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Multi-scale analysis on species diversity within a 40-ha old-growth temperate forest
Jie Gao, Peng Zhang, Xing Zhang, Yanhong Liu
Plant Diversity    2018, 40 (02): 45-49.   doi: 10.1016/j.pld.2017.12.003
Abstract378)      PDF (1145KB)(295)       Save

In order to better explore the maintenance mechanisms of biodiversity,data collected from a 40-ha undisturbed Pinus forest were applied to the Individual SpecieseArea Relationship model (ISAR) to determine distribution patterns for species richness.The ecological processes influencing species abundance distribution patterns were assessed by applying the same data set to five models:a LogNormal Model (LNM),a Broken Stick Model (BSM),a Zipf Model (ZM),a Niche Preemption Model (NPM),and a Neutral Model (NM).Each of the five models was used at six different sampling scales (10 m×10 m,20 m×20 m,40 m×40 m,60 m×60 m,80 m×80 m,and 100 m×100 m).Model outputs showed that:(1) Accumulators and neutral species strongly influenced species diversity,but the relative importance of the two types of species varied across spatial scales.(2) Distribution patterns of species abundance were best explained by the NPM at small scales (10 me20 m),whereas the NM was the best fit model at large spatial scales.(3) Species richness and abundance distribution patterns appeared to be driven by similar ecological processes.At small scales,the niche theory could be applied to describe species richness and abundance,while at larger scales the neutral theory was more applicable.

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Diversity and conservation of Chinese wild begonias
Daike Tian, Yan Xiao, Yi Tong, Naifeng Fu, Qingqing Liu, Chun Li
Plant Diversity    2018, 40 (03): 75-90.   doi: 10.1016/j.pld.2018.06.002
Abstract354)      PDF (9641KB)(353)       Save

Begonia, one of the most diverse plant taxa and the fifth or sixth largest angiosperm genus, consists of over 1800 accepted species. The number of species recognized within this genus has greatly increased over the past 20 years, rising from 80 to 200 species in China alone. Based on recent field surveys, the number of begonia species in China is predicted to be between 250 and 300. Given the large number of begonia species that still remain to be described, further taxonomical work is urgently required. This is especially true for Chinese Begonia, in which there is a huge diversity of habitat, habit, plant size, leaf type, flower and fruit morphology, and most species are narrowly distributed in isolated habitats that are subject to negative disturbances from climate change, as well as agricultural and industrial activities. Although the conservation status for the majority of species has been evaluated using the standards of the International Union for Conservation of Nature, the results don't represent the truth in many species, and also about 11.5% of which are data-absent. In addition, illegal collection and over-harvesting of wild begonias for ornamental or medicinal use has increased due to the rapid development of internet commerce. Far more often than predicted, these species should be categorized as rare and endangered and require immediate protection. Ex situ conservation of Chinese begonias started in 1995 and over 60% of the total species have been so far introduced into cultivation by several major botanical gardens in China. However, only few research institutions, limited funds and human resources have been involved in Begonia conservation; moreover, no project has conducted reintroduction. Therefore, more conservation-based work remains to be done. Improved conservation of Chinese begonias in the future depends on further field survey, an improved understanding of population diversity, and integrative approaches, including in situ and ex situ conservation, seed banking, and plant reintroduction. Speciestargeted conservation zones should be established for endangered species excluded from the existing nature reserves. Additionally, laws pertaining to plant protection should be extended to prevent the illegal collection and transaction of wild plants, particularly for those species with unique habitats and small populations.

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Genome-wide analysis indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) oligopeptide transporters gene family
Yanan Pu, Danni Yang, Xin Yin, Qiuli Wang, Qian Chen, Yunqiang Yang, Yongping Yang
Plant Diversity    2018, 40 (02): 57-67.   doi: 10.1016/j.pld.2018.03.001
Abstract219)      PDF (13033KB)(466)       Save

Oligopeptide transporters (OPTs) encode integral membrane-localized proteins and have a broad range of substrate transport capabilities.Here,28 BrrOPT genes were identified in the turnip.Phylogenetic analyses revealed two well-supported clades in the OPT family,containing 15 BrrOPTs and 13 BrrYSLs. The exon/intron structure of OPT clade are conserved but the yellow stripe-like (YSL) clade was different. The exon/intron of the YSL clade possesses structural differences,whereas the YSL class motifs structure are conserved.The OPT genes are distributed unevenly among the chromosomes of the turnip genome. Phylogenetic and chromosomal distribution analyses revealed that the expansion of the OPT gene family is mainly attributable to segmental duplication.For the expression profiles at different developmental stages,a comprehensive analysis provided insights into the possible functional divergence among members of the paralog OPT gene family.Different expression levels under a variety of ion deficiencies also indicated that the OPT family underwent functional divergence during long-term evolution. Furthermore,BrrOPT8.1,BrrYSL1.2,BrrYSL1.3,BrrYSL6 and BrrYSL9 responded to Fe (Ⅱ) treatments and BrrYSL7 responded to calcium treatments,BrrYSL6 responded to multiple treatments in root,suggesting that turnip OPTs may be involved in mediating cross-talk among different ion deficiencies.Our data provide important information for further functional dissection of BrrOPTs,especially in transporting metal ions and nutrient deficiency stress adaptation.

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Effect of vernalization on tuberization and flowering in the Tibetan turnip is associated with changes in the expression of FLC homologues
Yan Zheng, Landi Luo, Yuanyuan Liu, Yunqiang Yang, Chuntao Wang, Xiangxiang Kong, Yongping Yang
Plant Diversity    2018, 40 (02): 50-56.   doi: 10.1016/j.pld.2018.01.002
Abstract208)      PDF (7762KB)(210)       Save

The turnip (Brassica rapa var.rapa) is a biennial crop that is planted in late summer/early fall and forms fleshy tubers for food in temperate regions.The harvested tubers then overwinter and are planted again the next spring for flowering and seeds.FLOWERING LOCUS C (FLC) is a MADS-box transcription factor that acts as a major repressor of floral transition by suppressing the flowering promoters FT and SOC1.Here we show that vernalization effectively represses tuber formation and promotes flowering in Tibetan turnip.We functionally characterized four FLC homologues (BrrFLC1, FLC2,FLC3,and FLC5),and found that BrrFLC2 and BrrFLC1 play a major role in repressing flowering in turnip and in transgenic Arabidopsis.In contrast,tuber formation was correlated with BrrFLC1 expression in the hypocotyl and was repressed under cold treatment following the quantitative downregulation of BrrFLC1.Grafting experiments of non-vernalized and vernalized turnips revealed that vernalization independently suppressed tuberization in the tuber or hypocotyl of the rootstock or scion,which occurred in parallel with the reduction in BrrFLC1 activity.Together,our results demonstrate that the Tibetan turnip is highly responsive to cold exposure,which is associated with the expression levels of BrrFLC genes.

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A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing
Ying Guo, Guo-Qian Yang, Yun-Mei Chen, De-Zhu Li, Zhen-Hua Guo
Plant Diversity    2018, 40 (03): 106-116.   doi: 10.1016/j.pld.2018.04.001
Abstract190)      PDF (2029KB)(148)       Save

Obtaining high-quality plant materials for experiments is challenging for many research projects. Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on ddRADseq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species (Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the ddRAD-seq technique (MiddRAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA, regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The ddRAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by ddRAD-seq.

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NaPDR1 and NaPDR1-like are essential for the resistance of Nicotiana attenuata against fungal pathogen Alternaria alternata
Zhen Xu, Na Song, Lan Ma, Dunhuang Fang, Jinsong Wu
Plant Diversity    2018, 40 (02): 68-73.   doi: 10.1016/j.pld.2018.01.001
Abstract188)      PDF (2806KB)(279)       Save

Pleiotropic drug resistance (PDR) transporters are widely distributed membrane proteins catalyzing the export or import of a diverse array of molecules,and are involved in many plant responses to biotic and abiotic stresses.However,it is unclear whether PDRs are involved in Nicotiana attenuata resistance to the necrotic fungal pathogen Alternaria alternata.In this study,transcriptional levels of both NaPDR1 and NaPDR1-like were highly induced in N.attenuata leaves after A.alternata inoculation.Interestingly, silencing NaPDR1 or NaPDR1-like individually had little effect on N.attenuata resistance to A.alternata; however,when both genes were co-silenced plants became highly susceptible to the fungus,which was associated with elevated JA and ethylene responses.Neither NaPDR1 nor NaPDR1-like was significantly elicited by exogenous treatment with methyl jasmonate (MeJA),whereas both were highly induced by ethylene.The elicitation levels of both genes by A.alternata were significantly reduced in plants with impaired JA or ethylene signaling pathways.Thus,we conclude that both NaPDR1 and NaPDR1-like function redundantly to confer resistance against A.alternata in N.attenuata,and the elicitation of the transcripts of both genes by the fungus is partially dependent on ethylene and jasmonate signaling.

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Plastome characteristics of Cannabaceae
Huan-Lei Zhang, Jian-Jun Jin, Michael J. Moore, Ting-Shuang Yi, De-Zhu Li
Plant Diversity    2018, 40 (03): 127-137.   doi: 10.1016/j.pld.2018.04.003
Abstract181)      PDF (3701KB)(167)       Save

Cannabaceae is an economically important family that includes ten genera and ca.117 accepted species. To explore the structure and size variation of their plastomes,we sequenced ten plastomes representing all ten genera of Cannabaceae.Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes.The Inverted Repeat (IR) regions in five plastomes had experienced small expansions (330-983 bp) into the Large Single-Copy (LSC) region.The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs.The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR.A 270-bp inversion was detected in the Parasponia rugosa plastome,which might have been mediated by 18-bp inverted repeats.Repeat sequences,simple sequence repeats,and nucleotide substitution rates varied among these plastomes. Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified,which may be useful for further phylogenetic analysis and species identification.Our results show strong support for a sister relationship between Gironniera and Lozanell (BS=100).Celtis,Cannabis-Humulus,Chaetachme-Pteroceltis,and Trema-Parasponia formed a strongly supported clade,and their relationships were well resolved with strong support (BS=100).The availability of these ten plastomes provides valuable genetic information for accurately identifying species,clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.

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N-P fertilization did not reduce AMF abundance or diversity but alter AMF composition in an alpine grassland infested by a root hemiparasitic plant
Xue-Zhao Wang, Xiao-Lin Sui, Yan-Yan Liu, Lei Xiang, Ting Zhang, Juan-Juan Fu, Ai-Rong Li, Pei-Zhi Yang
Plant Diversity    2018, 40 (03): 117-126.   doi: 10.1016/j.pld.2018.05.001
Abstract178)      PDF (1821KB)(237)       Save

Fertilization has been shown to have suppressive effects on arbuscular mycorrhizal fungi (AMF) and root hemiparasites separately in numerous investigations, but its effects on AMF in the presence of root hemiparasites remain untested. In view of the contrasting nutritional effects of AMF and root hemiparasites on host plants, we tested the hypothesis that fertilization may not show strong suppressive effects on AMF when a plant community was infested by abundant hemiparasitic plants. Plants and soil samples were collected from experimental field plots in Bayanbulak Grassland, where N and P fertilizers had been applied for three continuous years for control against a spreading root hemiparasite, Pedicularis kansuensis. Shoot and root biomass of each plant functional group were determined. Root AMF colonization levels, soil spore abundance, and extraradical hyphae length density were measured for three soil depths (0-10 cm, 10-20 cm, 20-30 cm). Partial 18S rRNA gene sequencing was used to detect AMF diversity and community composition. In addition, we analyzed the relationship between relative abundance of different AMF genera and environmental factors using Spearman's correlation method. In contrast to suppressive effects reported by many previous studies, fertilization showed no significant effects on AMF root colonization or AMF species diversity in the soil. Instead, a marked increase in soil spore abundance and extraradical hyphae length density were observed. However, fertilization altered relative abundance and AMF composition in the soil. Our results support the hypothesis that fertilization does not significantly influence the abundance and diversity of AMF in a plant community infested by P. kansuensis.

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Pollination ecology in China from 1977 to 2017
Zongxin Ren, Yanhui Zhao, Huan Liang, Zhibin Tao, Hui Tang, Haiping Zhang, Hong Wang
Plant Diversity    2018, 40 (04): 172-180.   doi: 10.1016/j.pld.2018.07.007
Abstract171)      PDF (3389KB)(141)       Save

China is one of most biodiverse countries in the world, containing at least 10% of all angiosperm species. Therefore, we should anticipate a diverse, pollinator fauna. China also has a long history of applied ethnobiology, including a sustainable agriculture based on apiculture and plant-pollinator interactions. However, the science of pollination ecology is a far younger sub-discipline in China, compared to in the West. Chinese studies in pollination ecology began in the 1970s. For this review, we compiled a complete reference database (>600 publications) of pollination studies in China. Using this database, we identified and analyzed gaps and limitations in research on the pollination systems of native and naturalized species. Specifically, we asked the following questions:1) What do we know about the pollination systems of native, Chinese species? 2) How does Chinese pollination ecology compare with the development of pollination research abroad and which aspects of research should be pursued by Chinese anthecologists in the near future? 3) What research on pollination in China will advance our understanding and contribute to our ongoing analyses of endemism and conservation? Subsequently, we segregated and identified prospective lines of future research that are unique to China and can only be done in China. This requires discussing priorities within a systematic approach.

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Securing a future for China's plant biodiversity through an integrated conservation approach
Sergei Volis
Plant Diversity    2018, 40 (03): 91-105.   doi: 10.1016/j.pld.2018.04.002
Abstract166)      PDF (1060KB)(183)       Save

The severely threatened Chinese flora urgently needs a new, well adapted to China and properly formulated conservation strategy. The present review provides a detailed conservation methodology that complements previously described guidelines for preservation of plant species with extremely small populations (PSESP) in China. This review adds to the above concept in several aspects, making it relevant to all threatened Chinese plant species. The proposed integral conservation strategy has the following crucial components:
-ecoregional basis for conservation planning and implementation;
-a unified scoring system that is used in regional systematic planning for reserve design, monitoring and assessment of efficiency of a reserve network, and creation of seed banks and living collections;
-a focus on population demography and the presence of naturally occurring regeneration as the key criteria for defining the conservation status of a species and the appropriate major focus of the species recovery plan;
-creation of multi-species living collections that preserve species genetic variation and provide material for in situ actions;
-experimental translocation of threatened species into multiple locations within and outside their known range.
Adopting and implementing these strategies successfully and more fully in China requires that the country changes PA legislation and improves PA management, the National Science Foundation of China (NSFC) re-prioritizes the type of research that receives research funds, and local scientists improve their approach toward information sharing.

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A few words on our commemoration of 80 years at KIB
Hang Sun, Yongping Yang, Zhekun Zhou
Plant Diversity    2018, 40 (04): 139-140.   doi: 10.1016/j.pld.2018.08.001
Abstract158)      PDF (1981KB)(197)       Save
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Current understanding of maize and rice defense against insect herbivores
Jinfeng Qi, Saif ul Malook, Guojing Shen, Lei Gao, Cuiping Zhang, Jing Li, Jingxiong Zhang, Lei Wang, Jianqiang Wu
Plant Diversity    2018, 40 (04): 189-195.   doi: 10.1016/j.pld.2018.06.006
Abstract130)      PDF (1214KB)(126)       Save

Plants have sophisticated defense systems to fend off insect herbivores. How plants defend against herbivores in dicotyledonous plants, such as Arabidopsis and tobacco, have been relatively well studied, yet little is known about the defense responses in monocotyledons. Here, we review the current understanding of rice (Oryza sativa) and maize (Zea mays) defense against insects. In rice and maize, elicitors derived from insect herbivore oral secretions or oviposition fluids activate phytohormone signaling, and transcriptomic changes mediated mainly by transcription factors lead to accumulation of defense-related secondary metabolites. Direct defenses, such as trypsin protein inhibitors in rice and benzoxazinoids in maize, have anti-digestive or toxic effects on insect herbivores. Herbivory-induced plant volatiles, such as terpenes, are indirect defenses, which attract the natural enemies of herbivores. R gene-mediated defenses against herbivores are also discussed.

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Studies on diversity of higher fungi in Yunnan, southwestern China: A review
Bang Feng, Zhuliang Yang
Plant Diversity    2018, 40 (04): 165-171.   doi: 10.1016/j.pld.2018.07.001
Abstract130)      PDF (796KB)(147)       Save

Yunnan is exceedingly rich in higher fungi (Ascomycota and Basidiomycota). Given that the number of fungi (including lichens) occurring in a given area is, as Hawksworth suggested, roughly six times that of local vascular plants, a total of approximately 104,000 fungal species would be expected in Yunnan. However, to date only about 6000 fungal species, including roughly 3000 species of higher fungi, have been reported from the province. Although studies on Yunnan's fungi started in the late nineteenth century, significant progress has been made only in the last forty-five years. Over the first twenty-five years of this period, studies on fungal diversity in this area have largely been about taxonomy based on morphological characters and partially on geographical distribution. Over the past twenty years, the combination of both morphological and molecular phylogenetic approaches has become the preferred method to help understand the diversity and evolution of higher fungi. This review focuses on our current knowledge of how geological, geographical, and ecological factors may have contributed to the diversity patterns of higher fungi in Yunnan. Based on this knowledge, three aspects for future studies are suggested.

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The role of botanical gardens in scientific research, conservation, and citizen science
Gao Chen, Weibang Sun
Plant Diversity    2018, 40 (04): 181-188.   doi: 10.1016/j.pld.2018.07.006
Abstract127)      PDF (7787KB)(207)       Save

Plant diversity is currently being lost at an unprecedented rate, resulting in an associated decrease in ecosystem services. About a third of the world's vascular plant species face the threat of extinction due to a variety of devastating activities, including, over-harvesting and over exploitation, destructive agricultural and forestry practices, urbanization, environmental pollution, land-use changes, exotic invasive species, global climate change, and more. We therefore need to increase our efforts to develop integrative conservation approaches for plant species conservation. Botanical gardens devote their resources to the study and conservation of plants, as well as making the world's plant species diversity known to the public. These gardens also play a central role in meeting human needs and providing well-being. In this minireview, a framework for the integrated missions of botanical gardens, including scientific research, in/ex situ conservation, plant resource utilization, and citizen science are cataloged. By reviewing the history of the development of Kunming Botanical Garden, we illustrate successful species conservation approaches (among others, projects involving Camellia, Rhododendron, Magnolia, Begonia, Allium, Nepenthes, medicinal plants, ornamental plants, and Plant Species with Extreme Small Populations), as well as citizen science, and scientific research at Kunming Botanical Garden over the past 80 years. We emphasize that Kunming Botanical Garden focuses largely on the ex situ conservation of plants from Southwest China, especially those endangered, endemic, and economically important plant species native to the Yunnan Plateau and the southern Hengduan Mountains. We also discuss the future challenges and responsibilities of botanical gardens in a changing world, including:the negative effects of outbreeding and/or inbreeding depression; promoting awareness, study, and conservation of plant species diversity; accelerating global access to information about plant diversity; increasing capacity building and training activities. We hope this minireview can promote understanding of the role of botanical gardens.

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Current progress and future prospects in phylofloristics
Rong Li, Lishen Qian, Hang Sun
Plant Diversity    2018, 40 (04): 141-146.   doi: 10.1016/j.pld.2018.07.003
Abstract123)      PDF (1690KB)(197)       Save

The species composition of regional plant assemblages can in large part be explained by a long history of biogeographical and evolutionary events. Traditional attempts of floristic studies typically focus on the analyses of taxonomic composition, often ignoring the rich context that evolutionary history can provide. In 2014, Swenson and Umaña introduced the term ‘phylofloristics’ to define a phylogenetically enabled analysis of the species composition of regional floras. Integrating phylogenetic information into traditional floristic analysis can provide a promising way to explore the ecological, biogeographic, and evolutionary processes that drive plant assemblies at multiple spatial scales. In this review, we summarize the current progress on the phylogenetic structure, spatial phylogenetic pattern, origin and diversification, phylogenetic regionalization of floristic assemblages, and application of phylogenetic information in biodiversity conservation. These summaries highlight the importance of incorporating phylogenetic information to improve our understanding of floristic assembly from an evolutionary perspective. The review ends with a brief outlook on future challenges for phylofloristic studies, including generating a highly resolved species-level phylogenetic tree, compiling detailed and refined information regarding the geographic distribution of all plant life, extracting trait information from publications and herbarium specimens, and developing technological and methodological approaches for big data analysis.

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Taxonomy in the Kunming Institute of Botany (KIB): Progress during the past decade (2008-2018) and perspectives on future development
Xiangqin Yu, Chunlei Xiang, Hua Peng
Plant Diversity    2018, 40 (04): 147-157.   doi: 10.1016/j.pld.2018.07.002
Abstract112)      PDF (8017KB)(182)       Save

The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of "integrative taxonomy." Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.

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Physiological diversity of orchids
Shibao Zhang, Yingjie Yang, Jiawei Li, Jiao Qin, Wei Zhang, Wei Huang, Hong Hu
Plant Diversity    2018, 40 (04): 196-208.   doi: 10.1016/j.pld.2018.06.003
Abstract109)      PDF (9766KB)(177)       Save

The Orchidaceae is a diverse and wide spread family of flowering plants that are of great value in ornamental, medical, conservation, and evolutionary research. The broad diversity in morphology, growth form, life history, and habitat mean that the members of Orchidaceae exhibit various physiological properties. Epiphytic orchids are often characterized by succulent leaves with thick cell walls, cuticles, and sunken stomata, whereas terrestrial orchids possess rhizomes, corms, or tubers. Most orchids have a long juvenile period, slow growth rate, and low photosynthetic capacity. This reduced photosynthetic potential can be largely explained by CO2 diffusional conductance and leaf internal structure. The amount of light required for plant survival depends upon nutritional mode, growth form, and habitat. Most orchids can adapt to their light environments through morphological and physiological adjustments but are sensitive to sudden changes in irradiance. Orchids that originate from warm regions are susceptible to chilling temperatures, whereas alpine members are vulnerable to high temperatures. For epiphytic orchids, rapid water uptake by the velamen radicum, water storage in their pseudobulbs and leaves, slow water loss, and Crassulacean Acid Metabolism contribute to plant-water balance and tolerance to drought stress. The presence of the velamen radicum and mycorrhizal fungi may compensate for the lack of root hairs, helping with quick absorbance of nutrients from the atmosphere. Under cultivation conditions, the form and concentration of nitrogen affect orchid growth and flowering. However, the limitations of nitrogen and phosphorous on epiphytic orchids in the wild, which require these plants to depend on mycorrhizal fungi for nutrients throughout the entire life cycle, are not clearly understood. Because they lack endosperm, seed germination depends upon obtaining nutrients via mycorrhizal fungi. Adult plants of some autotrophic orchids also gain carbon, nitrogen, phosphorus, and other elements from their mycorrhizal partners. Future studies should examine the mechanisms that determine slow growth and flower induction, the physiological causes of variations in flowering behavior and floral lifespan, the effects of nutrients and atmospheric-nitrogen deposition, and practical applications of mycorrhizal fungi in orchid cultivation.

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Plant phylogenomics based on genome-partitioning strategies: Progress and prospects
Xiangqin Yu, Dan Yang, Cen Guo, Lianming Gao
Plant Diversity    2018, 40 (04): 158-164.   doi: 10.1016/j.pld.2018.06.005
Abstract107)      PDF (355KB)(128)       Save

The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genomepartitioning approaches in plant phylogenomics:genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.

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Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains
Shuai Chang, Jianguo Chen, Jianqiang Su, Yang Yang, Hang Sun
Plant Diversity    2018, 40 (05): 209-216.   doi: 10.1016/j.pld.2018.09.003
Abstract95)      PDF (8500KB)(47)       Save

Positive associations between alpine cushion plants and other species have been extensively studied. However, almost all studies have focused on the associations between macrofauna. Studies that have investigated positive associations between alpine cushion plants and rhizospheric microbes have been limited to the vegetation growing season. Here, we asked whether the positive effects that alpine cushion plants confer on rhizospheric microbe communities vary with seasons. We assessed seasonal variations in the bacterial diversity and composition in rhizosphere of two alpine cushion plants and surrounding bare ground by employing a high throughput sequencing method targeting the V3 region of bacterial 16S rRNA genes. Soil properties of the rhizosphere and the bare ground were also examined. We found that cushion rhizospheres harbored significantly more C, N, S, ammonia nitrogen, and soil moisture than the bare ground. Soil properties in cushion rhizospheres were not notably different, except for soil pH. Bacterial diversities within the same microhabitats did not vary significantly with seasons. We concluded that alpine cushion plants had positive effects on the rhizospheric bacterial communities, even though the strength of the effect varied in different cushion species. Cushion species and the soil sulfur content were probably the major factors driving the spatial distribution and structure of soil bacterial communities in the alpine communities dominated by cushion plants.

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The first complete plastid genome of Burmannia disticha L. from the mycoheterotrophic monocot family Burmanniaceae
Liuqing Ma, Pengfei Ma, Dezhu Li
Plant Diversity    2018, 40 (05): 232-237.   doi: 10.1016/j.pld.2018.07.004
Abstract55)      PDF (1924KB)(113)       Save

Burmanniaceae is one major group within the monocot order Dioscoreales that has not had its plastome sequenced. Members of Burmanniaceae are mostly achlorophyllous, although the genus Burmannia also includes autotrophs. Here, we report sequencing and analysis of the first Burmanniaceae plastid genome from Burmannia disticha L.. This plastome is 157,480 bp and was assembled as a circular sequence with the typical quadripartite structure of plant plastid genomes. This plastome has a regular number of potentially functional genes with a total of 111, including 78 protein coding genes, 4 ribosomal RNA (rRNA) genes, and 29 tRNA genes. The ratio of the total length of genic:intergenic DNA is 1.58:1, and the mean length of intergenic regions is 398 bp, the longest being 1918 bp. The overall GC content of the B. disticha plastome is 34.90%, and the IR regions in B. disticha are more GC rich (39.50%) than the LSC (32.30%) and SSC (28.80%) regions. Phylogenetic analysis of protein-coding sequences from plastomes of related species in the order Dioscoreales support a clade comprising Burmanniaceae and Dioscoreaceae. This phylogenetic placement is congruent with previous findings based on nuclear and mitochondrial evidence.

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Fast and abundant in vitro spontaneous haustorium formation in root hemiparasitic plant Pedicularis kansuensis Maxim. (Orobanchaceae)
Lei Xiang, Yanmei Li, Xiaolin Sui, Airong Li
Plant Diversity    2018, 40 (05): 226-231.   doi: 10.1016/j.pld.2018.07.005
Abstract40)      PDF (2107KB)(71)       Save

Haustorium formation is the characteristic feature of all parasitic plants and a vital process for successful parasitism. Previous investigations on haustorium initiation and development are constricted to induced processes by host-derived signals or synthetic analogs. Spontaneous haustorium formation in the absence of host signals, a process representing an early stage in the evolution of parasitic plants, remains largely unexplored. Lack of fast and frequent formation of spontaneous haustoria greatly hinders full understanding of haustorium formation in root hemiparasites. In this study, seedlings of Pedicularis kansuensis Maxim., a facultative root hemiparasitic species in Orobanchaceae observed to produce many spontaneous haustoria, were grown in autoclaved water agar in the absence of any known haustoriuminducing stimulants. We aimed to test the temporal and developmental pattern of spontaneous haustorium formation. Also, effects of sucrose supply and root contact on spontaneous haustorium formation were tested. Spontaneous haustoria were observed starting from six days after germination, much earlier than previously reported root hemiparasites. A majority of the spontaneous haustoria formed on lateral roots. Percentage of seedlings with spontaneous haustoria was 28.8% when grown on water agar plates, with a mean of four haustoria per seedling two weeks after germination. Haustorium formation by seedlings grown in water agar amended with 2% sucrose was more than twice of those without sucrose amendment. Singly grown seedlings were able to develop spontaneous haustoria at similar levels as those grown with another conspecific seedling. In view of the fast and abundant formation of spontaneous haustoria, P. kansuensis may be developed as an excellent experimental system in future investigations for unraveling endogenous regulation of haustorium initiation and development in root hemiparasitic plants.

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Mapping and breeding value evaluation of a semi-dominant semidwarf gene in upland rice
Xiaoqian Chen, Peng Xu, Jiawu Zhou, Dayun Tao, Diqiu Yu
Plant Diversity    2018, 40 (05): 238-244.   doi: 10.1016/j.pld.2018.09.001
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Plant height is an important trait related to yield potential and plant architecture. A suitable plant height plays a crucial role in improvement of rice yield and lodging resistance. In this study, we found that the traditional upland landrace ‘Kaowenghan’ (KWH) showed a special semi-dwarf phenotype. To identify the semi-dwarf gene from KWH, we raised BC2F4 semi-dwarf introgression lines (IL) by hybridization of the japonica rice cultivar ‘Dianjingyou1’ (DJY1) and KWH in a DJY1 background. The plant height of the homozygous semi-dwarf IL (IL-87) was significantly reduced compared with that of DJY1. The phenotype of the F1 progeny of the semi-dwarf IL-87 and DJY1 showed that the semi-dwarf phenotype was semidominant. QTL mapping indicated that the semi-dwarf phenotype was controlled by a major QTL qDH1 and was localized between the markers RM6696 and RM12047 on chromosome 1. We also developed near-isogenic lines (NIL) from the BC3F3 population, and found that the yield of homozygous NIL (NIL-2) was not significantly different compared to DJY1. Breeding value evaluation through investigation of the plant height of the progeny of NIL (NIL-2) and cultivars from different genetic background indicate that the novel semi-dwarf gene shows potential as a genetic resource for rice breeding.

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Diversity of desert rangelands of Tunisia
Mouldi Gamoun, Azaiez Ouled Belgacem, Mounir Louhaichi
Plant Diversity    2018, 40 (05): 217-225.   doi: 10.1016/j.pld.2018.06.004
Abstract38)      PDF (64502KB)(28)       Save

Plants are important components of any rangeland. However, the importance of desert rangeland plant diversity has often been underestimated. It has been argued that desert rangelands of Tunisia in good ecological condition provide more services than those in poor ecological condition. This is because rangelands in good condition support a more diverse mixture of vegetation with many benefits, such as forage for livestock and medicinal plants.
Nearly one-quarter of Tunisia, covering about 5.5 million hectares, are rangelands, of which 87% are located in the arid and desert areas (45% and 42%, respectively). Here, we provide a brief review of the floristic richness of desert rangelands of Tunisia. Approximately 135 species are specific to desert rangelands. The predominant families are Asteraceae, Poaceae, Brassicaceae, Chenopodiaceae, and Fabaceae. These represent approximately 50% of Tunisian desert flora.

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Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library of Cycas debaoensis
Yunhua Wang, Nan Li, Ting Chen, Yiqing Gong
Plant Diversity    2018, 40 (05): 245-252.   doi: 10.1016/j.pld.2018.09.002
Abstract37)      PDF (1879KB)(20)       Save

A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5' end of the RNA Transcript) technique. The titer of the original cDNA library was about 1.5×106 cfu·mL-1 and the average insertion size was about 1 kb with a high recombination rate (97%). The 5011 high-quality expressed sequence tags (ESTs) were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 (50.1%) unigenes were associated with 4082 Gene Ontology (GO) terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups (COG) functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase (RLK) genes were screened. Furthermore, a total of 94 simple sequence repeats (SSRs) were discovered, of which 20 loci were successfully amplified in C. debaoensis. This study is the first EST analysis for the coralloid roots of C. debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C. debaoensis and related cycad species.

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Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae
Ruisen Lu, Wuqin Xu, Qixiang Lu, Pan Li, Jocelyn Losh, Faiza Hina, Enxiang Li, Yingxiong Qiu
Plant Diversity    2018, 40 (06): 253-264.   doi: 10.1016/j.pld.2018.11.006
Abstract30)      PDF (3630KB)(47)       Save
The genus Croomia (Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia (EA) eEastern North America (ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study, we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala (ChFlower), flowers of C. japonica (CjFlower), and leaves of C. japonica (CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes (SCNGs) and 21,460 expression sequence tags-simple sequence repeats (ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade (SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
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Phospholipase D antagonist 1-butanol inhibited the mobilization of triacylglycerol during seed germination in Arabidopsis
Yanxia Jia, Weiqi Li
Plant Diversity    2018, 40 (06): 292-298.   doi: 10.1016/j.pld.2018.11.002
Abstract14)      PDF (9675KB)(0)       Save
Storage oil breakdown plays an important role in the life cycle of many plants by providing the carbon skeletons that support seedling growth immediately following germination. 1-Butanol, a specific inhibitor of phospholipase D (PLD)-dependent production of the signalling molecule phosphatidic acid (PA), inhibited Arabidopsis seed germination. N-Acylethanolamines (NAEs), which have been shown to inhibits PLDα1 activity, have no effect on seed germination. However, mobilization profile of triacylglycerols (TAG) that induced by each compound has not been reported. To gain deeper insights into the mode of mobilization of TAG during NAE 12:0 or 1-butanol treatment, we conducted a detailed comparative analysis of the effect of NAE 12:0, DMSO, 1-butanol and tert-butanol on Arabidopsis seed germination and fatty acid composition, tert-butanol and DMSO served as the corresponding controls treatment respectively. Our data show that 1-butanol, but not the inactive tert-butanol isomer, inhibited Arabidopsis seed germination, which is accompanied by a with retardation of the mobilization of triacylglycerols (TAG). In contrast, NAE 12:0 did not affect mobilization of TAG, nor did it significantly delay seed germination as monitored by radicle and cotyledon emergence. 1-Butanol induced RNA degradation in seeds and seedlings. We speculate that the large-scale degradation of RNA under the induction of 1-butanol may lead to abnormal gene expression in genes necessary for seed germination, including the genes needed for the mobilization of oil bodies, and thus cause a delay of seed germination. To the best of our knowledge, we report for the first time that 1-butanol delays the mobilization of TAG.
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Factors limiting the recruitment of Quercus schottkyana, a dominant evergreen oak in SW China
Ke Xia, Roy Turkington, Hong-yu Tan, Lei Fan
Plant Diversity    2018, 40 (06): 277-283.   doi: 10.1016/j.pld.2018.11.004
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Quercus schottkyana is a dominant species of oak in the Asian evergreen broad-leaved forests in southwestern China but seedlings are uncommon and recruitment is rare. Annual acorn production by Q. schottkyana is variable and the acorns are exposed to a series of mortality risks. Understanding the factors that limit recruitment of the oak requires knowledge of the oak's life cycle from acorn production to germination and seedling establishment. In this study, we first tested the effects of acorn density on establishment of seedlings by placing batches of acorns at different densities throughout the study area. Second, we tested the effects of herbivores on seedling survival by erecting fences around both natural and transplanted seedling populations. Our results show that even though the rate of seedling establishment increases as acorn density increases (for 32-8000 acorns·m-2), survival rates of seedlings in the field were generally low (0-0.6%). We show that seedling recruitment of Q. schottkyana is mainly limited to the acorn stage where 88% of the acorns died from the combined effects of desiccation and predation by weevils (Curculio) and bark beetles (Coccotrypes sp.). Herbivory results in the death of some seedlings and consequently also affects the recruitment of seedlings of Q. schottkyana.
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The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)
Changkun Liu, Zhenyan Yang, Lifang Yang, Junbo Yang, Yunheng Ji
Plant Diversity    2018, 40 (06): 265-276.   doi: 10.1016/j.pld.2018.11.001
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Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine proteincoding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.
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Morphological plasticity and adaptation level of distylous Primula nivalis in a heterogeneous alpine environment
Aysajan Abdusalam, Qingjun Li
Plant Diversity    2018, 40 (06): 284-291.   doi: 10.1016/j.pld.2018.11.003
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Plant populations at high elevation face extreme climatic conditions and resource limitations. The existence of distylous species at different elevations can help us investigate their adaptation to high altitudes, the evolution of their morphological characteristics, as well as their responses to limited resources. Here, 17 populations of Primula nivalis at different elevations were evaluated regarding variations in plant morphological characteristics, biomass allocation, and morphological plasticity in a heterogeneous environment. Our results demonstrate that heterogeneous environments can affect plant morphological characteristics and resource allocation in each sexual morph of these plants. Moreover, environmental variations reduced morphological plasticity in the two plant morphs, and the plasticity of long style (LS) plants was greater than that of short style (SS) plants. There were significant negative correlations between morphological characteristics and elevation, rainfall, temperature, and sunshine, and these are the main variables that affect morphological characteristics and resource allocation of both morphs of P. nivalis plants in heterogeneous environments. The morphological characteristics of P. nivalis plants transplanted from high to lower elevations were not significantly different in either population. LS plants had greater morphological plasticity and adaptability in heterogeneous environments than SS plants. Elevational gradients and heterogeneous environments differentiated both morphs of P. nivalis plants with regards to morphology as well as adaptations. LS plants showed a higher level of adaptability than SS plants.
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