Chromosome-level genome assembly and demographic history of Euryodendron excelsum in monotypic genus endemic to China.

Euryodendron excelsum is in a monotypic genus Euryodendron, endemic to China. It has intermediate morphisms in the Pentaphylacaceae or Theaceae families, which make it distinct. Due to anthropogenic disturbance, E. excelsum is currently found in very restricted and fragmented areas with extremely small populations. Although much research and effort has been applied towards its conservation, its long-term survival mechanisms and evolutionary history remain elusive, especially from a genomic aspect. Therefore, using a combination of long/short whole genome sequencing, RNA sequencing reads, and Hi-C data, we assembled and annotated a high-quality genome for E. excelsum. The genome assembly of E. excelsum comprised 1,059,895,887 bp with 99.66% anchored into 23 pseudo-chromosomes and a 99.0% BUSCO completeness. Comparative genomic analysis revealed the expansion of terpenoid and flavonoid secondary metabolite genes, and displayed a tandem and/or proximal duplication framework of these genes. E. excelsum also displayed genes associated with growth, development, and defence adaptation from whole genome duplication. Demographic analysis indicated that its fluctuations in population size and its recent population decline were related to cold climate changes. The E. excelsum genome assembly provides a highly valuable resource for evolutionary and ecological research in the future, aiding its conservation, management, and restoration.

The complete chloroplast genome of Stichorkis gibbosa (Orchidaceae: Malaxideae).

Stichorkis gibbosa is a rare orchid species of the tribe Malaxideae mainly distributed in tropical Asia. This is the only species of the genus Stichorkis Thouars which has been reported to occur in China. Despite the importance of this genus, previous molecular studies based on few markers have resulted in limited phylogenetic resolution. With the decline of habitats, the wild population of S. gibbosa has decreased in recent years. In this study, we first reported the complete chloroplast (cp) genome of S. gibbosa. The entire cp genome was determined to be 158,056 bp in length with overall GC content of 36.9%, containing a pair of inverted repeat regions (IRs) of 27,006 bp, separated by a large single-copy (LSC, 86,280 bp) and a small single-copy (SSC, 17,764 bp). A total of 133 unique genes were annotated, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic tree indicated that S. gibbosa was a sister group of the genus Oberonia and the epiphytic Liparis alliance with strong support.

Ovule Development and in Planta Transformation of Paphiopedilum Maudiae by Agrobacterium-Mediated Ovary-Injection.

In this paper, the development of the Paphiopedilum Maudiae embryo sac at different developmental stages after pollination was assessed by confocal laser scanning microscopy. The mature seeds of P. Maudiae consisted of an exopleura and a spherical embryo, but without an endosperm, while the inner integument cells were absorbed by the developing embryo. The P. Maudiae embryo sac exhibited an Allium type of development. The time taken for the embryo to develop to a mature sac was 45-50 days after pollination (DAP) and most mature embryo sacs had completed fertilization and formed zygotes by about 50-54 DAP. In planta transformation was achieved by injection of the ovaries by Agrobacterium, resulting in 38 protocorms or seedlings after several rounds of hygromycin selection, corresponding to 2, 7, 5, 1, 3, 4, 9, and 7 plantlets from Agrobacterium-mediated ovary-injection at 30, 35, 42, 43, 45, 48, 50, and 53 DAP, respectively. Transformation efficiency was highest at 50 DAP (2.54%), followed by 2.48% at 53 DAP and 2.45% at 48 DAP. Four randomly selected hygromycin-resistant plants were GUS-positive after PCR analysis. Semi-quantitative PCR and quantitative real-time PCR analysis revealed the expression of the hpt gene in the leaves of eight hygromycin-resistant seedlings following Agrobacterium-mediated ovary-injection at 30, 35, 42, 43, 45, 48, 50, and 53 DAP, while hpt expression was not detected in the control. The best time to inject P. Maudiae ovaries in planta with Agrobacterium is 48-53 DAP, which corresponds to the period of fertilization. This protocol represents the first genetic transformation protocol for any Paphiopedilum species and will allow for expanded molecular breeding programs to introduce useful and interesting genes that can expand its ornamental and horticulturally important characteristics.

The complete chloroplast genome of Pholidota yunnanensis Rolfe (Orchidaceae: Coelogyninae).

In this study, the complete chloroplast genome of Pholidota yunnanensis is presented, which represents first complete plastid genome of the genus Pholidota in the subtribe Coelogyninae. The chloroplast genome size is 159,729 bp, including a GC content of 37.3% and 135 genes (89 protein-coding genes, 38 tRNA genes, 8 rRNA genes). The genome structure is typical quadripartite, consisting of a pair of inverted repeat regions (26,638 bp) separated by a large single-copy region (LSC, 87,610 bp) and a small single-copy region (SSC, 18,843 bp). Phylogenetic analysis among 15 species based on cp genomes recovered a well-supported phylogenetic tree and indicated a close relationship between Pholidota yunnanensis and Pleione bulbocodioides.

Characterization of the complete chloroplast genome of Coelogyne fimbriata (Orchidaceae).

Coelogyne fimbriata has been classified as a national second-class protected orchid species in China. In this study, we report and characterize the complete chloroplast (cp) genome sequence of C. fimbriata in an effort to provide genomic resources useful for promoting its conservation and systematic research. The complete genome is 159,010 bp in length and the overall GC content is 43.3%. The cp genome sequence has a typical quadripartite structure, comprising two inverted repeats (IRA and IRB) regions, which are separated by a small single-copy (SSC) region and a large single-copy (LSC) region. Moreover, a total of 135 functional genes were annotated, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis recovered a close relationship between C. fimbriata and Pleione formosana, and both species are placed within the tribe Arethuseae (Orchidaceae).

Liparisnapoensis (Orchidaceae), a new species from Guangxi, China.

Liparisnapoensis, a new orchid species belonging to section Cestichis from Guangxi, China is described and illustrated. It occurs in the karst limestone forest. The new species is morphologically similar to L.viridiflora and L.somae, but can be readily distinguished by having narrowly oblong-falcate petals; flabellate-quadrate lip distinctly concave at base and emarginate at apex; conspicuously arcuate column with a pair of wedge-shaped wings.

The taxonomic identities of Pholidota wenshanica and P. subcalceata (Orchidaceae, Coelogyninae).

P. wenshanica S.C.Chen & Z.H.Tsi and P. subcalceata Gagnep. have long been recognized as synonyms of P. leveilleana Schltr. In the present study, detailed morphological comparisons suggest that specimens referred to as P. wenshanica and P. subcalceata differ significantly in both vegetative and floral characters from those of P. leveilleana. Here we resurrect P. wenshanica and P. subcalceata as independent species. Key diagnostic characters essential for delineating identities of these species are presented.

Bulbophyllumchrysolabium (Orchidaceae, Epidendroideae, Malaxideae), a new species from Yunnan, China.

Bulbophyllumchrysolabium, a new species belonging to section Racemosae from Yunnan, China is described and illustrated. The species is related to B.orientale and B.morphologorum, but differs by having the following set of characters: obliquely broadly-based triangular petals with a long filiform apex; lip densely glandular papillose and conspicuously ciliolate along margins; lip auricles well developed, narrowly falcate, tapering to a long sharp point at the apex; stelidia subulate and twisted inwards, slightly exceeding operculum. The conservation status of B.chrysolabium is assessed and taxonomic notes are provided.

Embryo development in association with asymbiotic seed germination in vitro of Paphiopedilum armeniacum S. C. Chen et F. Y. Liu.

This paper documents the key anatomical features during the development of P. armeniacum zygotic embryos and their ability to germinate asymbiotically in vitro. This study also examines the effect of media and seed pretreatments on seed germination and subsequent seedling growth. Seeds collected from pods 45 days after pollination (DAP) did not germinate while 95 DAP seeds displayed the highest seed germination percentage (96.2%). Most seedlings (50%) developed to stage 5 from 110 DAP seeds whose compact testa had not yet fully formed. Suspensor cells were vacuolated, which enabled the functional uptake of nutrients. The optimum basal medium for seed germination and subsequent protocorm development was eighth-strength Murashige and Skoog (1/8MS) for 95 DAP seeds and »MS for 110 DAP seeds. Poor germination was displayed by 140 DAP seeds with a compact testa. Pretreatment of dry mature seeds (180 DAP) with 1.0% sodium hypochlorite solution for 90 min or 40 kHz of ultrasound for 8 min improved germination percentage from 0 to 29.2% or to 19.7%, respectively. Plantlets that were at least 5 cm in height were transplanted to a Zhijing stone substrate for orchids, and 85.3% of plantlets survived 180 days after transplanting.

Lanthanide doping-facilitated growth of ultrasmall monodisperse Ba2LaF7 nanocrystals with excellent photoluminescence.

Lanthanide doping not only works as sensitizer and activator, but also plays an important role to facilitate the growth of nanocrystal and to control the size, shape, and property of nanocrystals. Here, reported was the synthesis of monodisperse Ba(2)LaF(7) nanocrystals with the size of sub-10nm through a solvothermal method. We found the dopants of Ho(3+), Er(3+), or Yb(3+) facilitated the growth of Ba(2)LaF(7) nanocrystals obviously to a certain size within a shorter reaction time. Similar phenomenon can also be observed in the synthesis of LaF(3) nanocrystals. We find that Ln(3+) (e.g., Ho(3+), Er(3+), or Yb(3+)) with smaller radius can reduce the nucleation energy and lead to heterogeneous nucleation, which favors the growth of Ba(2)LaF(7) nanocrystals obviously. In addition, intense upconversion emission can be observed from Ln(3+)-doped Ba(2)LaF(7) nanocrystals under the 980 nm laser excitation, providing great potential application in biological imaging. Especially, Ba(2)LaF(7):Yb/Er (20/1 mol%) nanocrystals present more intense upconversion emission than α-NaYF(4):Yb/Er (20/1 mol%) nanocrystals under the same conditions.

Computational comparison of the conventional multislice method and the real space multislice method for simulating exit wavefunctions.

The simulation of exit wavefunctions of a TEM sample is carried out by both the conventional multislice (C-MS) method and the real space multislice (RS-MS) method, with a series of different slice thicknesses. Surprisingly, the results calculated by the RS-MS method remain constant to seven significant figures when the slice thicknesses are changed within a wide range, while those calculated by the C-MS method change significantly. From the mathematical point of view, the C-MS method is only a first order approximation of the RS-MS method. Thus, the calculation precision of the RS-MS method is much higher than that of the C-MS method. Or to achieve the same precision, the slice thickness for the RS-MS method can be taken as two orders of magnitude larger than for the C-MS method in the simulation. As a result, the calculation speed for the RS-MS method may be even faster than that for the C-MS method in some cases. For the two advantages stated above, the RS-MS method may be more suitable for precise calculations.

Half analytical method with application to the high order Laue zone effects in monoclinic and triclinic crystals.

The simulation of the high order Laue zone (HOLZ) diffractions of monoclinic and triclinic crystals is a very complicated problem. The conventional multislice (MS) method suffers from the problem of infinity of the phase grating size. To avoid the difficulty of the infinity, Chen et al. arranged the phase grating plane along the ab plane of the crystal lattice. In this paper we introduce a new method which allows the incident and exit wavefunction planes perpendicular to the zone axis without the difficulty of infinity. We name the method half analytical method. The results calculated by half analytical method are in good agreement with those calculated by the conventional MS method.