Abstract Background: Phalaenopsis is a taxonomically controversial genus and the most horticulturally valuable group in the family Orchidaceae. Inconsistencies among morphological characteristics and the lack of genomic resources have greatly impeded studies of the taxonomy and evolutionary relationships of this particular genus. The chloroplast genomes of Phalaenopsis wilsonii f. wilsonii and Phalaenopsis braceanum remains pending. Results: Here, we successfully obtained the entire chloroplast genome sequences of P. wilsonii f. wilsonii and P. braceanum and subsequently compared them with chloroplast genomes of various other species. Our aim was to enhance our understanding of the taxonomy of Phalaenopsis , as well as aid the utilization of wild orchid resources. The chloroplast genomes of Phalaenopsis wilsonii f. wilsonii and Phalaenopsis braceanum exhibited similar lengths, measuring 145,874 bp and 145,935 bp, respectively. These genomes comprised a total of 128 genes, which consisted of 75 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 7 pseudogenes. The GC content was 36.79%. By conducting a comparative analysis of these two chloroplast genomes, we observed a significant resemblance in their structural properties, amino acids frequencies, and codon usage bias. The biased usage of certain amino acid codons in deciduous orchids might be associated with their resistance to various types of adverse conditions (e.g., drought and nutrient deficiency). Among the four types simple sequence repeats (SSRs) that have been identified, A/T repeats constituted the highest occurrence. Seven protein-coding genes, including petN , psaI , psbH , psbM , rpl33 , rpl23 , and rps16 , were under positive selection.Ten InDel markers greater than 10 bp were developed and used to distinguish between these two species. Phylogenetic analysis revealed that P. braceanum was sister to P. stobariana ; the combined P. braceanum + P. stobariana clade was sister to P. wilsonii . Conclusions: Our study provided novel findings concerning the chloroplast genomes of P. wilsonii f. wilsonii and P. braceanum . Our data provide key molecular resources for Phalaenopsis species that will aid future studies of the genetic evolution and environmental adaptation of orchids. The divergent hotspots identified could be serve as valuable resources for the creation of molecular markers, enabling the identification of Phalaenopsis species and facilitating phylogenetic investigations between closely related species or individuals with morphological traits similar to those of Phalaenopsis .
Dendrobium nobile Lindl. ( D. nobile ), as an important traditional Chinese medicine and highly ornamental value plant, has attracted more and more people’s attention. In order to meet the needs of tracking and testing the growth status of D. nobile , the visible-near infrared hyperspectral imaging technology was proposed for nitrogen nutrients detection in vivo in its different growth stages. Firstly, collecting the hyperspectral images of D . nobile in spectral range 400-1000 nm. Secondly, extracting the region of interesting (ROI). The 2G-R-B algorithm was used to segment the background and plants, and then the RGB threshold method was used to separate the leaf sheath and stems. Removing noise by two masks’ or-operations, and then the ROI area was finally extracted by selecting the largest area. After that, the reflectance spectrum of the ROI area was extracted, and then two kinds of feature extraction methods and two kinds of optimizing band selection methods were researched for dimension reduction of hyperspectral images. Finally, Support vector machine (SVM) model was established to classify the nitrogen level of D. nobile . The results showed that the LDA combined with the SVM algorithm had the highest classification accuracy. The classification accuracy of training sets in the three growth stages were 97.47%, 95.03%, and 95.97%, respectively, and the classification accuracy of test set reached 97.00%, 88.8%, 92.67%. The visible-near infrared hyperspectral imaging technology combining LDA-SVM classification model could effectively distinguish D. nobile cultivated by gradient nitrogen in each growth stage. It is a potential technology applied in decision-making of precise nutrition supply. Keywords: facility gardening, hyperspectral imaging technology, Dendrobium nobile Lindl., nitrogen detection, SVM DOI:  10.33440/j.ijpaa.20200302.87  Citation: Long T, Long Y B, Liu H C, Liu H L, Wang Z H, Zhao J. Nitrogen detection of Dendrobium nobile based on hyperspectral images.  Int J Precis Agric Aviat, 2020; 3(2): 73–82.
Abelmoschus is an economically and phylogenetically valuable genus in the family Malvaceae. Owing to coexistence of wild and cultivated form and interspecific hybridization, this genus is controversial in systematics and taxonomy and requires detailed investigation. Here, we present whole chloroplast genome sequences and annotation of three important species: A . moschatus , A . manihot and A . sagittifolius , and compared with A . esculentus published previously. These chloroplast genome sequences ranged from 163121 bp to 163453 bp in length and contained 132 genes with 87 protein-coding genes, 37 transfer RNA and 8 ribosomal RNA genes. Comparative analyses revealed that amino acid frequency and codon usage had similarity among four species, while the number of repeat sequences in A . esculentus were much lower than other three species. Six categories of simple sequence repeats (SSRs) were detected, but A . moschatus and A . manihot did not contain hexanucleotide SSRs. Single nucleotide polymorphisms (SNPs) of A/T, T/A and C/T were the largest number type, and the ratio of transition to transversion was from 0.37 to 0.55. Abelmoschus species showed relatively independent inverted-repeats (IR) boundary traits with different boundary genes compared with the other related Malvaceae species. The intergenic spacer regions had more polymorphic than protein-coding regions and intronic regions, and thirty mutational hotpots (≥200 bp) were identified in Abelmoschus , such as start-psbA , atpB-rbcL , petD-exon2-rpoA , clpP-intron1 and clpP-exon2 .These mutational hotpots could be used as polymorphic markers to resolve taxonomic discrepancies and biogeographical origin in genus Abelmoschus . Moreover, phylogenetic analysis of 33 Malvaceae species indicated that they were well divided into six subfamilies, and genus Abelmoschus was a well-supported clade within genus Hibiscus .
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