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Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land., A draft genome sequence of the hornwort Anthoceros augustus confirms the phylogenetic relationships among the three clades of bryophytes and provides insight into the unique characteristics of hornworts and their adaptations to live on land.

Begonia daunhitam, a new species from West Kalimantan, Indonesia with strongly bullate black leaves is described and illustrated here, and details of the distribution, ecology and conservation status are provided.

Quaternary climate and environment oscillations have profoundly shaped the population dynamic history and geographic distributions of current plants. However, how the endangered and rare tree species respond to the climatic and environmental fluctuations in the subtropical regions of China in East Asia still needs elucidation. In this study, we collected 36 natural populations of an endangered and rare tree species Magnolia sprengeri Pamp. in subtropical China to determine the demographic history, and modeled the changes of geographic distributions of this species in East Asia based on the MaxEnt ecological niche analyses. In addition, we sequenced three maternally inherited chloroplast DNA fragments (matK, trnH-psbA, and rbcL) for all the natural populations which covered the whole geographic distributions of M. sprengeri. Population genetic analysis showed that the endangered tree species have a low level of chloroplast DNA diversity. However, the genetic variation contribution within populations was greater than that among populations (FST = 0.276), which demonstrated a high level of genetic differentiation. Interestingly, some unique chloroplast DNA haplotypes and higher genetic variations were identified in the Qinling-Daba Mountains, Central China, and Tianmu Mountains of Zhejiang province, East of China in East Asia. Combining with the species distribution modeling, we speculated that these areas might be the potential glacial refugia for the endangered plant M. sprengeri. Phylogeographic analysis demonstrated that the geographic factors (e.g., mountains, rivers, and other isolation barriers) had little effect on the genetic divergence among populations. Ecological niche modeling further revealed that the natural populations of M. sprengeri did not experience significant geographic distribution changes from the last glacial maximum to the present time. These findings are in line with the analysis results of the multimodal mismatch patterns of the chloroplast DNA variations. To protect the endangered species M. sprengeri, in situ and ex situ conservation strategies should be formulated for the natural populations with higher genetic variations.

Magnolia sinostellata Chiu & Chen is a rare and endangered species endemic to subtropical China. Here we assembled and annotated the complete chloroplast (cp) genome of M. sinostellata. The chloroplast genome of M. sinostellata is 160,076 bp in length and encodes 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. The maximum-likelihood (ML) phylogenetic analysis result reveals that M. sinostellata is most closely related to M. biondii.

Gnetum chinensesp. nov., a new lianoid species of Gnetaceae, is described from southwestern China. The new species is morphologically similar to G. montanum Markgr. in its oblong elliptic leaves and the ovoid to ellipsoid chlamydosperm, but differs from the latter by its shorter male spikes having fewer involucral collars (7–10 vs. 13–18 in G. montanum). We also did a new molecular analysis using one nuclear marker (i.e. nrITS) and four chloroplast markers (i.e. matK gene, rpoC1 intron, psbB-rps12 IGS, and trnF-trnV IGS). The result suggests that this specific clade is sister to a large clade consisting of all other known Chinese lianoid species of Gnetum except G. parvifolium (Warb.) W.C. Cheng.

Modern gnetophytes consist of three families, i.e. the Ephedraceae, the Gnetaceae, and the Welwitschiaceae, which show diversified morphology. The basal group Ephedraceae possesses an extremely reduced female cone with only the uppermost pair/whorl being fertile, while both the Gnetaceae and the Welwitschiaceae bear female cones/spikes with multiple whorls of fertile bracts. Here, we describe a new ephedroid macrofossil, Liaoningia decussata Yang et Lin, gen. et sp. nov., from the Lower Cretaceous Yixian Formation of western Liaoning in China. This species has typical ephedroid morphology, e.g. the dichasial branching shoot system, swollen nodes, internodes having many fine longitudinal striations, and decussate phyllotaxy, lengthy linear leaves possessing two parallel veins, and female cones consisting of paired bracts. This new genus is similar to the Ephedraceae in its vegetative organs, but differs from the latter by the female spikes with multiple pairs of fertile bracts. In this respect Liaoningia is similar to both the Gnetaceae and the Welwitschiaceae, but distinctly differs from the latter two genera in its vegetative organs. As a result, our new genus shows intermediate morphology between the Ephedaceae and the other two families of the gnetophytes, and is probably a missing link in the evolutionary process from the Ephedraceae to the clade including the Gnetaceae and the Welwitschiaceae.

Begonia puerensis sp. nov., a new tuberous species of Begonia sect. Reichenheimia (Begoniaceae) from Yunnan, China is described and illustrated. The morphological similarity between the new species and the similar species B. discreta, B. harmandii and B. qingchengshanensis is compared and discussed and a key to Begonia sect. Reichenheimia in China is provided. The new species is assessed as Endangered (EN) following the IUCN Red List Categories and Criteria.

Orchids are one of the most diverse flowering plant families, yet possibly maintain the smallest number of the nucleotide-binding site-leucine-rich repeat (NBS-LRR) type plant resistance (R) genes among the angiosperms. In this study, a genome-wide search in four orchid taxa identified 186 NBS-LRR genes. Furthermore, 214 NBS-LRR genes were identified from seven orchid transcriptomes. A phylogenetic analysis recovered 30 ancestral lineages (29 CNL and one RNL), far fewer than other angiosperm families. From the genetics aspect, the relatively low number of ancestral R genes is unlikely to explain the low number of R genes in orchids alone, as historical gene loss and scarce gene duplication has continuously occurred, which also contributes to the low number of R genes. Due to recent sharp expansions, Phalaenopsis equestris and Dendrobium catenatum having 52 and 115 genes, respectively, and exhibited an "early shrinking to recent expanding" evolutionary pattern, while Gastrodia elata and Apostasia shenzhenica both exhibit a "consistently shrinking" evolutionary pattern and have retained only five and 14 NBS-LRR genes, respectively. RNL genes remain in extremely low numbers with only one or two copies per genome. Notably, all of the orchid RNL genes belong to the ADR1 lineage. A separate lineage, NRG1, was entirely absent and was likely lost in the common ancestor of all monocots. All of the TNL genes were absent as well, coincident with the RNL NRG1 lineage, which supports the previously proposed notion that a potential functional association between the TNL and RNL NRG1 genes.

Magnolia denudata var. glabrata Y. L. Wang et S. Z. Zhang var. nov. is described and illustrated from Hunan, China. The variety occurs mainly in semi-evergreen forest of south Hunan at altitudes between 700 and 1260 m a.s.l. It differs from M. denudata var. denudata by its green and glabrous twigs and leaves which are glabrous above and have some white pubescence underneath. With its white flowers consisting of mostly 9 tepals, it differs from M. sprengeri Pamp. which mainly has 12 tepals in various shades of red/pink to white. The new variety is rare and considered endangered due to habitat destruction.

Taxonomists are divided over the infrageneric classification and species delimitation within the genus Cycas. The division is largely determined by whether a broad or narrow species concept is adopted, the latter approach being based on apparently minor morphological differences. It is well known that cytokinesis in the cells of pollen provides important evidence for plant taxonomy, particularly at the higher taxonomic level. Here we present the first broad comparison of the cytokinesis of male meiosis in five species of Cycas. A comparative analysis of microsporogenesis in Cycas was carried out using conventional microscopy, semi‐thin sectioning, histochemistry, and fluorescence microscopy with a focus on the cytokinesis of meiosis in the pollen of dividing cells. Our observations confirmed that, contrary to previous reports, the cytokinesis in male meiosis of five species in Cycas is simultaneous at the end of second meiosis. The basic model of microsporogenesis and its systematic implications in Cycas is discussed based both on previous reports and our new results.

Here, we report a completely sequenced plastome using Illumina/Solexa sequencing-by-synthesis (SBS) technology. The plastome of Magnolia kwangsiensis Figlar & Noot. is 159 667 bp in length with a typical quadripartite structure: 88 030 bp large single-copy (LSC) and 18 669 bp small single-copy (SSC) regions, separated by two 26 484 bp inverted repeat (IR) regions. The overall predicted gene number is 129, among which 17 genes are duplicated in IR regions. The plastome of M. kwangsiensis is identical in its gene order to previously published plastomes of magnoliids. Furthermore, the C-to-U type RNA editing frequency of 114 seed plants is positively correlated with plastome GC content and plastome length, whereas plastome length is not correlated with GC content. A total of 16 potential putative barcoding or low taxonomic level phylogenetic study markers in Magnoliaceae were detected by comparing the coding and noncoding regions of the plastome of M. kwangsiensis with that of Liriodendron tulipifera L. At least eight markers might be applied not only to Magnoliaceae but also to other taxa. The 86 mononucleotide cpSSRs that distributed in single-copy noncoding regions are highly valuable to study population genetics and conservation genetics of this endangered rare species.

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for 26 species representing 11 genera of the tribe Oryzeae and three outgroup species. The sequenced fragments varied from 1522 base pairs (bp) to 1534 bp in length with 15.4% variable and 7.9% phylogenetically informative sites when the outgroups were excluded. The aligned sequences were analyzed by maximum parsimony and neighbor-joining methods. Analyses of the sequence data indicated that species of Oryzeae form a strongly supported monophyletic group, concordant with previous morphological and anatomical evidence. The tribe Oryzeae can be divided into two monophyletic lineages, corresponding to the traditionally recognized subtribes Oryzinae and Zizaniinae. The first subtribe consists of Oryza and Leersia, while the subtribe Zizaniinae includes the remaining genera. The matK sequence data did not support the close affinities of the monoecious genera in Oryzeae, implying the possibility of multiple origins of the floral structures in the tribe. It is noteworthy that Porteresia coarctata is closely related to Oryza species, suggesting that it should be treated as a member in the genus Oryza rather than a separate monotypic genus.

To analyze the genetic diversity and differentiation degree of five Lonicera confusa populations.Random Amplified Polymorphic DNA (RAPD) markers were perfomed to amplify the discernible loci.A total of 100 loci were obtained for all populations using ten primers, 87.00% of which were polymorphic (PPL = 87.00%). Analyzed by POPGENE, the average percentage of polymorphic loci was 58.86%. Nei's genetic diversity (H = 0.2647) and Shannon's information index (I = 0.4022) indicated that Lonicera confusa had a higher level of genetic diversity. The high value of differentiation( G(st) = 0.3839) showed that geographic isolation strongly influenced genetic differentiation among populations and there was a significant correlation between genetic distance and geographic distance (r = 0.8504, P = 96.80%). The clustering analysis was performed using softwares POPGENE and NTSYS-pc. Five populations were divided into 2 clusters, named cluster 1 (LFS, XX and NN) and cluster 2 (XW and HK).Management strategies were proposed for species conservation and resource utilization of Lonicera confusa, including the protection from human disturbance to facilitate natural regeneration, construction of germplasm resources and cultivation of plants collected from different populations, in order to select elite lines for good agricultural practice (GAP) of medicinal materials.

The chloroplast mat-K region and rpL16 intron region were sequenced for 14 species of Schisandraceae, representing both genera Kadsura Kaempf. ex Juss. and Schisandra Michx, to discuss the phylogeny of this family. Analyses were performed both in separate and combined sequence data sets (including the rbc-L sequence), with Illicium angustispealum A. C. Smith as the out-group. The results showed that the Schisandraceae are monophyletic. In all the analyses, Schisandra propinqua var. chinensis Oliva and Schisandra plena A. C. Smith were nested within Kadsura, which implies that the genera Kadsura and Schisandra are closely related. They might have originated from a common ancestor, but then evolved via different routes. The result inferred from the combined data showed a greater resolution within Schisandra than those from the two separate data sets. High bootstrap values supported the monophyly of most subgenera according to Law's system (1996). A combination of morphological, anatomical, and chemical analyses indicates that S. chinensis and S. rubriflora may be the primitive taxa in Schisandra.

A new species, Petrocosmea hexiensis, is described and illustrated from Hexi in the Nanchuan district of Chongqing, China. The new species is similar to Petrocosmea duclouxii , but differs mainly in having a longer corolla tube and ovate-rhombic to rhombic leaves with truncated bases. Cytological and phylogenetic studies of the new species demonstrate that it has the same chromosome number as other species of Petrocosmea and that its closest relative is P. duclouxii .