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Abstract Background Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. Description Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses. Conclusion OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.

Cymbidium sinense is one of the most important traditional Chinese Orchids due to its unique and highly ornamental floral organs. Although the ABCDE model for flower development is well-established in model plant species, the precise roles of these genes in C. sinense are not yet fully understood. In this study, four SEPALLATA-like genes were isolated and identified from C. sinense. CsSEP1 and CsSEP3 were grouped into the AGL9 clade, while CsSEP2 and CsSEP4 were included in the AGL2/3/4 clade. The expression pattern of CsSEP genes showed that they were significantly accumulated in reproductive tissues and expressed during flower bud development but only mildly detected or even undetected in vegetative organs. Subcellular localization revealed that CsSEP1 and CsSEP4 were localized to the nucleus, while CsSEP2 and CsSEP3 were located at the nuclear membrane. Promoter sequence analysis predicted that CsSEP genes contained a number of hormone response elements (HREs) and MADS-box binding sites. The early flowering phenotype observed in transgenic Arabidopsis plants expressing four CsSEP genes, along with the expression profiles of endogenous genes, such as SOC1, LFY, AG, FT, SEP3 and TCPs, in both transgenic Arabidopsis and C. sinense protoplasts, suggested that the CsSEP genes played a regulatory role in the flowering transition by influencing downstream genes related to flowering. However, only transgenic plants overexpressing CsSEP3 and CsSEP4 caused abnormal phenotypes of floral organs, while CsSEP1 and CsSEP2 had no effect on floral organs. Protein-protein interaction assays indicated that CsSEPs formed a protein complex with B-class CsAP3-2 and CsSOC1 proteins, affecting downstream genes to regulate floral organs and flowering time. Our findings highlighted both the functional conservation and divergence of SEPALLATA-like genes in C. sinense floral development. These results provided a valuable foundation for future studies of the molecular network underlying floral development in C. sinense.

Transcription factors (TFs) of the WRKY family play pivotal roles in defense responses and secondary metabolism of plants. Although WRKY TFs are well documented in numerous plant species, no study has performed a genome-wide investigation of the WRKY gene family in Cymbidium sinense. In the present work, we found 64 C. sinense WRKY (CsWRKY) TFs, and they were further divided into eight subgroups. Chromosomal distribution of CsWRKYs revealed that the majority of these genes were localized on 16 chromosomes, especially on Chromosome 2. Syntenic analysis implied that 13 (20.31%) genes were derived from segmental duplication events, and 17 orthologous gene pairs were identified between Arabidopsis thaliana WRKY (AtWRKY) and CsWRKY genes. Moreover, 55 of the 64 CsWRKYs were detectable in different plant tissues in response to exposure to plant hormones. Among them, Group III members were strongly induced in response to various hormone treatments, indicating their potential essential roles in hormone signaling. We subsequently analyzed the function of CsWRKY18 in Group III. The CsWRKY18 was localized in the nucleus. The constitutive expression of CsWRKY18 in Arabidopsis led to enhanced sensitivity to ABA-mediated seed germination and root growth and elevated plant tolerance to abiotic stress within the ABA-dependent pathway. Overall, our study represented the first genome-wide characterization and functional analysis of WRKY TFs in C. sinense, which could provide useful clues about the evolution and functional description of CsWRKY genes.

Heavy metal pollution in agricultural soil has a wide range of sources and an enormous scope of influence, bringing about severe environmental risk. In this study, we used Pearson correlation analysis, combined with principal component and cluster analysis (PCA/CA) to comprehensively analyze the sources of soil heavy metal contamination in a mango plantation area in Panzhihua City. We performed a spatial distribution of heavy metal contamination levels via ArcGIS for single factor and Nemerow Contamination Index. The results showed that PTEs exceeded background values of soil pollution in Sichuan Province. The enrichment of Cr, Ni and Zn were caused by the development of local industry. Cu is mainly from atmospheric dust. Various pollution sources controlled the accumulation of Cd, whereas that of As and Pb were related to agricultural activities and transportation. The spatial distribution of the pollution indices indicated that the soil in the study area was mild to severe pollution with compound PTEs. Chemical speciation analysis showed that the ecological risk of PTEs enrichment in the study area was slight. This study highlights the geographic distribution of heavy metal contamination levels and source resolution, providing targeting for local regulatory authorities to improve soil environmental quality. [ABSTRACT FROM AUTHOR]

This study collected 49 topsoil samples in agricultural soil from Panxi district (Sichuan, China), investigating the contamination status and probabilistic health risk of their heavy metal(loid)s (HMs). The average concentrations (mg/kg) of As, Cd, Cr, Cu, Ni, Pb and Zn were 18.18, 1.66, 294.05, 143.37, 70.18, 31.70 and 139.18, respectively. The pollution index (Pi) of the seven HMs were in the descending order of Cd > Cr > Cu > As > Zn > Ni > Pb, and the comprehensive Nemeiro risk index (PN) was 2.67, indicating that the study area was a moderate pollution by HMs. Meanwhile, Cd showed major contribution to the soil pollution among these HMs. The spatial distribution of HMs revealed that the southwestern part of the study area was the contamination hotspots. The hazard index (Hi) for children and adults were 1.621 and 0.346, respectively, and the total non-carcinogenic risk for children exceeded the threshold of 1. The carcinogenic risks associated with Cr (adults:, children:) and Ni (adults:) far exceeded the safe level of 1E-04; Monte Carlo simulations showed that humans locating in the study area suffered from a relatively significant carcinogenic risk; and the children were at higher risk than the adults. Among the three exposure pathways (ingestion, inhalation, and dermal contact), the ingestion was the most important way for HMs to harm human health. Overall, this study provides a scientific basis for both controlling HMs contamination and reducing the potential health risks in studied soils. [ABSTRACT FROM AUTHOR]