A Set of Novel Microsatellite Markers Developed for a Distylous Species Luculia gratissima (Rubiaceae)

Luculia gratissima (Wall.) Sweet (Rubiaceae) is a perennial shrub distributed in the southeast margin of the Tibetan Plateau in southwest China and adjacent region of Nepal and Myanmar. The plant is a distylous species with reciprocally placed stigmas and anthers in each floral morph. By using the Fast Isolation by Amplified Fragment Length Polymorphism (AFLP) of Sequences Containing (FIASCO) repeats protocol, 19 primer sets were identified in two wild populations. Of these primers, 10 displayed polymorphisms and nine were monomorphic. The number of alleles per locus ranged from two to five, values for observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.289 to 0.760, with averages of 0.303 and 0.555, respectively. These microsatellite loci will facilitate further studies on breeding system, gene flow patterns, and population structure of L. gratissima and its allied species

A generalized deceptive pollination system of Doritis pulcherrima (Aeridinae: Orchidaceae) with non-reconfigured pollinaria

<p>Abstract</p> <p>Background</p> <p>As one of largest angiosperm families, orchids have long fascinated evolutionary biologists with their staggering diversity in floral design and display to promote outcrossing. Two of the most intriguing aspects of orchid pollination that promote cross-pollination are pollinarium reconfiguration (PR) and deceptive pollination. PR and generalized food deception employ virtually antagonistic methods of promoting cross-pollination: PR occurs through delayed pollination, involving the relatively long visitation periods that are typically observed for the pollinators of one flower or inflorescence; conversely, generalized food deception leads to reductions in the visitation periods of pollinators to one flower or inflorescence. Thus, it is logical to hypothesize that PR is unnecessary or PR happens soon in generalized food-deceptive orchids in the promotion of cross-pollination. Using <it>Doritis pulcherrima</it> as a model, the aim of this study was to understand the following: (1) the pollination and breeding system of <it>D. pulcherrima</it>; (2) the morphological interactions between orchids and their pollinators; and (3) whether PR is necessary in the promotion of cross-pollination in <it>D. pulcherrima</it>.</p> <p>Results</p> <p>Our observations indicated that <it>Doritis pulcherrima</it> is pollinated almost exclusively by <it>Amegilla nigritar</it> (Hymenoptera: Apidae) and possesses pollinia that are deposited on the “occiputs” (cervical membranes) of these insects. All of evidences are indicated that <it>D. pulcherrima</it> is a generalized food-deceptive orchid. Our morphometric measurements of the flowers and pollinators show that the heights of the “occiputs” with un-oriented pollinaria were equal to the distances between stigmas and surfaces of the middle lobes, suggesting that pollinarium reconfiguration is not necessary in <it>Doritis pulcherrima</it>.</p> <p>Conclusions</p> <p>Our observation and analyses supported the hypothesis that pollinarium reconfiguration is unnecessary in generalized food-deceptive orchids, such as <it>Doritis pulcherrima</it>, for the promotion of cross-pollination. This conclusion was indirectly supported by the abundance of deceptive orchids that do not exhibit pollinarium reconfiguration. There are two mechanisms (i.e. clone-growing characteristics and a long flowering season) that promote fruit sets in the epiphytic food-deceptive orchids in tropical regions.</p

Hybrid minigene splicing assay verifies the pathogenicity of a novel splice site variant in the COL1A1 gene of a chinese patient with osteogenesis imperfecta type I

Abstract(#br)Background(#br)Osteogenesis imperfecta (OI) is a rare genetic bone disease associated with brittle bones and fractures. Among all known types, OI type I is the most common type and characterized by increased bone fragility, low bone mass, distinctly blue-gray sclera, and susceptibility to conductive hearing loss beginning in adolescence. Mutations in genes encoding type I collagen ( COL1A1 and COL1A2 ) contribute to the main pathogenic mechanism of OI.(#br)Methods(#br)Subtle mutation of the COL1A1 gene in the proband was detected by targeted next-generation sequencing (NGS) and confirmed by Sanger sequencing. We then assessed the effect of the mutation on the splicing of the COL1A1 gene by bioinformatics prediction and hybrid minigene splicing assay (HMSA).(#br)Results(#br)A novel splice site mutation c.1821+1 G > C was discovered in the proband by NGS and further confirmed by Sanger sequencing, which was also simultaneously identified from the proband’s mother and elder sister. Bioinformatics predicted that this mutation would result in a disappearance of the 5′ donor splice site in intron 26, thereby leading to abnormal splicing and generation of premature stop codon. The follow-up experimental data generated by HMSA was consistent with this prediction.(#br)Conclusion(#br)Our study identified a novel splice site mutation that caused OI type I in the proband by abnormal splicing and demonstrated that combined applications of NGS, bioinformatics and HMSA are comprehensive and effective methods for diagnosis and aberrant splicing study of OI

Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA

BACKGROUND: Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2)regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. CONCLUSIONS: Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification.Jingyuan Song, Linchun Shi, Dezhu Li, Yongzhen Sun, Yunyun Niu, Zhiduan Chen, Hongmei Luo, Xiaohui Pang, Zhiying Sun, Chang Liu, Aiping Lv, Youping Deng, Zachary Larson-Rabin, Mike Wilkinson and Shilin Che

The first complete plastid genome of Burmannia disticha L. from the mycoheterotrophic monocot family Burmanniaceae

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. Keywords: Burmannia disticha, Burmanniaceae, Plastome, Phylogenetic analysi

Distribution of Holttumochloa (Poaceae: Bambusoideae) in China with description of a new species revealed by morphological and molecular evidence

Holttumochloa has previously only been recorded from Malaysia. Here we describe and illustrate a new species, Holttumochloa hainanensis sp. nov., from the lowland montane forests of Diaoluo Mountain on the Island of Hainan, South China. Morphologically, H. hainanensis is similar to Holttumochloa korbuensis, but can be clearly distinguished from it in having larger culms covered by white wax, longer leaf blades, larger pseudospikelets and anthers. Furthermore, molecular phylogeny based on the nuclear gene GBSSI corroborates the identification of the new species and its affinity. The biogeographical significance of the new record of Holttumochloa in South China is also highlighted in this study

Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation

is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and th

The reproductive strategy of a pollinator-limited Himalayan plant, Incarvillea mairei (Bignoniaceae)

BACKGROUND: Plants may adapt to alpine habitats by specialization in the reproductive strategy and functional aspects of their flowers and pollination systems. Alpine habitats reduce the opportunities for cross-pollination in a relatively high proportion of alpine plant species, and self-pollination may be favored in these adverse conditions. Here, we investigated the mating system and pollination of Incarvillea mairei, a perennial Himalayan herb typically found at altitudes between 3000 and 4500 m. RESULTS: Analyses of floral morphology, observation of plant-pollinator interactions, and hand pollination experiments were conducted in three natural populations. Outcrossing rates and effective numbers of pollen donors were assessed in 45 open-pollinated families by using progeny analysis based on seven microsatellite markers. Incarvillea mairei displayed a set of apparently specialized floral traits, the stigma is sensitive to touch and close immediately and its reopening allows a second opportunity for the receipt of pollen. The species is fully self-compatible but employs a predominantly outcrossing mating system according to parentage analysis (t(m) > 0.9). Fruit set was low (26.3%), whereas seed set was high (67.2%), indicating that this species suffers pollinator limitation. Its main effective pollinator was Halictus sp., and visitation frequency was low. CONCLUSIONS: Floral features such as having a sensitive stigma and anther-prongs, in conjunction with pollinator behavior, function together contributing to a set of unique reproductive adaptations that enhance outcrossing success. The increased floral longevity and high pollination efficiency operated as compensatory mechanisms to counteract low pollinator visitation frequency

Space-Time Adaptive Processing Clutter-Suppression Algorithm Based on Beam Reshaping for High-Frequency Surface Wave Radar

In high-frequency surface wave radar (HFSWR) systems, clutter is a common phenomenon that causes objects to be submerged. Space-time adaptive processing (STAP), which uses two-dimensional data to increase the degrees of freedom, has recently become a crucial tool for clutter suppression in advanced HFSWR systems. However, in STAP, the pattern is distorted if a clutter component is contained in the main lobe, which leads to errors in estimating the target angle and Doppler frequency. To solve the main-lobe distortion problem, this study developed a clutter-suppression method based on beam reshaping (BR). In this method, clutter components were estimated and maximally suppressed in the side lobe while ensuring that the main lobe remained intact. The results of the proposed algorithm were evaluated by comparison with those of standard STAP and sparse-representation STAP (SR-STAP). Among the tested algorithms, the proposed BR algorithm had the best suppression performance and the most accurate main-lobe peak response, thereby preserving the target angle and Doppler frequency information. The BR algorithm can assist with target detection and tracking despite a background with ionospheric clutter

Content Linking for UGC based on Word Embedding Model

There are huge amounts of User Generated Contents (UGCs) consisting of authors’ articles of different themes and readers’ on-line comments on social networks every day. Generally, an article often gives rise to thousands of readers’ comments, which are related to specific points of the originally published article or previous comments. Hence it has suggested the urgent need for automated methods to implement the content linking task, which can also help other related applications, such as information retrieval, summarization and content management. So far content linking is still a relatively new issue. Because of the unsatisfactory of traditional ways based on feature extraction, we look forward to using deeper textual semantic analysis. The Word Embedding model based on deep learning has performed well in Natural Language Processing (NLP), especially in mining deep semantic information recently. Therefore, we study further on the Word Embedding model trained by different neural network models from which we can learn the structure, principles and training ways of the neural network language model in more depth to complete deep semantic feature extraction. With the aid of the semantic features, we expect to do further research on content linking between comments and their original articles from social networks, and finally verify the validity of the proposed method by comparison with traditional ways based on feature extraction