Literature DB >> 28337391

An efficient field and laboratory workflow for plant phylotranscriptomic projects.

Ya Yang1, Michael J Moore2, Samuel F Brockington3, Alfonso Timoneda3, Tao Feng3, Hannah E Marx4, Joseph F Walker1, Stephen A Smith1.   

Abstract

PREMISE OF THE STUDY: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. METHODS AND
RESULTS: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms. These included difficult mucilaginous tissues such as those of Cactaceae and Droseraceae.
CONCLUSIONS: Our workflow is not only cost effective (ca. $270 per sample, as of August 2016, from tissue to reads) and time efficient (less than 50 h for 10-12 samples including all laboratory work and sample curation), but also has proven robust for extraction of difficult samples such as tissues containing high levels of secondary compounds.

Entities:  

Keywords:  Caryophyllales; RNA; cryogenic field sampling; phylogenomics; phylotranscriptomics

Year:  2017        PMID: 28337391      PMCID: PMC5357122          DOI: 10.3732/apps.1600128

Source DB:  PubMed          Journal:  Appl Plant Sci        ISSN: 2168-0450            Impact factor:   1.936


Phylotranscriptomics, or using transcriptome sequences to investigate phylogenetic relationships and gene family evolution in nonmodel plants, has gained popularity in recent years due to decreases in cost and improvements in analysis pipelines (Wickett et al., 2014; Edger et al., 2015; Li et al., 2015; Yang et al., 2015; McKain et al., 2016). It is often possible to recover at least 15,000 genes from the target species using de novo–assembled transcriptome data (Yang and Smith, 2013). Among these, approximately 5000 are shared among most species within an order (Yang et al., 2015), with the rest being tissue- and/or taxon-specific. Together they provide enormously rich data both for phylogenetic reconstruction and for investigating gene family evolution that underlies lineage-specific adaptations. Generating plant phylotranscriptomic data has become much easier over the past few years due to improvements in sequencing and extraction protocols but may still be challenging for a variety of reasons. Previous literature on phylotranscriptomic methods has focused on RNA extraction and fragment analyses of those extracted RNA samples (Johnson et al., 2012; Yockteng et al., 2013; Jordon-Thaden et al., 2015) and sequence data analyses (Yang and Smith, 2013, 2014). However, as phylotranscriptomic studies expand to nonmodel systems that often require field sampling, the logistics of obtaining fresh tissues becomes a limiting factor. Likewise, some taxa such as cacti pose special challenges due to high levels of mucilage (Jordon-Thaden et al., 2015). Moving forward, the issues of long-term preservation and curation of cryogenic genetic materials will also be of the utmost importance for laboratories seeking to pursue these studies. From 2012 to 2015, we conducted field expeditions to remote localities in both the southwestern United States and northern Mexico to support National Science Foundation–funded projects on the evolution of Caryophyllales and gypsum-endemic plants. Together with samples from living collections, we generated a transcriptome data set of 200 species of plants (Appendix 1). During the process we have developed an optimized workflow, which is described below. In addition, we discuss alternative procedures that we tested, as well as considerations for project planning.

METHODS AND RESULTS

Taxon sampling

The Caryophyllales phylotranscriptomics project emphasized a combination of broad taxon sampling across the order and in-depth sampling of lineages with key evolutionary transitions. These key transitions include the gain and loss of plant carnivory; the gain and loss of betalain pigmentation; transitions to saline, dry, or alpine habitats, and/or to specialized soil types; and transitions to C4 and CAM photosynthesis. Of the transcriptomes we have generated for the Caryophyllales phylotranscriptomic project, half were collected from the field, with the remaining half from living collections (Appendix 1). Additional transcriptomes and genomes were obtained from publicly available databases such as Phytozome (Goodstein et al., 2012), the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), and the 1000 Plants Initiative (1KP; Matasci et al., 2014).

Field collection

We timed our field trips to coincide with the beginning of the flowering season as much as possible to optimize the chance of obtaining young flower and leaf buds. Our experience has been that mature vegetative tissue is more difficult to work with due to its low concentration of nuclear RNA (Johnson et al., 2012) and high level of chloroplast RNA and secondary compounds compared to developing tissues. It is also important to emphasize that field conditions are more difficult to control than greenhouse conditions. While this may impose limitations for researchers wishing to study differential gene expression, this is less problematic for phylotranscriptomic studies. Compared to tissue preservation using an RNA stabilization solution (such as RNAlater; Thermo Fisher Scientific, Waltham, Massachusetts, USA), tissue frozen in the field allows for biochemical analyses such as characterization of betalain and anthocyanin pigmentation, in addition to DNA and RNA sequencing, and hence this was our primary (and recommended) means of collection (Appendix 2). For all individuals frozen in liquid nitrogen, we also collected silica-preserved tissue from the same individual as a DNA backup, as well as herbarium specimens whenever possible. Because DNA may degrade relatively quickly for some groups in silica (e.g., Onagraceae), it is important to remove silica from the leaves once dried and place them in a −20°C freezer for long-term storage (Neubig et al., 2014).

RNA extraction (less than 6 h for six samples)

We tested five alternative RNA extraction protocols. These include TRIzol option 1 from Jordon-Thaden et al. (2015), the Aurum Total RNA Mini Kit (Bio-Rad Laboratories, Hercules, California, USA) following the manufacturer’s protocol, the QIAGEN RNeasy Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s protocol, the PureLink protocol (Appendix 3; Yockteng et al., 2013), and the hot acid phenol-LiCl-RNeasy Mini Kit protocol (Appendix 4, modified from Protocol 12 of Johnson et al. [2012]). We had approximately 10–30% success rate (see below for quality control) with Bio-Rad, QIAGEN, and TRIzol protocols, whereas the PureLink protocol had close to 100% success rate and only failed when the sample itself was degraded or highly mucilaginous. Although more time consuming, the hot acid phenol-LiCl-RNeasy Mini Kit protocol had great success with tissues that are highly mucilaginous like cacti (Appendix 4).

Quality control and DNase digestion (less than 3 h for 12 samples)

For quality control of RNA, we used agarose gel for an initial assessment. If RNA was evident, removal of DNA was carried out following Jordon-Thaden et al. (2015) with minor modifications (Appendix 5). After that, we followed fig. 2 of Jordon-Thaden et al. (2015) for evaluating integrity of RNA on a 2100 Bioanalyzer (Agilent, Santa Clara, California, USA) or a Fragment Analyzer (Advanced Analytical Technologies, Ankeny, Iowa, USA). RNA concentration was measured with either a NanoDrop Spectrophotometer (Thermo Fisher Scientific) or a Qubit fluorometer (Thermo Fisher Scientific). We considered an RNA integrity number (RIN) of 6 or higher and concentration of 20 ng/μL or higher as successful. When RNA extraction failed, it was often due to either pellet loss (resulting in a completely empty gel with no DNA or RNA trace) or degradation (which shows up as smeared ribosomal RNA bands). RNA degradation can happen during collection, shipping, or in a suboptimal extraction, as for example with too much starting tissue. For difficult tissues that are mucilaginous, we reduced the amount of starting tissue by half. RNA samples prepared at the Brockington Laboratory at the University of Cambridge, United Kingdom, were shipped on dry ice in cardboard freezer boxes to the University of Michigan for library preparation and sequencing. Dry ice shipments were sent on Monday or Tuesday to avoid delay over the weekend.

Library preparation (less than 20 h for 12 samples)

We tested four different library preparation protocols. In 2012, we started with Illumina TruSeq version 2 (Illumina, San Diego, California, USA), with and without additional strand-specific steps (see Supplementary Methods in Yang et al. [2015]). In 2013, we began using the newly released TruSeq Stranded mRNA Library Prep Kit (“the Illumina kit”; Illumina), which was more streamlined and produced much higher strand specificity than the previous stranded protocol. In 2014, we switched to the KAPA Stranded mRNA-Seq kit (“the KAPA kit”; KAPA Biosystems, Wilmington, Massachusetts, USA; Appendix 6), which is considerably cheaper than the Illumina kit with indistinguishable results in terms of both success rate and strand specificity. The KAPA kit is also more streamlined with fewer bead washing steps and required roughly 15% less time. The cost is ca. US$30 per sample for the KAPA kit itself plus ca. US$20 per sample for consumables (magnetic beads, tips, tubes, and additional chemicals; we used leftover adapters from the Illumina kit, which lasted through more than 150 additional libraries from one 48-sample Illumina kit). We modified the manufacturer’s protocol slightly to accommodate the increasing read length of newer Illumina platforms (125- or 150-bp paired-end; Appendix 6). Quality control of the library was done at the University of Michigan DNA Sequencing Core using an Agilent 2100 Bioanalyzer followed by confirmation using qPCR. Although the minimal concentration of the library and percentage of adapter contamination allowed differ among sequencing platforms, we followed a few general rules. First, the peak of the library fragment size distribution should be approximately the read length plus adapter size. For example, for paired-end 125-bp sequencing on Illumina platforms, peak of library size distribution should be approximately 60 bp (adapter) + 125 bp (read) in each direction, making a total of 370 bp for the optimum library size (see Appendix 6 for modifications in library preparation to adjust library sizes). Second, although we do not quantify the library concentration in the laboratory, we visualized the library by loading 3 μL of library mixed with GelRed fluorescent stain (Biotium, Fremont, California, USA) onto a 1.5% agarose gel. As a rule of thumb, if the libraries were visible from the gel (even if only barely visible), they were sent to the DNA Sequencing Core for further quantification. Libraries were walked to the on-campus University of Michigan DNA Sequencing Core immediately in ambient temperature, or stored in −20°C for less than a month before walking to the sequencing core in ambient temperature.

Sample curation (less than 1 h per sample)

We store all RNAs in a −80°C freezer on standard storage racks. Ideally, they would be stored long-term in liquid nitrogen vapor freezers. To prevent freeze/thaw of sensitive samples, we placed samples into labeled cardboard freezer boxes and recorded the sample locations in a database that is properly backed up (Appendix 7).

CONCLUSIONS

We have developed an effective phylotranscriptomics workflow involving cryogenic tissue collection in the field, RNA extraction of diverse taxa with close to 100% success rate, library preparation for Illumina platforms, and sample storage and curation. Future efforts should focus on streamlining the workflow given specific laboratory and field settings and as sequencing technologies continue to evolve. In addition, it would be ideal to collaborate with major tissue and seed banks such as the Millennium Seed Bank (Royal Botanic Gardens, Kew) and the Global Genome Initiative (Smithsonian Institution) (Gostel et al., 2016) when designing phylotranscriptomic projects.
Appendix 1.

Voucher information for the accessions used in this study.

FamilyTaxon nameCollection or accession no. (Herbarium)[a,b]Collection localityField or cultivated?RNA extractionSRA accession no. (Publication)
AchatocarpaceaeAchatocarpus gracilis H. WalterMichael J. Moore et al. 2704 (OC)Jalisco, Mexico: La Huerta, Estacion Biologica Chamela, along Sendero PericoFieldPureLinkUnpublished
AchatocarpaceaePhaulothamnus spinescens A. GrayMichael J. Moore 1677 (OC)Texas, USA: Kleberg, along Kleberg County Rd. 1155 S, approx. 0.1 mi. N of jct. w/ FM 771.FieldBio-RadSRX998856 (Brockington et al., 2015)
AgdestidaceaeAgdestis clematidea Moc. & Sessé ex DC.Michael J. Moore et al. 2669 (OC)Veracruz, Mexico: San Andres Tuxtla, in thicket immediately adjacent to rd. in MontepioFieldPureLinkUnpublished
AmaranthaceaeFroelichia latifolia R. A. McCauleyMichael J. Moore 1665 (OC)Texas, USA: Caldwell, along FM 713 betw. McMahan and Delhi, just W of jct. w/ Taylorville Rd.FieldBio-RadSRX998855 (Brockington et al., 2015)
AmaranthaceaeGomphrena decumbens Jacq.Michael J. Moore et al. 2734 (OC)Distrito Federal, Mexico: Coyoacan, at Instituto de Biologia at UNAMCultivatedPureLinkUnpublished
AmaranthaceaeGossypianthus lanuginosus (Poir.) Moq.Michael J. Moore 1807 (OC)Texas, USA: Llano, along TX 71 at roadside historical marker, where Honey Creek passes under the hwy.FieldBio-RadUnpublished
AmaranthaceaeGuilleminea densa (Humb. & Bonpl. ex Schult.) Moq.Michael J. Moore et al. 2445 (OC)Chihuahua, Mexico: N end of Sierra de Fernando, on Rancho Puerto de LobosFieldBio-RadUnpublished
AmaranthaceaeIresine arbuscula Uline & W. L. BrayMichael J. Moore et al. 2678 (OC)Veracruz, Mexico: San Andres Tuxtla, Estacion Biologica Los Tuxtlas, along stream bed approx. 100 m upstream of path crossingFieldPureLinkUnpublished
AmaranthaceaeIresine rhizomatosa Standl.Michael J. Moore & J. Lee 2943 (OC)Cultivated at Missouri Botanical GardenCultivatedPureLinkUnpublished
AmaranthaceaeNelsia quadrangula (Engl.) SchinzMillennium Seed Bank accession 0468510Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
AmaranthaceaeNitrophila occidentalis (Moq.) S. WatsonMichael J. Moore et al. 3242 (OC)California, USA: Inyo, along CA 190 approx. 1.3 mi. NE of jct. w/ US 395 in Olancha, just S of Owens Lake bedFieldPureLinkUnpublished
AmaranthaceaePolycnemum majus A. BraunGudrun Kadereit s.n.Cultivated at Universitat MainzCultivatedPureLinkUnpublished
AmaranthaceaeTidestromia lanuginosa (Nutt.) Standl.Michael J. Moore et al. 2259 (OC)New Mexico, USA: Sierra, E side of Caballo Mountains, ca. 0.3 mi. N of jct. of Slater Rd. and Apache Gap Ranch entranceFieldBio-RadUnpublished
AnacampserotaceaeGrahamia kurtzii (Bacigalupo) G. D. RowleySukkulenten-Sammlung Zürich accession 100046/0Cultivated at Sukkulenten-Sammlung ZürichCultivatedBio-RadUnpublished
AnacampserotaceaeTalinopsis frutescens A. GrayMichael J. Moore et al. 2441 (OC)Chihuahua, Mexico: N end of Sierra de Fernando, on Rancho Puerto de LobosFieldTrizolUnpublished
AncistrocladaceaeAncistrocladus robertsoniorum J. LéonardMichael J. Moore & J. Lee 2940 (OC)Missouri Botanical Garden, cultivated in ClimatronCultivatedPureLinkUnpublished
ApiaceaeHeracleum mantegazzianum Sommier & LevierHannah E. Marx 2014-016 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
ApiaceaeHeracleum sphondylium L.Hannah E. Marx 2014-010 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
ApiaceaeMeum athamanticum Jacq.Hannah E. Marx 2014-027 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
AsteraceaeCentaurea uniflora TurraHannah E. Marx 2014-028 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
AsteraceaeGaillardia multiceps GreeneMichael J. Moore 1737 (OC)Texas, USA: Winkler, along Winkler County Rd. 101, ca. 5 mi. N of jct. w/ TX 302FieldBio-RadUnpublished
BasellaceaeAnredera cordifolia (Ten.) SteenisCultivated at Cambridge University Botanic Garden 19770198Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
BoraginaceaeTiquilia hispidissima (Torr. & A. Gray) A. T. RichardsonMichael J. Moore 1736 (OC)Texas, USA: Winkler, along Winkler County Rd. 101, ca. 5 mi. N of jct. w/ TX 302FieldBio-RadUnpublished
BrassicaceaeNerisyrenia linearifolia (S. Watson) GreeneMichael J. Moore 1755 (OC)Texas, USA: Culberson, along FM 652 ca. 25 mi. W of OrlaFieldBio-RadUnpublished
CactaceaeOpuntia arenaria Engelm.Michael J. Moore et al. 2911 (OC)New Mexico, USA: Dona Ana, cultivated at UTEP Botanical Garden; originally collected from Anapra, NMCultivatedPureLinkUnpublished
CactaceaeRhipsalis baccifera (Sol.) Stearn subsp. bacciferaMichael J. Moore 2938 (OC)Cultivated at Oberlin College greenhouseCultivatedPureLinkUnpublished
CaryophyllaceaeArenaria serpyllifolia L.Michael J. Moore 1164 (OC)Ohio, USA: Erie, in lawn behind my house (4910 State Route 113 E)FieldBio-RadUnpublished
CaryophyllaceaeCerastium alpinum L. var. lanatum (Lam.) Hegetschw.Alplains accession 07471.06Cultivated at Matthaei Botanical Gardens, University of MichiganCultivatedPureLinkUnpublished
CaryophyllaceaeCerastium arvense L.Michael J. Moore 1767 (OC)New Mexico, USA: Otero, along NM 130 a few mi. E of jct. w/ rd. to SunspotFieldBio-RadSRX998858 (Brockington et al., 2015)
CaryophyllaceaeCerastium fontanum Baumg. subsp. vulgare (Hartm.) Greuter & BurdetMichael J. Moore 1163 (OC)Ohio, USA: Erie, in lawn behind my house (4910 State Route 113 E)FieldBio-RadUnpublished
CaryophyllaceaeCorrigiola litoralis L.Cultivated at Cambridge University Botanic Garden SFB_221Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeDrymaria cordata (L.) Willd. ex Schult.Lucas C. Majure 3403 (FLAS)Florida, USA: Alachua, Gainesville, University of Florida campusFieldBio-RadSRX998854 (Brockington et al., 2015)
CaryophyllaceaeDrymaria sp.Michael J. Moore et al. 2679 (OC)Veracruz, Mexico: Coscomatepec, along paved rd. from Fortin to Huatusco, a few km N of CoscomatepecFieldPureLinkUnpublished
CaryophyllaceaeDrymaria subumbellata I. M. Johnst.Michael J. Moore et al. 2503 (OC)Durango, Mexico: on the W side of the Sierra de TlahualiloFieldBio-RadUnpublished
CaryophyllaceaeEremogone hookeri (Nutt. ex Torr. & A. Gray) W. A. Weber subsp. desertorum (Maguire) W. A. WeberAlplains accession 35665.38Cultivated at Matthaei Botanical Gardens, University of MichiganCultivatedBio-RadUnpublished
CaryophyllaceaeEremogone procera (Spreng.) Rchb.Gudrun Kadereit s.n.Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeGypsophila repens L.Cambridge University Botanic Garden 10007025, 19610163, 19860039Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeHerniaria latifolia Lapeyr.Cambridge University Botanic Garden 10005718Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeHonckenya peploides (L.) Ehrh.Millennium Seed Bank accession 0286981Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeIllecebrum verticillatum L.N/ACultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeLepyrodiclis stellarioides Fisch. & C. A. Mey.Millennium Seed Bank accession 0653842Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeParonychia drummondii Torr. & A. GrayMichael J. Moore 1670 (OC)Texas, USA: Caldwell, along FM 713 between McMahan and Delhi, just W of jct. w/ Taylorville Rd.FieldPureLinkUnpublished
CaryophyllaceaeParonychia jamesii Torr. & A. GrayMichael J. Moore et al. 2931 (OC)New Mexico, USA: Eddy, along gravel rd. leading W from US 285 along N edge of Seven Rivers HillsFieldPureLinkUnpublished
CaryophyllaceaeSchiedea globosa H. MannCambridge University Botanic Garden SFB_256Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeScleranthus polycarpos L.Gudrun Kadereit s.n.Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeSilene acaulis (L.) Jacq. subsp. acaulescens Hitchc. & MaquireAlplains accession 01224.31Cultivated at Matthaei Botanical Gardens, University of MichiganCultivatedBio-RadUnpublished
CaryophyllaceaeSpergularia marina (L.) BesserMichael J. Moore et al. 3185 (OC)California, USA: Kern, Tejon Ranch: Amargo SpringsFieldPureLinkUnpublished
CaryophyllaceaeTelephium imperati L.Cambridge University Botanic Garden 19910346Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
CaryophyllaceaeVelezia rigida L.Gudrun Kadereit s.n.Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
ChenopodiaceaeAnabasis articulata (Forssk.) Moq.LS168Cultivated at Universitat MainzCultivatedPureLinkUnpublished
ChenopodiaceaeArthrocnemum macrostachyum (Moric.) K. KochLS33Cultivated at Universitat MainzCultivatedPureLinkUnpublished
ChenopodiaceaeAtriplex sp.Michael J. Moore et al. 3295 (OC)Utah, USA: Wayne, a few hundred yards W of Coal Mine Rd., approx. 3.2 mi. N of jct. w/ UT 24FieldPureLinkUnpublished
ChenopodiaceaeCaroxylon vermiculatum (L.) Akhani & RoalsonLS178Cultivated at Universitat MainzCultivatedPureLinkUnpublished
ChenopodiaceaeChenopodiastrum murale (L.) S. Fuentes, Uotila & BorschMichael J. Moore et al. 2991 (OC)New Mexico, USA: Chaves, along gravel rd. just N of US 380 opposite rest areaFieldPureLinkUnpublished
ChenopodiaceaeCorispermum hyssopifolium L.Millennium Seed Bank accession 0000170Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
ChenopodiaceaeEokochia saxicola (Guss.) Freitag & G. KadereitLS70Cultivated at Universitat MainzCultivatedPureLinkUnpublished
ChenopodiaceaeExtriplex californica Moq.Michael J. Moore et al. 3214 (OC)California, USA: San Luis Obispo, Morro Bay State Park/Morro Estuary Natural Preserve: just E of State Park Rd./Main St., approx. 0.7 mi. SW of jct. w/ S Bay Blvd.FieldBio-RadUnpublished
ChenopodiaceaeGrayia spinosa (Hook.) Moq.Michael J. Moore et al. 3268 (OC)Nevada, USA: Douglas, near two-track rd. that runs S from Mel DriveFieldBio-RadUnpublished
ChenopodiaceaeKali collina (Pall.) Akhani & RoalsonMillennium Seed Bank accession 0496298Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
ChenopodiaceaeKalidium cuspidatum (Ung.-Sternb.) GrubovLS97Cultivated at Universitat MainzCultivatedPureLinkUnpublished
ChenopodiaceaeKrascheninnikovia lanata (Pursh) A. Meeuse & A. SmitMichael J. Moore et al. 2311 (OC)New Mexico, USA: Sierra, along WSMR Rte. 6 just S of Big Gyp MountainFieldTrizolUnpublished
ChenopodiaceaeSalsola sp.N/ACultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
ChenopodiaceaeSarcocornia pacifica (Standl.) A. J. ScottMichael J. Moore et al. 3216 (OC)California, USA: San Luis Obispo, Morro Bay State Park/Morro Estuary Natural Preserve: just E of State Park Rd./Main St., approx. 0.7 mi. SW of jct. w/ S Bay Blvd.FieldPureLinkUnpublished
ChenopodiaceaeStutzia covillei (Torr. ex S. Watson) S. WatsonMichael J. Moore et al. 3228 (OC)California, USA: Inyo, along Searles Dry Lake Rd., approx. 0.5 mi. E of jct. w/ Trona-Wildrose Rd.FieldPureLinkUnpublished
ChenopodiaceaeSuaeda linearis (Elliott) Moq.Michael J. Moore 1679 (OC)Texas, USA: Kleberg, Riviera Beach, along beach just N of parking area at end of FM 771. GPS coordinates refer to parking area.FieldBio-RadUnpublished
ChenopodiaceaeTecticornia pergranulata (J. M. Black) K. A. Sheph. & Paul G. WilsonLS28Cultivated at Universitat MainzCultivatedPureLinkUnpublished
CyperaceaeCarex capillaris L.Hannah E. Marx 2014-030 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
CyperaceaeCarex nigra (L.) ReichardHannah E. Marx 2014-031 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
DidiereaceaeAlluaudia dumosa (Drake) DrakeDesert Botanical Garden accession 1987-0301-0201Cultivated at Desert Botanical GardenCultivatedPureLinkUnpublished
DidiereaceaeAlluaudia humbertii ChouxDesert Botanical Garden accession 1974-0229-01-1Cultivated at Desert Botanical GardenCultivatedPureLinkUnpublished
DidiereaceaeAlluaudia procera (Drake) DrakeDesert Botanical Garden accession 1956-5744-02-3 GCultivated at Desert Botanical GardenCultivatedPureLinkUnpublished
DidiereaceaeAlluaudiopsis marnieriana RauhSukkulenten-Sammlung Zürich accession 81 2213/0Cultivated at Sukkulenten-Sammlung ZürichCultivatedHot acid PhenolUnpublished
DidiereaceaeCeraria pygmaea (Pillans) G. D. RowleySukkulenten-Sammlung Zürich accession 90 1893/bCultivated at Sukkulenten-Sammlung ZürichCultivatedHot acid PhenolUnpublished
DidiereaceaeDecarya madagascariensis ChouxMichael J. Moore & J. Lee 2944 (OC)Missouri Botanical Garden, cultivated in nonpublic arid plant greenhouseCultivatedPureLinkUnpublished
DidiereaceaeDidierea madagascariensis Baill.Desert Botanical Garden accession 1996-0312-01-1Cultivated at Desert Botanical GardenCultivatedPureLinkUnpublished
DidiereaceaeDidierea trollii Capuron & RauhDesert Botanical Garden accession 1984-0024-0202 GCultivated at Desert Botanical GardenCultivatedPureLinkUnpublished
DidiereaceaePortulacaria afra Jacq.Desert Botanical Garden accession 1988-0583-02-1 GCultivated at Desert Botanical GardenCultivatedPureLinkUnpublished
DroseraceaeAldrovanda vesiculosa L.Michael J. Moore 1652 (OC)Virginia, USA: Caroline, ponds at Meadowview Biological StationCultivatedBio-RadSRX998847 (Brockington et al., 2015)
DroseraceaeDrosera binata Labill.Cambridge University Botanic GardenCultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
DroseraceaeDrosera burmannii VahlMatthaei Botanical GardensCultivated at Matthaei Botanical Gardens, University of MichiganCultivatedPureLinkUnpublished
DrosophyllaceaeDrosophyllum lusitanicum (L.) LinkCambridge University Botanic GardenCultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
FabaceaeLotus corniculatus L.Hannah E. Marx 2014-026 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
FrankeniaceaeFrankenia salina (Molina) I. M. Johnst.Michael J. Moore et al. 3209 (OC)California, USA: San Luis Obispo, Morro Bay State Park/Morro Estuary Natural Preserve: just E of State Park Rd./Main St., approx. 0.7 mi. SW of jct. w/ S Bay Blvd.FieldPureLinkUnpublished
GeraniaceaeGeranium sylvaticum L.Hannah E. Marx 2014-014 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
GisekiaceaeGisekia pharnaceoides L.Millennium Seed Bank accession 0586315Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
HydrophyllaceaeNama carnosa (Woot.) C. L. Hitchc.Michael J. Moore 1750 (OC)Texas, USA: Culberson, along FM 652 ca. 25 mi. W of OrlaFieldBio-RadUnpublished
KewaceaeKewa bowkeriana (Sond.) Christenh.Botanischen Gartens, Technische Universität Dresden accession 99 Bonn 931 (B:09964)Cultivated at Cambridge University Botanic GardenCultivatedHot acid PhenolUnpublished
LentibulariaceaePinguicula vulgaris L.Hannah E. Marx 2014-021 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
LimeaceaeLimeum aethiopicum Burm. f.Cultivated at Cambridge University Botanic Garden s.n.Cultivated at Cambridge University Botanic GardenCultivatedHot acid PhenolUnpublished
LoasaceaeMentzelia humilis (Urb. & Gilg) J. Darl.Michael J. Moore 1749 (OC)Texas, USA: Culberson, along FM 652 ca. 25 mi. W of OrlaFieldBio-RadUnpublished
MacarthuriaceaeMacarthuria australis Hügel ex Endl.Kevin Thiele 5141 (UWA)Western Australia, Australia: Perth. Cultivated at Cambridge University Botanic Garden.CultivatedPureLinkUnpublished
MelanthiaceaeVeratrum album L.Hannah E. Marx 2014-025 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
MolluginaceaeGlinus lotoides L. var. virens FenzlMillennium Seed Bank accession 0197698Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
MolluginaceaePharnaceum exiguum AdamsonMillennium Seed Bank accession 0467649Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
MolluginaceaeSuessenguthiella caespitosa FriedrichMillennium Seed Bank accession 0467650Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
MontiaceaeCalandrinia grandifloraCambridge University Botanic Garden 20070025Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
MontiaceaeCalyptridium pygmaeum Parish ex Rydb.Michael J. Moore et al. 3165 (OC)California, USA: San Bernardino, approx. 0.2 mi. N of Forest Rd. 2N86, approx. 0.4 mi. NE of Bluff LakeFieldPureLinkUnpublished
MontiaceaeCalyptridium umbellatum (Torr.) HershkovitzMichael J. Moore et al. 3142 (OC)California, USA: San Bernardino, Mt. Baldy ski areaFieldBio-RadUnpublished
MontiaceaeCistanthe grandiflora (Lindl.) Schltdl.Chileflora s.n.Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
MontiaceaeClaytonia nevadensis S. WatsonThomas R. Stoughton et al. 2027 (RSA)California, USA: Alpine, about 250 yards W of Round Top Lake, near trailFieldBio-RadUnpublished
MontiaceaeClaytonia virginica L.Michael J. Moore 1156 (OC)Ohio, USA: Erie, in woods behind my house (4910 State Route 113 E)FieldBio-RadUnpublished
MontiaceaeLewisia nevadensis (A. Gray) B. L. Rob.Michael J. Moore et al. 3168 (OC)California, USA: San Bernardino, near edge of meadow, along small creek that feeds into Bluff LakeFieldPureLinkUnpublished
MontiaceaeMontia chamissoi (Ledeb. ex Spreng.) GreeneMichael J. Moore et al. 3167 (OC)California, USA: San Bernardino, near edge of meadow, along small creek that feeds into Bluff LakeFieldPureLinkUnpublished
MontiaceaePhemeranthus parviflorus (Nutt.) KigerMichael J. Moore et al. 2214 (OC)New Mexico, USA: Socorro, just E of Quebradas Backcountry BywayFieldTrizolUnpublished
NepenthaceaeNepenthes alata BlancoCambridge University Botanic Garden 20160588, 20160946Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
NepenthaceaeNepenthes ventricosa BlancoCambridge University Botanic Garden 20050134Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
NyctaginaceaeAbronia bigelovii HeimerlMichael J. Moore et al. 2189 (OC)New Mexico, USA: Sandoval, just N of Cabezon Rd., N of White Mesa Bike TrailsFieldBio-RadUnpublished
NyctaginaceaeAbronia fragrans Nutt. ex Hook.Michael J. Moore et al. 2992 (OC)New Mexico, USA: Chaves, along gravel rd. just N of US 380 opposite rest areaFieldPureLinkUnpublished
NyctaginaceaeAbronia glabrifolia Standl.Michael J. Moore et al. 3318 (OC)Colorado, USA: Mesa, along Mitchell Rd. approx. 1.0 mi. W of jct. w/ CO 139FieldPureLinkUnpublished
NyctaginaceaeAbronia latifolia Eschsch.Michael J. Moore et al. 3204 (OC)California, USA: San Luis Obispo, Montana de Oro State Park: along path from parking lot at end of Sand Spit Rd. to beach, just up the dunes from the beachFieldPureLinkUnpublished
NyctaginaceaeAbronia maritima Nutt. ex S. WatsonMichael J. Moore et al. 3217 (OC)California, USA: San Luis Obispo, Morro Strand State Beach: just W of Hwy. 1 in CayucosFieldTrizolUnpublished
NyctaginaceaeAbronia nealleyi Standl.Michael J. Moore 1751 (OC)Texas, USA: Culberson, along FM 652 ca. 25 mi. W of OrlaFieldBio-RadSRX998850 (Brockington et al., 2015)
NyctaginaceaeAbronia umbellata Lam.Michael J. Moore et al. 3203 (OC)California, USA: San Luis Obispo, Montana de Oro State Park: along path from parking lot at end of Sand Spit Rd. to beach, approx. 100 yards from parking lotFieldPureLinkUnpublished
NyctaginaceaeAcleisanthes acatitensis M. J. Moore & E. Loke (ined.)Michael J. Moore et al. 2505 (OC)Durango, Mexico: on the W side of the Sierra de TlahualiloFieldPureLinkUnpublished
NyctaginaceaeAcleisanthes acutifolia Standl.Michael J. Moore et al. 2447 (OC)Chihuahua, Mexico: N end of Sierra de Fernando, on Rancho Puerto de LobosFieldBio-RadUnpublished
NyctaginaceaeAcleisanthes chenopodioides (A. Gray) R. A. LevinMichael J. Moore et al. 2246 (OC)New Mexico, USA: Sierra, Armendaris Ranch, along rd. leading to highest point in Fra Cristobal MountainsFieldBio-RadUnpublished
NyctaginaceaeAcleisanthes lanceolata (Wooton) R. A. Levin var. lanceolataMichael J. Moore 1741 (OC)Texas, USA: Winkler, along Winkler County Rd. 101, ca. 5 mi. N of jct. w/ TX 302FieldBio-RadSRX998849 (Brockington et al., 2015)
NyctaginaceaeAcleisanthes obtusa (Choisy) Standl.Michael J. Moore 1697 (OC)Texas, USA: Zapata, immediately behind the Holiday Inn Express on the S side of Zapata, along US 83FieldBio-RadSRX998848 (Brockington et al., 2015)
NyctaginaceaeAnulocaulis annulatus (Coville) Standl.Michael J. Moore et al. 3237a (OC)California, USA: Inyo, mouth of Surprise CanyonFieldPureLinkUnpublished
NyctaginaceaeAnulocaulis eriosolenus (A. Gray) Standl.Michael J. Moore et al. 2362 (OC)Chihuahua, Mexico: along MEX 16 in Sierra PeguisFieldBio-RadUnpublished
NyctaginaceaeAnulocaulis leiosolenus (Torr.) Standl. var. gypsogenus (Waterf.) Spellenb. & T. WoottenMichael J. Moore 1070 (OC)Texas, USA: Culberson, along FM 652 25 mi. W of jct. w/ US 285 in OrlaFieldBio-RadSRX717838 (Yang et al., 2015)
NyctaginaceaeBoerhavia ciliata BrandegeeMichael J. Moore et al. 2760 (OC)Nuevo Leon, Mexico: Mier y Noriega, large gypsum exposure about 35 km SSW of Doctor ArroyoFieldPureLinkUnpublished
NyctaginaceaeBoerhavia purpurascens A. GrayMichael J. Moore et al. 2201 (OC)New Mexico, USA: Socorro, along wash E of County Rd. 12FieldBio-RadUnpublished
NyctaginaceaeBoerhavia torreyana (S. Watson) Standl.Michael J. Moore et al. 2202 (OC)New Mexico, USA: Socorro, along wash E of County Road 12FieldBio-RadUnpublished
NyctaginaceaeBougainvillea stipitata Griseb. var. grisebachiana HeimerlKew Living Collection #1986-4920Cultivated at Royal Botanic Gardens, KewCultivatedPureLinkSRX718672 (Yang et al., 2015)
NyctaginaceaeColignonia ovalifolia HeimerlCrug Farms accession BSWJ10644Cultivated at Cambridge University Botanic GardenCultivatedHot acid PhenolUnpublished
NyctaginaceaeCommicarpus scandens (L.) Standl.Michael J. Moore et al. 2726B (OC)Jalisco, Mexico: Autlan de Navarro, along gravel rd. leading from the outskirts of El Grullo to El ChacalitoFieldPureLinkUnpublished
NyctaginaceaeCyphomeris gypsophiloides (M. Martens & Galeotti) Standl.Michael J. Moore 1714 (OC)Texas, USA: Val Verde, along US 90 W of LangtryFieldBio-RadSRX998857 (Brockington et al., 2015)
NyctaginaceaeGuapira obtusata (Jacq.) LittleKew Living Collection #2011-994Cultivated at Royal Botanic Gardens, KewCultivatedPureLinkSRX718384 (Yang et al., 2015)
NyctaginaceaeMirabilis multiflora (Torr.) A. GrayMichael J. Moore 1771 (OC)New Mexico, USA: Lincoln, along NM 55 approx. 0.5 mi. W of jct. w/ US 54FieldBio-RadSRX998851 (Brockington et al., 2015)
NyctaginaceaeMirabilis pringlei Weath.Michael J. Moore et al. 2725 (OC)Jalisco, Mexico: Autlan de Navarro, along gravel rd. leading from the outskirts of El Grullo to El ChacalitoFieldPureLinkUnpublished
NyctaginaceaeNeea psychotrioides Donn. Sm.Michael J. Moore et al. 2675 (OC)Veracruz, Mexico: San Andres Tuxtla, Estacion Biologica Los Tuxtlas, near the collections buildingFieldPureLinkUnpublished
NyctaginaceaeNyctaginia capitata ChoisyMichael J. Moore et al. 2585 (OC)Coahuila, Mexico: in Valle Padilla along rd. leading W away from ranch houseFieldBio-RadUnpublished
NyctaginaceaeOkenia hypogaea Schltdl. & Cham.Michael J. Moore et al. 2673 (OC)Veracruz, Mexico: San Andres Tuxtla, along the face and near the base of large foredunes near the beachFieldPureLinkUnpublished
NyctaginaceaePisonia aculeata L.Kew Living Collection #2011-448Cultivated at Royal Botanic Gardens, KewCultivatedPureLinkSRX718389 (Yang et al., 2015)
NyctaginaceaePisonia umbellifera (J. R. Forst. & G. Forst.) Seem.Kew Living Collection #1986-3623Cultivated at Royal Botanic Gardens, Kew, United KingdomCultivatedPureLinkSRX998852 (Brockington et al., 2015)
NyctaginaceaeSalpianthus purpurascens (Cav. ex Lag.) Hook. & Arn.Michael J. Moore et al. 2724 (OC)Jalisco, Mexico: Autlan de Navarro, along arroyo bed across the street from the campus of CUCSUR in Autlan de NavarroFieldPureLinkUnpublished
NyctaginaceaeTripterocalyx carneus (Greene) L. A. GallowayMichael J. Moore et al. 3027 (OC)New Mexico, USA: Socorro, along US 380 at picnic area a few mi. W of BinghamFieldPureLinkUnpublished
NyctaginaceaeTripterocalyx crux-maltae (Kellogg) Standl.Michael J. Moore et al. 3267 (OC)Nevada, USA: Douglas, approx. 0.6 mi. S along two-track road that runs S from Mel DriveFieldBio-RadUnpublished
OrchidaceaeDactylorhiza alpestris (Pugsley) Aver.Hannah E. Marx 2014-019 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
OrobanchaceaeBartsia alpina L.Hannah E. Marx 2014-020 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
PetiveriaceaeMonococcus echinophorus F. Muell.I. R. Telford & G. Butler 9043 (CANB)Queensland, Australia: Moreton, Mount French, 6 km SW of Boonah. [Cultivated at Booderee National Park, Jervis Bay Territory.]CultivatedPureLinkUnpublished
PetiveriaceaeRivina humilis L.Michael J. Moore 1651 (OC)CultivatedCultivatedBio-RadSRX718277 (Yang et al., 2015)
PetiveriaceaeSeguieria aculeata Jacq.Kew Living Collection #1991-169Cultivated at Royal Botanic Gardens, KewCultivatedPureLinkSRX718486 (Yang et al., 2015)
PetiveriaceaeTrichostigma octandrum (L.) H. WalterMichael J. Moore et al. 3358 (OC)Florida, USA: Miami-Dade, The Kampong: S fenceline immediately adjacent to Biscayne BayCultivatedPureLinkUnpublished
PhytolaccaceaeAnisomeria littoralis (Poepp. & Endl.) Moq.Chileflora s.n.Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
PhytolaccaceaeErcilla volubilis (Bertero) Moq.Michael J. Moore 1649 (OC)Oberlin greenhouseCultivatedBio-RadSRX998846 (Brockington et al., 2015)
PhytolaccaceaePhytolacca dioica L.Kew Living Collection #1963-34101Cultivated at Royal Botanic Gardens, Kew, United KingdomCultivatedPureLinkSRX998853 (Brockington et al., 2015)
PlumbaginaceaeAcantholimon lycopodioides (Girard) Boiss.Euroseeds s.n.; Cultivated at Cambridge University Botanic Garden 20150471Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
PlumbaginaceaeAegialitis annulata R. Br.David Warmington s.n.Queensland, Australia: near Cairns. Cultivated at Cambridge University Botanic Garden.CultivatedPureLinkUnpublished
PlumbaginaceaeLimonium californicum (Boiss.) A. HellerMichael J. Moore et al. 3210 (OC)California, USA: San Luis Obispo, Morro Bay State Park/Morro Estuary Natural Preserve: just E of State Park Rd./Main St., approx. 0.7 mi. SW of jct. w/ S Bay Blvd.FieldPureLinkUnpublished
PlumbaginaceaePlumbago auriculata Lam.Michael J. Moore et al. 3360 (OC)Florida, USA: Miami-Dade, The Kampong: betw. tennis court and main houseCultivatedPureLinkUnpublished
PoaceaeDactylis glomerata L.Hannah E. Marx 2014-011 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
PoaceaeDeschampsia cespitosa (L.) P. Beauv.Hannah E. Marx 2014-012 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
PolemoniaceaePolemonium caeruleum L.Hannah E. Marx 2014-004 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
PolygonaceaeAntigonon leptopus Hook. & Arn.Michael J. Moore 1811 (OC)Texas, USA: Travis, in overgrown lot on N side of house at 3104 Tom Green St., AustinFieldBio-RadSRX998859 (Brockington et al., 2015)
PolygonaceaeBistorta bistortoides (Pursh) SmallMichael J. Moore et al. 3333 (OC)Colorado, USA: Larimer, approx. 0.25 mi. E of Forest Rd. 69, S of Red Feather LakesFieldPureLinkUnpublished
PolygonaceaeChorizanthe angustifolia Nutt.Michael J. Moore et al. 3201 (OC)California, USA: San Luis Obispo, Montana de Oro State Park: along path from parking lot at end of Sand Spit Rd. to beach, approx. 100 yards from parking lotFieldPureLinkUnpublished
PolygonaceaeCoccoloba pubescens L.Michael J. Moore & J. Lee 2942 (OC)Missouri Botanical Garden, cultivated in ClimatronCultivatedPureLinkUnpublished
PolygonaceaeCoccoloba uvifera (L.) L.Michael J. Moore 2665 (OC)Oberlin greenhouseCultivatedPureLinkUnpublished
PolygonaceaeDedeckera eurekensis Reveal & J. T. HowellMichael J. Moore et al. 3138 (OC)California, USA: Los Angeles. Cultivated at Rancho Santa Ana Botanic Garden.CultivatedPureLinkUnpublished
PolygonaceaeEmex spinosa (L.) Campd.Millennium Seed Bank accession 0210373Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
PolygonaceaeEriogonum arcuatum Greene var. arcuatumMichael J. Moore et al. 2215 (OC)New Mexico, USA: Socorro, just E of Quebradas Backcountry BywayFieldPureLinkUnpublished
PolygonaceaeEriogonum callistum RevealMichael J. Moore et al. 3179 (OC)California, USA: Kern, Tejon Ranch: Tehachapi Mtns., on calcareous outcrop near crestFieldPureLinkUnpublished
PolygonaceaeEriogonum deflexum Torr.Lucas C. Majure and Michael J. Moore 5367 (DES)Arizona, USA: Maricopa, Desert Botanical GardenFieldPureLinkUnpublished
PolygonaceaeEriogonum inflatum Torr. subsp. inflatumMichael J. Moore et al. 3227 (OC)California, USA: Kern, along Short Canyon Rd., approx. 2.6 mi. W of BradysFieldPureLinkUnpublished
PolygonaceaeEriogonum longifolium Nutt. var. longifoliumMichael J. Moore et al. 2918 (OC)New Mexico, USA: Eddy, Yeso Hills, on long WNW/ENE trending ridge of gypsum, approx 1.0 mi. along gravel rd. leading E from US 62/180FieldPureLinkUnpublished
PolygonaceaeEriogonum rotundifolium Benth.Michael J. Moore 1769 (OC)New Mexico, USA: Otero, next to parking lot at Holiday Inn Express, near US 54/70 jct. in southern end of AlamogordoFieldPureLinkUnpublished
PolygonaceaeMuehlenbeckia platyclada (F. J. Müll.) Meisn.Michael J. Moore 1170 (OC)Cultivated at Oberlin greenhouseCultivatedBio-RadUnpublished
PolygonaceaeOxytheca perfoliata Torr. & A. GrayMillennium Seed Bank accession 0266864Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
PolygonaceaePersicaria virginiana (L.) Gaertn.Michael J. Moore 1162 (OC)Ohio, USA: Erie, along the bank of the creek behind my houseFieldBio-RadUnpublished
PolygonaceaePodopterus cordifolius Rose & Standl.Michael J. Moore et al. 2714 (OC)Jalisco, Mexico: La Huerta, behind farmhouse approx. 0.5 km landward from main coastal hwy.FieldPureLinkUnpublished
PolygonaceaePodopterus mexicanus Humb. & Bonpl.Michael J. Moore et al. 2721 (OC)Jalisco, Mexico: La Huerta, Estacion Biologica Chamela, along Arroyo Colorado near the end of the Eje CentralFieldPureLinkUnpublished
PolygonaceaePolygonum sp.Michael J. Moore et al. 3219 (OC)California, USA: San Luis Obispo, Morro Strand State Beach: just W of Hwy. 1 in CayucosFieldPureLinkUnpublished
PolygonaceaePolygonum sp.Michael J. Moore et al. 3263 (OC)California, USA: alpine, along Round Top Lake TrailFieldPureLinkUnpublished
PolygonaceaePolygonum aviculare L.Michael J. Moore 2667 (OC)Ohio, USA: Lorain, adjacent to Woodland St. parking lot on campus of Oberlin CollegeFieldBio-RadUnpublished
PolygonaceaePolygonum dentoceras T. M. Schust. & RevealMichael J. Moore et al. 3353 (OC)Florida, USA: Highlands, just S of the Denny’s parking lot on the E side of US 27, approx. 0.6 mi. N of jct. w/ Schumacher Rd./Sebring Pkwy.FieldPureLinkUnpublished
PolygonaceaePterostegia drymarioides Fisch. & C. A. Mey.Millennium Seed Bank accession 0496863Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
PolygonaceaeRumex alpinus L.Hannah E. Marx 2014-013 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
PolygonaceaeRumex arifolius AitonHannah E. Marx 2014-015 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
PolygonaceaeRuprechtia coriacea (H. Karst.) S. F. BlakeMichael J. Moore et al. 3364 (OC)Florida, USA: Miami-Dade, The Kampong: N side of Bay Breeze Ave. near main entrance to property. Area B1. Original collecting locality: Venezuela, Sangre de Toro, BiscochitoCultivatedPureLinkUnpublished
PolygonaceaeRuprechtia salicifolia (Cham. & Schltdl.) C. A. Mey.Sunshine Seeds s.n.Cultivated at Cambridge University Botanic GardenCultivatedPureLinkUnpublished
PolygonaceaeSidotheca caryophylloides (Parry) RevealMichael J. Moore et al. 3164 (OC)California, USA: San Bernardino, just S of CA 18 approx. 80 yards E of jct. w/ Rim of the World Dr.FieldPureLinkUnpublished
PolygonaceaeStenogonum salsuginosum Nutt.Michael J. Moore et al. 3060 (OC)New Mexico, USA: San Juan, along Rd. 6893 approx. 2.4 mi. N of jct. w/ US 64FieldPureLinkUnpublished
PolygonaceaeTriplaris weigeltiana (Rchb.) KuntzeMichael J. Moore & J. Lee 2941 (OC)Missouri Botanical Garden, cultivated in ClimatronCultivatedPureLinkUnpublished
PrimulaceaePrimula auriculata Lam.Hannah E. Marx 2014-006 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
PrimulaceaePrimula farinosa L.Hannah E. Marx 2014-001 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
PrimulaceaePrimula grandis Trautv.Hannah E. Marx 2014-003 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
RanunculaceaeCaltha fistulosa Schipcz.Hannah E. Marx 2014-009 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
RanunculaceaeCaltha palustris L.Hannah E. Marx 2014-002 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
RanunculaceaeRanunculus aconitifolius L.Hannah E. Marx 2014-022 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
RanunculaceaeRanunculus acris L.Hannah E. Marx 2014-017 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
RanunculaceaeRanunculus caucasicus M. Bieb.Hannah E. Marx 2014-005 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
RanunculaceaeTrollius europaeus L.Hannah E. Marx 2014-018 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
RosaceaeAlchemilla mollis (Buser) Rothm.Hannah E. Marx 2014-007 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: invaded plotFieldPureLinkUnpublished
RosaceaeAlchemilla xanthochlora Rothm.Hannah E. Marx 2014-008 (UI)Provence-Alpes-Côte d’Azur, France: Hautes-Alpes, Villar-d’Arêne: Jardin Botanique Alpin du Lautaret: native plotFieldPureLinkUnpublished
SarcobataceaeSarcobatus vermiculatus (Hook.) Torr.Michael J. Moore 1773 (OC)New Mexico, USA: Torrance, along US 60 ca 5 mi. E of jct. w/ NM 42, near S end of Laguna del PerroFieldBio-RadUnpublished
ScrophulariaceaeLeucophyllum frutescens (Berl.) I. M. Johnst.Michael J. Moore 1810 (OC)Texas, USA: Travis, on the campus of the University of Texas, behind the Littlefield HouseCultivatedBio-RadUnpublished
StegnospermataceaeStegnosperma halimifolium Benth.Desert Botanical Garden accession 1973-0120-01-1 WCultivated at Desert Botanical GardenCultivatedBio-RadUnpublished
TalinaceaeTalinum paniculatum (Jacq.) Gaertn.Michael J. Moore 1789 (OC)Cultivated; purchased from Oasis Nursery in Stillwater, OKCultivatedBio-RadUnpublished

Herbaria codes are from Index Herbariorum (http://sweetgum.nybg.org/science/ih/).

For samples without herbaria listed, we have provided the accession number from the living collection (e.g., Cambridge University Botanic Garden, Sukkulenten-Sammlung Zürich), seed bank (e.g., Millennium Seed Bank), or seed supplier.

  14 in total

1.  The butterfly plant arms-race escalated by gene and genome duplications.

Authors:  Patrick P Edger; Hanna M Heidel-Fischer; Michaël Bekaert; Jadranka Rota; Gernot Glöckner; Adrian E Platts; David G Heckel; Joshua P Der; Eric K Wafula; Michelle Tang; Johannes A Hofberger; Ann Smithson; Jocelyn C Hall; Matthieu Blanchette; Thomas E Bureau; Stephen I Wright; Claude W dePamphilis; M Eric Schranz; Michael S Barker; Gavin C Conant; Niklas Wahlberg; Heiko Vogel; J Chris Pires; Christopher W Wheat
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-22       Impact factor: 11.205

2.  Phylotranscriptomic analysis of the origin and early diversification of land plants.

Authors:  Norman J Wickett; Siavash Mirarab; Nam Nguyen; Tandy Warnow; Eric Carpenter; Naim Matasci; Saravanaraj Ayyampalayam; Michael S Barker; J Gordon Burleigh; Matthew A Gitzendanner; Brad R Ruhfel; Eric Wafula; Joshua P Der; Sean W Graham; Sarah Mathews; Michael Melkonian; Douglas E Soltis; Pamela S Soltis; Nicholas W Miles; Carl J Rothfels; Lisa Pokorny; A Jonathan Shaw; Lisa DeGironimo; Dennis W Stevenson; Barbara Surek; Juan Carlos Villarreal; Béatrice Roure; Hervé Philippe; Claude W dePamphilis; Tao Chen; Michael K Deyholos; Regina S Baucom; Toni M Kutchan; Megan M Augustin; Jun Wang; Yong Zhang; Zhijian Tian; Zhixiang Yan; Xiaolei Wu; Xiao Sun; Gane Ka-Shu Wong; James Leebens-Mack
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-29       Impact factor: 11.205

3.  Phytozome: a comparative platform for green plant genomics.

Authors:  David M Goodstein; Shengqiang Shu; Russell Howson; Rochak Neupane; Richard D Hayes; Joni Fazo; Therese Mitros; William Dirks; Uffe Hellsten; Nicholas Putnam; Daniel S Rokhsar
Journal:  Nucleic Acids Res       Date:  2011-11-22       Impact factor: 16.971

4.  Modified CTAB and TRIzol protocols improve RNA extraction from chemically complex Embryophyta.

Authors:  Ingrid E Jordon-Thaden; Andre S Chanderbali; Matthew A Gitzendanner; Douglas E Soltis
Journal:  Appl Plant Sci       Date:  2015-05-13       Impact factor: 1.936

5.  Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.

Authors:  Ya Yang; Stephen A Smith
Journal:  Mol Biol Evol       Date:  2014-08-25       Impact factor: 16.240

6.  Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing.

Authors:  Ya Yang; Michael J Moore; Samuel F Brockington; Douglas E Soltis; Gane Ka-Shu Wong; Eric J Carpenter; Yong Zhang; Li Chen; Zhixiang Yan; Yinlong Xie; Rowan F Sage; Sarah Covshoff; Julian M Hibberd; Matthew N Nelson; Stephen A Smith
Journal:  Mol Biol Evol       Date:  2015-04-02       Impact factor: 16.240

7.  A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.

Authors:  Michael R McKain; Haibao Tang; Joel R McNeal; Saravanaraj Ayyampalayam; Jerrold I Davis; Claude W dePamphilis; Thomas J Givnish; J Chris Pires; Dennis Wm Stevenson; James H Leebens-Mack
Journal:  Genome Biol Evol       Date:  2016-04-21       Impact factor: 3.416

8.  Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.

Authors:  Marc T J Johnson; Eric J Carpenter; Zhijian Tian; Richard Bruskiewich; Jason N Burris; Charlotte T Carrigan; Mark W Chase; Neil D Clarke; Sarah Covshoff; Claude W Depamphilis; Patrick P Edger; Falicia Goh; Sean Graham; Stephan Greiner; Julian M Hibberd; Ingrid Jordon-Thaden; Toni M Kutchan; James Leebens-Mack; Michael Melkonian; Nicholas Miles; Henrietta Myburg; Jordan Patterson; J Chris Pires; Paula Ralph; Megan Rolf; Rowan F Sage; Douglas Soltis; Pamela Soltis; Dennis Stevenson; C Neal Stewart; Barbara Surek; Christina J M Thomsen; Juan Carlos Villarreal; Xiaolei Wu; Yong Zhang; Michael K Deyholos; Gane Ka-Shu Wong
Journal:  PLoS One       Date:  2012-11-21       Impact factor: 3.240

9.  A method for extracting high-quality RNA from diverse plants for next-generation sequencing and gene expression analyses.

Authors:  Roxana Yockteng; Ana M R Almeida; Stephen Yee; Thiago Andre; Colin Hill; Chelsea D Specht
Journal:  Appl Plant Sci       Date:  2013-12-09       Impact factor: 1.936

10.  Early genome duplications in conifers and other seed plants.

Authors:  Zheng Li; Anthony E Baniaga; Emily B Sessa; Moira Scascitelli; Sean W Graham; Loren H Rieseberg; Michael S Barker
Journal:  Sci Adv       Date:  2015-11-20       Impact factor: 14.136

View more
  5 in total

1.  A protocol for high-throughput, untargeted forest community metabolomics using mass spectrometry molecular networks.

Authors:  Brian E Sedio; Cristopher A Boya P; Juan Camilo Rojas Echeverri
Journal:  Appl Plant Sci       Date:  2018-04-02       Impact factor: 1.936

Review 2.  Practical considerations for plant phylogenomics.

Authors:  Michael R McKain; Matthew G Johnson; Simon Uribe-Convers; Deren Eaton; Ya Yang
Journal:  Appl Plant Sci       Date:  2018-04-02       Impact factor: 1.936

3.  Pilot RNA-seq data from 24 species of vascular plants at Harvard Forest.

Authors:  Hannah E Marx; Stacy A Jorgensen; Eldridge Wisely; Zheng Li; Katrina M Dlugosch; Michael S Barker
Journal:  Appl Plant Sci       Date:  2021-02-14       Impact factor: 1.936

4.  Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.

Authors:  Jacob D Washburn; James C Schnable; Gavin C Conant; Thomas P Brutnell; Ying Shao; Yang Zhang; Martha Ludwig; Gerrit Davidse; J Chris Pires
Journal:  Sci Rep       Date:  2017-10-19       Impact factor: 4.379

Review 5.  Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects.

Authors:  Fernando Faria Franco; Danilo Trabuco Amaral; Isabel A S Bonatelli; Monique Romeiro-Brito; Milena Cardoso Telhe; Evandro Marsola Moraes
Journal:  Genes (Basel)       Date:  2022-03-01       Impact factor: 4.096

  5 in total

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