Systematics of Xanthorrhoeaceae Sensu Lato, with an Emphasis on Bulbine

We provide here results of a combined analysis of plastid genes rbcL, matK, and ndhF for Xanthorrhoeaceae s.l., the Asphodelaceae/Xanthorrhoeaceae/Hemerocallidaceae clade, which are well supported by the DNA data. Xanthorrhoea (often treated as the sole member of Xanthorrhoeaceae) is sister to the hemerocallid clade (former Hemerocallidaceae); and the asphodelid clade (formerly Asphodelaceae) is sister to them both. For additional species of Bulbine and Jodrellia (both Asphodeloideae), we also collected rps16 intron and ITS nuclear ribosomal DNA sequences to better assess their relationships. Bulbine, with Jodrellia, embedded are sister to the collective genera of subfamily Alooideae in which all species are characterized by strongly bimodal and nearly identical karyotypes, whereas that of Bulbine is much more variable. Cytological studies have previously shown Bulbine to possess a range of karyotypes from graduated to clearly bimodal (although never exactly like the aloid genera) and point toward a lower level of bimodality in the Australian members, all of which are autotetraploid, than in the African members, all of which are diploid. Therefore, there have been two events of particular interest within Bulbine, a change in ploidy and a long-range dispersal event

Multigene Analyses of Monocot Relationships

We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear I8S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atp1 DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79-82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87- 92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported

Field-based species identification in eukaryotes using real-time nanopore sequencing

Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored1,2. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere3–5. However, the generation of datasets from large, complex genomes has been constrained to laboratories6,7. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.)8 has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification-by-sequencing and de novo phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, “al fresco” laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible. These technological advances are set to revolutionise research in the biological sciences9 and have broad implications for conservation, taxonomy, border agencies and citizen science

Rapid, raw-read reference and identification (R4IDs): a flexible platform for rapid generic species ID using long-read sequencing technology

The versatility of the current DNA sequencing platforms and the development of portable, nanopore sequencers means that it has never been easier to collect genetic data for unknown sample ID. DNA barcoding and meta-barcoding have become increasingly popular and barcode databases continue to grow at an impressive rate. However, the number of canonical genome assemblies (reference or draft) that are publically available is relatively tiny, hindering the more widespread use of genome scale DNA sequencing technology for accurate species identification and discovery. Here, we show that rapid raw-read reference datasets, or R4IDs for short, generated in a matter of hours on the Oxford Nanopore MinION, can bridge this gap and accelerate the generation of useable reference sequence data. By exploiting the long read length of this technology, shotgun genomic sequencing of a small portion of an organism’s genome can act as a suitable reference database despite the low sequencing coverage. These R4IDs can then be used for accurate species identification with minimal amounts of re-sequencing effort (1000s of reads). We demonstrated the capabilities of this approach with six vascular plant species for which we created R4IDs in the laboratory and then re-sequenced, live at the Kew Science Festival 2016. We further validated our method using simulations to determine the broader applicability of the approach. Our data analysis pipeline has been made available as a Dockerised workflow for simple, scalable deployment for a range of uses

Genome characterization of brugmansia latent virus, a novel tobamovirus

A novel tobamovirus, brugmansia latent virus (BrLV), was discovered during a study of brugmansia (Brugmansia spp.) in the living collections held at the Royal Botanic Gardens, Kew. Here, we report the complete genome sequence of BrLV, which is 6,397 nucleotides long and contains the four open reading frames (RNA-dependent RNA polymerase, methyltransferase/helicase, movement, and coat proteins) typical of tobamoviruses. The complete genome sequence of BrLV shares 69.7% nucleotide sequence identity with brugmansia mild mottle virus (BrMMV) and 66.7 to 68.7% identity with other tobamoviruses naturally infecting members of the Solanaceae plant family. Phylogenetic analysis of the complete genome nucleotide sequence and the deduced amino acid sequences of the four tobamovirus proteins place BrLV in a subcluster with BrMMV within the Solanaceae-infecting tobamovirus subgroup as a new species

Benstonea ornata Callm. & Buerki, comb. nova.

29. Benstonea ornata (Solms) Callm. & Buerki, comb. nova. ≡ Pandanus ornatus Solms in Linnaea 42: 11. 1878. Lectotypus (designated here): MALAYSIA. Malacca: 1837, Gaudichaud 108 (G [G00164258]!; isolecto-: B [B1002 79958] image seen, P [P01751483, P01751484, P0175 1486, P01751487]!). = Pandanus monotheca Martelli in Boll. Soc. Bot. Ital. 1904: 303. 1904. Lectotypus (designated here): MALAYSIA. Malacca: Gunong Tundok, 1891, Ridley 10821 (FI [FI00 3937] image seen; isolecto-: G [G00353796]!; SING [SING0059013]!), syn. nov. Distribution and ecology. – Benstonea ornata is distributed from Peninsular Malaysia to Borneo (through Sumatra and Singapore) and Thailand. It grows in forest understory on hilltops, often on poor soils, at an altitude of 300 to 1350 m (STONE, 1978). Observations. – Pandanus ornatus was first illustrated by GAUDICHAUD (1841) in the invalidely published genus Fisquetia Gaudich. This name was then invalidly transferred by KURZ (1869) to Pandanus, without a description. SOLMS- LAUBACH (1878), while attempting to transfer it to Pandanus, in fact described it as new, designating two syntypes: Gaudichaud’s drawing and a Gaudichaud collection in the Delessert herbarium in G (Gaudichaud 108). His description thus validates the name as P.ornatus, even though he believed he was simply making a new combination. Gaudichaud 108 has both an infructescence and leaves, and is here designated as the lectotype. Benstonea ornata is characterized by a sub-cylindric cephalia (varying in length from 5 to 23 cm), pendent on a long peduncle (up to 50 cm) with sharp, proximally arcuate styles up to 5 mm in length (Fig. 4C). This species is wonderfully illustrated in GAUDICHAUD (1841: Tab. 5, Figs. 1, 8-9). MARTELLI (1904) described Pandanus monotheca based on Ridley 10821. The holotype deposited at CAL was not found by Stone, neither in 1968 nor in 1974 (STONE, 1978), and this entity was therefore regarded by him as a poorly known species. Drupes of this collection (with neither leaves nor syncarps) were, however, subsequently found in both FI and G. The FI collection, here designated as lectotype, clearly belongs to Benstonea ornata, and Pandanus monotheca is therefore treated as a synonym.Published as part of Callmander, Martin W., Lowry Ii, Porter P., Forest, Félix, Devey, Dion S., Beentje, Henk & Buerki, Sven, 2012, Benstonea Callm. & Buerki (Pandanaceae): characterization, circumscription, and distribution of a new genus of screw-pines, with a synopsis of accepted species, pp. 323-345 in Candollea 67 (2) on pages 336-337, DOI: 10.15553/c2012v672a12, http://zenodo.org/record/579000

Benstonea parva Callm. & Buerki, comb.nova.

31. Benstonea parva (Ridl.) Callm. & Buerki, comb.nova. ≡ Pandanus parvus Ridl. in J. Straits Branch Roy. Asiat. Soc. 33: 171. 1900. Typus: SINGAPORE. PulauUbin: Kranji, 1892, Ridley 8928 (lecto-: SING [SING0059862]!) (designated by ST. JOHN, 1963: 337). Distribution and ecology. – Benstonea parva grows in lowland to montane rainforests (from sea level to 1500 m) and is distributed from Peninsular Malaysia through Singapore to Borneo (Sabah). Observations. – This small terrestrial herbaceous species is characterized by its short monocaulous habit (up to 60 cm high), its broad but small leaves that are abruptly caudateacuminate in the distal part, glaucous on the abaxial surface, and its rather small globose terminal syncarp (Fig. 5A). It remains difficult to differentiate B.parva from B.unguiculata (Ridl.) Callm. & Buerki (with slightly narrower leaves and larger fruit), and further collections are needed to confirm whether they are distinct.Published as part of Callmander, Martin W., Lowry Ii, Porter P., Forest, Félix, Devey, Dion S., Beentje, Henk & Buerki, Sven, 2012, Benstonea Callm. & Buerki (Pandanaceae): characterization, circumscription, and distribution of a new genus of screw-pines, with a synopsis of accepted species, pp. 323-345 in Candollea 67 (2) on page 337, DOI: 10.15553/c2012v672a12, http://zenodo.org/record/579000

Benstonea lauterbachii Callm. & Buerki, comb. nova.

24. Benstonea lauterbachii (K. Schum. & Warb.) Callm. & Buerki, comb. nova. Ξ Pandanus lauterbachii K. Schum. & Warb. in Engl., Pflanzenr. 3(IV, 9): 81. 1900. Typus: PAPUA NEW GUINEA. Madang Prov.: Gogol, 28.X.1890, Lauterbach 863 (holo-: B [B100216880] image seen). Distribution and ecology. – Benstonea lauterbachii grows on wet soils, in swamps or near mangroves in New Guinea (West Papua, Papua and Papua New Guinea) and innorthern Australia (Queensland)(WILSON, 2011).Published as part of Callmander, Martin W., Lowry Ii, Porter P., Forest, Félix, Devey, Dion S., Beentje, Henk & Buerki, Sven, 2012, Benstonea Callm. & Buerki (Pandanaceae): characterization, circumscription, and distribution of a new genus of screw-pines, with a synopsis of accepted species, pp. 323-345 in Candollea 67 (2) on page 335, DOI: 10.15553/c2012v672a12, http://zenodo.org/record/579000

Benstonea alticola Callm. & Buerki, comb. nova.

3. Benstonea alticola (Holttum & H. St. John) Callm. & Buerki, comb. nova. ≡ Pandanus alticola Holttum & H. St. John in Pacific Sci. 16: 218. 1962. Typus: MALAYSIA. Johore (Peninsular Malaysia): Sungei Kayu, Mawai-Jemaluang rd., II.1935, Corner s.n. (holo-: SING [SING0169801]!). Distribution and ecology. – Benstonea alticola is found in montane forest and is an epiphyte growing to 12 m above ground, or a terrestrial shrub on limestone domes in Peninsular Malaysia (Bukit Takun, Selangor; Gua Musang, Kelantan) and Borneo (Sarawak) at an altitude of c. 700-1500 m. Observations. – This facultative epiphytic shrub, with one large clump of leaves on a very short stem, has only a single terminal syncarp. Abroader species concept, including other facultative epiphytes recognized here as distinct species such as B. inquilina (B. C. Stone) Callm. & Buerki, may ultimately prove to be more appropriate, but further fieldwork will be required to determine the preferable circumscription of species.Published as part of Callmander, Martin W., Lowry Ii, Porter P., Forest, Félix, Devey, Dion S., Beentje, Henk & Buerki, Sven, 2012, Benstonea Callm. & Buerki (Pandanaceae): characterization, circumscription, and distribution of a new genus of screw-pines, with a synopsis of accepted species, pp. 323-345 in Candollea 67 (2) on page 330, DOI: 10.15553/c2012v672a12, http://zenodo.org/record/579000