e0165176.
Article
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10.
Article
Google Scholar
BBMap short read aligner, and other bioinformatic tools. https://sourceforge.net/projects/bbmap/. Accessed 29 Jan 2019.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Article
CAS
Google Scholar
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.
Article
CAS
Google Scholar
https://pythonhosted.org/ORG.asm/. Accessed 29 Jan 2019.
Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2016;45(4):e18.
PubMed Central
Google Scholar
Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol. 2012;13(6):R56.
Article
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997. 2013.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;19(9):e112963.
Article
Google Scholar
Choudhuri SK, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale.