Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.
It is well known that mitogen‐activated protein kinase (MAPK) pathways are modules involved in the transduction of extracellular signals to intracellular targets in all eukaryotes. In plants, it has been shown that MAPKs play a role in the signalling of biotic and abiotic stresses. To characterize signalling pathways involved in heavy metal‐induced stress responses, we examine whether plant MAPKs are also involved in this process. The analyses of mRNA levels of OsMAPK genes have shown that only OsMAPK2 mRNA transcripts increased within 12 h upon CuCl 2 treatment in suspension cells and roots. An in‐gel kinase assay revealed that three protein kinases, approximate 42, 50, and 64‐kDa, were activated by CuCl 2 treatments. The approximate 42‐kDa protein kinase displayed MAPK properties. Antioxidant, GSH, prevented copper‐induced kinase activity. Furthermore, we found that rice roots underwent a rapid cell death upon this copper treatment. The copper‐induced cell death of rice roots was partially blocked by MAPK kinase inhibitor, PD98059. These results suggest that the MAPK cascades may function in the plant heavy metal induced‐signalling pathway.
In the original published version of this article, some of the language was misleading and allowed for misinterpretation of the article. In order to fix this issue, the following revisions have been made: In the Abstract, the sentence "The horizontally-transferred Phytophthora genes are abundant transposons that "transmit" exogenous gene to Phytophthora species thus bring about the gene recombination possibility" has been revised to "The horizontally-transferred Phytophthora genes are from abundant transposon activities that "transmit" exogenous genes to Phytophthora species and thus bring about the gene recombination possibility." In 2.3.5 Horizontal gene transfer, the paragraph "Most pervasive HGT genes are transposons, which is able to mobile and amplify in the host genome, which make them more prone to horizontal transfer. And horizontal transfer is an important way which wold allow the element to evade a seemingly inevitable vertical extinction in its original host lineage resulting from genetic drift, natural selection or mutational inactivation. It was result that transposition "transmitting" foreign genes to Phytophthora species from HGT" has been revised to "It is inferred that most transposons in the genome may be related to horizontal gene transfer, which is able to mobile and amplify in the host genome. And horizontal transfer is an important way which would allow the element to evade a seemingly inevitable vertical extinction in its original host lineage resulting from genetic drift, natural selection or mutational inactivation. It is speculated that transposition may serve as vectors to connect exogenous genes and Phytophthora species, which could be compared to "transmit" to Phytophthora from HGT." In 3. Conclusions, "Horizontally transferred genes in P. fragariae and P. rubi from plants, fungi, bacteria, molluscs, and insects are often transposons that impact genes involved in plant defence resistance mechanisms. Some" has been revised to "It may be postulated that HGTs in P. fragariae and P. rubi from plants, fungi, bacteria, molluscs, and insects might impact genes those are involved in plant defense mechanisms." The authors apologize for the errors. Both the HTML and PDF versions of the article have been updated to correct the errors. Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in cropsGao et al.HeliyonFebruary 23, 2021In BriefPhytophthora; Genome; Phylogenetic; Pathogenicity; Horizontally gene transfer. Full-Text PDF Open Access
Long-term grazing changes the plant diversity and their growth significantly. At the metabolite level, the contents and compositions of the specialized metabolic compounds in plants could also be altered under long-term grazing conditions. To understand the metabolic changes caused by the grazing stress, in this study, we compared the contents and compositions of major phenolic compounds, together with total flavonoid contents, in two grazing-tolerant plants, Carex duriuscula and Aster hispidus, and two grazing-non-tolerant plants, Carex pediformus and Aster alphinus, and a local native plant Stipa baicalensus under long-term grazing conditions in Mongolia. Our results showed that long-term grazing has altered the contents and compositions of phenolic compounds and flavonoids both in above-ground tissues and roots of the analyzed five plants. Interestingly, such effects could appear to differ depending on plant species. These results provide the first comparative study of metabolite changes in grazing-tolerant and grazing-non-tolerant plants under overgrazing stress in the country.
Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current next-generation sequencing platforms, many of which are already used in plant laboratories. The third part summarizes the state of orchid transcriptome and genome sequencing and illustrates current achievements. The genetic sequences currently obtained will not only provide a broad scope for the study of orchid biology, but also serves as a starting point for uncovering the mystery of orchid evolution.
Mitogen-activated protein kinase (MAPK) pathways are modules involved in the transduction of extracellular signals to intracellular targets in all eukaryotes. In plants, it has been evidenced that MAPKs play a role in the signaling of biotic and abiotic stresses, plant hormones, and cell cycle cues. However, the effect of heavy metals on plant MAPKs has not been well examined. The Northern blot analysis of OsMAPK mRNA levels has shown that only OsMAPK2, but not OsMAPK3 and OsMAPK4, expressed in suspension-cultured cells in response to 100–400 µM Cd treatments. The OsMAPK2 transcripts increased within 12 h upon 400 µM Cd treatment. In addition, we found that 42- and 50-kDa MBP kinases were significantly activated by Cd treatment in rice suspension-cultured cells. And 40-, 42-, 50- and 64-kDa MBP kinases were activated in rice roots. Furthermore, GSH inhibits Cd-induced 40-kDa MBP kinase activation. By immunoblot analysis and immunoprecipitation followed by in-gel kinase assay, we confirmed that Cd-activated 42-kDa MBP kinase is a MAP kinase. Our results suggest that a MAP kinase cascade may function in the Cd-signalling pathway in rice.
Abstract Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that defect in the ELONGATED HYPOCOTYL 5 ( HY5 ) transcription factor gene results in tolerance to Pi deficiency in Arabidopsis. The primary root length of hy5 was only slightly inhibited under Pi deficient condition and its fresh weight was significantly higher than that of wild type. The Pi deficiency-tolerant phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5slr1, without lateral roots also showed tolerance to phosphate deficiency, indicating that the tolerance of hy5 does not result from increase of external Pi uptake and may be related to internal Pi utilization or recycling. Moreover, we found that blue light negatively regulates tolerance to Pi-deficiency and that hy5 exhibits tolerance to Pi deficiency due to blockage of blue-light responses. Collectively, this study points out light quality may play an important role in the regulation of internal Pi recycling and utilization efficiency. Also, it may contribute to reducing Pi fertilizer requirements in plants through a proper illumination.
Abstract Orchid gynostemium, the fused organ of the androecium and gynoecium, and ovule development are unique developmental processes. Two DROOPING LEAF/CRABS CLAW (DL/CRC) genes, PeDL1 and PeDL2, were identified from the Phalaenopsis orchid genome and functionally characterized. Phylogenetic analysis indicated that the most recent common ancestor of orchids contained the duplicated DL/CRC-like genes. Temporal and spatial expression analysis indicated that PeDL genes are specifically expressed in the gynostemium and at the early stages of ovule development. Both PeDLs could partially complement an Arabidopsis crc-1 mutant. Virus-induced gene silencing (VIGS) of PeDL1 and PeDL2 affected the number of protuberant ovule initials differentiated from the placenta. Transient overexpression of PeDL1 in Phalaenopsis orchids caused abnormal development of ovule and stigmatic cavity of gynostemium. PeDL1, but not PeDL2, could form a heterodimer with Phalaenopsis equestris CINCINNATA 8 (PeCIN8). Paralogous retention and subsequent divergence of the gene sequences of PeDL1 and PeDL2 in P. equestris might result in the differentiation of function and protein behaviors. These results reveal that the ancestral duplicated DL/CRC-like genes play important roles in orchid reproductive organ innovation.
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