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Shi, Xiao-Ling, Kang, Yang, Liu, Yu-Ying, Tu, Song, Peng, Hong-Jun, Liu, Zhong-Jian, Peng, Dong-Hui (2023): Malaxis henanensis (Orchidaceae, Malaxideae), a new species from China. Phytotaxa 589 (3): 293-295, DOI: 10.11646/phytotaxa.589.3.9, URL: http://dx.doi.org/10.11646/phytotaxa.589.3.9

The YABBY gene family plays an important role in plant growth and development, such as response to abiotic stress and lateral organ development. YABBY TFs are well studied in numerous plant species, but no study has performed a genome-wide investigation of the YABBY gene family in Melastoma dodecandrum. Therefore, a genome-wide comparative analysis of the YABBY gene family was performed to study their sequence structures, cis-acting elements, phylogenetics, expression, chromosome locations, collinearity analysis, protein interaction, and subcellular localization analysis. A total of nine YABBY genes were found, and they were further divided into four subgroups based on the phylogenetic tree. The genes in the same clade of phylogenetic tree had the same structure. The cis-element analysis showed that MdYABBY genes were involved in various biological processes, such as cell cycle regulation, meristem expression, responses to low temperature, and hormone signaling. MdYABBYs were unevenly distributed on chromosomes. The transcriptomic data and real-time reverse transcription quantitative PCR (RT-qPCR) expression pattern analyses showed that MdYABBY genes were involved in organ development and differentiation of M. dodecandrum, and some MdYABBYs in the subfamily may have function differentiation. The RT-qPCR analysis showed high expression of flower bud and medium flower. Moreover, all MdYABBYs were localized in the nucleus. Therefore, this study provides a theoretical basis for the functional analysis of YABBY genes in M. dodecandrum.

Cymbidium, which includes approximately 80 species, is one of the most ornamental and cultivated orchid genera. However, a lack of markers and sparse sampling have posed great challenges to resolving the phylogenetic relationships within the genus. In the present study, we reconstructed the phylogenetic relationships by utilizing one nuclear DNA (nrITS) and seven plastid genes (rbcL, trnS, trnG, matK, trnL, psbA, and atpI) from 70 species (varieties) in Cymbidium. We also examined the occurrence of phylogenetic conflict between nuclear (nrITS) and plastid loci and investigated how phylogenetic conflict bears on taxonomic classification within the genus. We found that phylogenetic conflict and low support values may be explained by hybridization and a lack of informative characteristics. Our results do not support previous classification of the subgenera and sections within Cymbidium. Discordance between gene trees and network analysis indicate that reticulate evolution occurred in the genus Cymbidium. Overall, our study indicates that Cymbidium has undergone a complex evolution., Highlights • A comprehensive understanding of Cymbidium phylogeny. • Reticulate evolution occurred in the genus Cymbidium. • Cymbidium has a complex evolution.

Cymbidium goeringii is one of the important ornamental orchids, but its high-quality genome has not been previously published. Here, we report a chromosome-level genome of C. goeringii and report the gene family expansion, and contraction of the C. goeringii genome and the regulation mechanism of MADS-box genes in floral organ development. We constructed the pathways of carotenoids and anthocyanins that contribute to the different flower colors of C. goeringii and the metabolic pathways of the main components of flower fragrance. Moreover, we found the genes that regulate colourful leaves and analyzed the resistance genes involved in the adaptive evolution of C. goeringii. Our results provide valuable genomic resources for the improvement of orchids and other ornamental plants.

Due to the small degree of morphological and karyotype variations, the Pleione formosana, a well-known and valuable ornamental orchid, was treated as one member of the P. bulbocodioides complex including P. bulbocodioides, P. pleionoides and P. limprichtii, as well. The taxonomy of this complex remains problematic. P. hui was described in Anfu, Jiangxi, China, but was treated as synonym of P. formosana latter, making its taxonomic status remains controversy. In this study, we used molecular, morphological and cytological analyses to identify the relationship of P. formosana and other related species. Results base on phylogenetic analyses of chloroplast DNA and nuclear ribosomal Internal Transcribed Spacer sequence datasets indicated that Anfu samples were obviously separated from the P. formosana accessions. Network analysis showed three different groups: the P. formosana group, the P. bulbocodioides complex and the hybrid group. Morphological analysis also showed that Anfu population was significantly different from other P. formosana populations. Results of chromosome ploidy analyses showed that P. formosana was diploid and Anfu population was tetraploid, indicating that they are not the same species. In conclusion, we suggest to exclude P. formosana from P. bulbocodiodes complex, and restore the speceies rank of P. hui.

Based on morphological and molecular evidence, Luisia yunnanensis (Epidendroideae, Orchidaceae), a new species from Yunnan, China, is described and illustrated. A detailed comparison between the newly discovered orchid and other members of Luisia is presented. Molecular analysis of nrITS and plastid DNA (matK, rbcL) sequence data show that L. yunnanensis is sister to L. filiformis with strong support.

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Analyses of the genome sequences and expression data for two closely related mycoheterotrophic orchid species provide insights into the genomic basis underlying the evolution of mycoheterotrophy. To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.

The basic helix-loop-helix (bHLH) transcription factors are widely distributed across eukaryotic kingdoms and participate in various physiological processes. To date, the bHLH family has been identified and functionally analyzed in many plants. However, systematic identification of bHLH transcription factors has yet to be reported in orchids. Here, 94 bHLH transcription factors were identified from the Cymbidium ensifolium genome and divided into 18 subfamilies. Most CebHLHs contain numerous cis-acting elements associated with abiotic stress responses and phytohormone responses. A total of 19 pairs of duplicated genes were found in the CebHLHs, of which 13 pairs were segmentally duplicated genes and six pairs were tandemly duplicated genes. Expression pattern analysis based on transcriptome data revealed that 84 CebHLHs were differentially expressed in four different color sepals, especially CebHLH13 and CebHLH75 of the S7 subfamily. The expression profiles of CebHLH13 and CebHLH75 in sepals, which are considered potential genes regulating anthocyanin biosynthesis, were confirmed through the qRT-PCR technique. Furthermore, subcellular localization results showed that CebHLH13 and CebHLH75 were located in the nucleus. This research lays a foundation for further exploration of the mechanism of CebHLHs in flower color formation.

Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family.

A new species, Bredia malipoensis D. H. Peng, S. Jin Zeng & Z. Y. Wen, from China, is described and illustrated here. Bredia malipoensis is morphologically similar to B. longiradiosa C. Chen in having cordate leaf blades, umbellate inflorescence and undulate petals with unguiculate bases and retuse apices. It is characterized by its terete stem and petioles, green calyx lobes, purple anthers, yellow connective appendages and white filaments. It is also morphologically similar to B. velutina Diels in having a woody stem, unequal and cordate leaf blades, but it is differentiated by having no reddish trichomes, larger and semiorbicular calyx lobes, and unguiculate petal bases. Bredia malipoensis differs markedly from the former relatives by its densely tomentose indumentum (with uniseriate non-glandular and sparse glandular trichomes) both on vegetative and floral parts, basal leaf venation and purplish-red petals. Our phylogenetic analyses using nuclear ribosomal ITS and chloroplast trnV-trnM regions strongly support the generic placement of B. malipoensis and its relatives B. longiradiosa and B. velutina within Bredia.

Melastomataceae have abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the first chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size was 299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum, Eucalyptus grandis and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. We found that the SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.

With an increase in aging populations worldwide, age-related diseases such as Alzheimer’s disease (AD) have become a global concern. At present, a cure for neurodegenerative disease is lacking. There is an urgent need for a biomarker that can facilitate the diagnosis, classification, prognosis, and treatment response of AD. The recent emergence of highly sensitive mass-spectrometry platforms and high-throughput technology can be employed to discover and catalog vast datasets of small metabolites, which respond to changed status in the body. Metabolomics analysis provides hope for a better understanding of AD as well as the subsequent identification and analysis of metabolites. Here, we review the state-of-the-art emerging candidate biomarkers for AD.

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

Paphiopedilum purpuratum, an endangered terrestrial orchid distributed in southwestern and south of China. In this study, the complete chloroplast genome (cpDNA) sequence of P. purpuratum was determined from Illumina pair-end sequencing data. With a total length of 158,459 bp in length and includes two inverted repeat regions (IRs) of 34,484 bp each, which were separated by a large single-copy region (LSC) 88,022 bp and a small single-copy region (SSC) 1,469 bp. The chloroplast genome contained 126 genes, including 74 protein conding genes,38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that P. purpuratum, P. dianthum, P. niveum, P. delenatii, and P. armeniacum cluster together, placed them within genus Paphiopedilum. The complete chloroplast genome sequence of P. purpuratum will provide a useful resource for the evolutionary biology study of phylogenetic studies in Orchidaceae.

Plants in Michelia, presented by Magnolia figo DC, are wonderful resources in Magnoliaceae, covering a series of aromatic plants. Despite extensive studies in this family, the M. figo complete chloroplast genome and the taxonomical status based on the whole chloroplast sequences remain unclear. Herein, we report the complete chloroplast genome of M. figo. The chloroplast genome was 160,113 bp in length, with a large single-copy (LSC) region of 88,113 bp and a small single-copy (SSC) region of 18,797 bp, separated by two inverted repeat (protein-coding) regions of 26,602 bp. A total of 135 CDSs were found, including 129 genes, 85 protein-coding mRNAs, 36 tRNA genes, and eight rRNA genes. The overall GC content was 39.3%, and GC percentages range from 34.3% to 43.2% throughout LSC, IRs, and SSC regions. Phylogenetic analysis showed that M. figo is most closely to Michelia odora and displayed a relationship that three Michelia were nested inside Magnolia. This announcement of the complete M. figo cp genome sequence could provide valuable information for further breeding, cp genetic modification, and phylogenetic study in Magnoliaceae.

Blastus pauciflorus, a shrub endemic to Hong Kong and Guangdong, south China, growing on low-altitude hillsides, under the forest. The species is controversial in classification. Herein, we report the complete chloroplast genome sequence assembled from Illumina pair-end sequencing data, with aims to resolve its relationship with the related species. The complete chloroplast genome was 155,983 bp in length, includes two inverted repeat regions (IRs) of 26,716 bp each, which were separated by a large single copy region (LSC) 86,101 bp and a small single copy region (SSC) 16,450 bp. The chloroplast genome contained 129 genes, including 82 protein-coding genes, 2 pseudogenes, 37 tRNA genes and 8 rRNA genes. The overall GC content in the chloroplast genome of B. pauciflorus was 37.0%. Phylogenetic analysis showed that B. pauciflorus is closed to B. cochinchinensis.

Plants in Michelia, presented by Magnolia figo DC, are wonderful resources in Magnoliaceae, covering a series of aromatic plants. Despite extensive studies in this family, the M. figo complete chloroplast genome and the taxonomical status based on the whole chloroplast sequences remain unclear. Herein, we report the complete chloroplast genome of M. figo. The chloroplast genome was 160,113 bp in length, with a large single-copy (LSC) region of 88,113 bp and a small single-copy (SSC) region of 18,797 bp, separated by two inverted repeat (protein-coding) regions of 26,602 bp. A total of 135 CDSs were found, including 129 genes, 85 protein-coding mRNAs, 36 tRNA genes, and eight rRNA genes. The overall GC content was 39.3%, and GC percentages range from 34.3% to 43.2% throughout LSC, IRs, and SSC regions. Phylogenetic analysis showed that M. figo is most closely to Michelia odora and displayed a relationship that three Michelia were nested inside Magnolia. This announcement of the complete M. figo cp genome sequence could provide valuable information for further breeding, cp genetic modification, and phylogenetic study in Magnoliaceae.

ABSTACT Phalaenopsis mannii, one of the native Phalaenopsis in China, is an important parent for breeding new varieties. However, its position has been unclear in Phalaenopsis. The obtained high-quality P. mannii chloroplast genome will provide useful information for phylogenetic and future breeding of Phalaenopsis. Herein, we reported a complete chloroplast genome of P. mannii from Yunnan, China. The sequencing data obtained from BGISEQ-500 platform were assembled. This sequence had a circular molecular length of 148,596 bp and contained a total of 127 genes with an average GC content of 36.7%. Phylogenetic analysis indicated that Phalaenopsis was monophyletic with strong support, in which the P.mannii was the sister-group of Phalaenopsis aphrodite subsp. formosas, Phalaenopsis ‘TinyStar’ and Phalaenopsis equestris.

Cymbidium maguanense is a valuable orchid endemic to China, with delicate smelling, ivory white flower, and showy yellow labellum. Herein, we reported the complete chloroplast genome of C. maguanen...

Paphiopedilum micranthum is a rare species of terrestrial herb in the Orchidaceae. It is naturally distributed in southwestern China and north of Vietnam. Here, we reported the first complete chlor...

Paphiopedilum purpuratum, an endangered terrestrial orchid distributed in southwestern and south of China. In this study, the complete chloroplast genome (cpDNA) sequence of P. purpuratum was determined from Illumina pair-end sequencing data. With a total length of 158,459 bp in length and includes two inverted repeat regions (IRs) of 34,484 bp each, which were separated by a large single-copy region (LSC) 88,022 bp and a small single-copy region (SSC) 1,469 bp. The chloroplast genome contained 126 genes, including 74 protein conding genes,38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that P. purpuratum, P. dianthum, P. niveum, P. delenatii, and P. armeniacum cluster together, placed them within genus Paphiopedilum. The complete chloroplast genome sequence of P. purpuratum will provide a useful resource for the evolutionary biology study of phylogenetic studies in Orchidaceae.

Blastus Lour. belongs to tribe Sonerileae (Melastomataceae), comprising about 18 species worldwide. Herein, we presented, assembled, and annotated the first complete chloroplast genome of Blastus (...

The plant genus Melastoma of the family Melastomataceae is comprised of nine species and one variety in China. Melastoma dodecandrum is the only creeping species of this genus. Previous study has r...

Blastus pauciflorus, a shrub endemic to Hong Kong and Guangdong, south China, growing on low-altitude hillsides, under the forest. The species is controversial in classification. Herein, we report ...

Cyphotheca, a shrub narrowly endemic to Yunnan, southwest China, is a monotypic genus of Sonerileae in Melastomataceae. The species, Cyphotheca montana, is dwindling and is listed as ‘Near Threaten...

In view of the grass-roots level radar equipment maintenance and testing difficulty is big, the efficiency is low, limited technical conditions, etc, put forward a kind of intelligent fault diagnosis expert system model suitable for the radar equipment, and focus on the basic structure of the model, knowledge acquisition and the relevant reasoning mechanism. According to the characteristics of the grass-roots level radar fault diagnosis, the system combines automatic test technology and expert system and can improve the efficiency and reliability of fault diagnosis.

The optimal group is an important problem of histogram algorithm, and how to confirm group number has not a quantitative rule. So the concept of the close degree is imported to make the close degree between the upper contour line of histogram and the PDF(probability density function) of parameter as the judging criteria of optimal group. With the unknown of the PDF of parameter, the improved kernel density estimation algorithm can pre-select and estimate the PDF. This improved kernel density estimation algorithm combine the selection of fixed window and variable window's width to achieve the window's width automatic adjustment value between the different estimation points based on the sample distribution. In the parameter analysis of radar emitter signal, the algorithm based on improved kernel density estimation and close degree is used to determine optimal group, and the result indicate that this method is effective and can search the optimal group automatically.

The CRTSⅠslab ballastless track structure was the research object of this thesis and the truck vehicle-track dynamics coupled model had established in this thesis. Germany track interference spectrum was used as the track irregularity. The study analyzed the force conditions of the CRTSⅠslab ballastless track under the action of heavy freight trains in 110km/h, as well as the wheel-rail vertical force, vertical displacement and acceleration of the rail and rail board changes with time. The results show that the CRTSⅠslab ballastless track can meet the basic requirements of freight line.

UAV system with a wireless data link for the calibration and test objects, designed and implemented a wireless data link system calibration equipment, medium-range UAV system to solve the simple means of technical support, equipment calibration testing process takes a long time, personnel, results poor reliability and accuracy problems. Test and results showed that the use of force: a reasonable system design, calibration, testing methods of science, advanced technology, stable performance, with medium-range UAV wireless data link for the key performance indicators calibration and testing functions. Keywords-unmanned aerial vehicles, wireless data link, transmit power, receiver sensitivity, bit error rate I. INTRODUCTION UAV system, wireless data link system performance impact of its operational use is always a key factor in grassroots units not equipped with the appropriate testing equipment, only use low-power near-field signal for qualitative features observed; separated by aircraft and ground stations 5 km away from the high power signal pull test, the wireless data link to a rough assessment of the technical state of the system. Sometimes the signal is unstable and smooth and can not clear why. Through to the transmit power, receive sensitivity, bit error rate measurement parameters, comprehensive and accurate assessment of the UAV data link system wireless technology performance, provide the basis for the UAV operational commanders. Medium-range UAV system to the existing test methods based qualitative test, test indicator species, a small number of test results unreliable, difficult to accurately assess medium-range UAV system-wide performance. In the medium-range UAV wireless data link control loop calibration test in the test methods introduced in order to send remote commands and receive telemetry data, through two lines to send and receive, in the process of calibration and testing form a closed signal detection loop, build a dynamic online test environment, the state controlled UAV system calibration and testing of integrated performance. Detection method to solve a single system, low accuracy, quantitative analysis of the problem can not be.

Changnienia Chien (1935: 89) is a monotypic genus of tribe Calypsoeae endemic to eastern and central China (Chen et al. 1999, 2009, Freudenstein 2005), previously with only the species C. amoena Chien (1935: 90), which was listed in the Chinese Redbook in 1992 (Fu 1992). Yang & Zhu (1984) reported a chromosome number for it of 2n=46. Sun et al. (2006) observed pollination and found that Bombus trifasciatus was its pollinator. Zhai et al. (2013) confirmed the phylogenetic placement of this species as a member of tribe Calypsoeae (sensu Pridgeon et al. 2005). A new species of Changnienia is described and illustrated here based on molecular and morphological evidence. It is discovered in Malipo, Yunnan Province, China.