title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1114 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.) link: https://peerj.com/articles/9310 last-modified: 2020-06-10 description: Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis. creator: Weina Zhang creator: Zhongjian Chen creator: Yichen Kang creator: Yanling Fan creator: Yuhui Liu creator: Xinyu Yang creator: Mingfu Shi creator: Kai Yao creator: Shuhao Qin uri: https://doi.org/10.7717/peerj.9310 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells link: https://peerj.com/articles/9163 last-modified: 2020-06-10 description: P-glycoprotein (P-gp) is one of the highly expressed cancer cell efflux transporters that cause the failure of chemotherapy. To reverse P-gp induced multidrug resistance, we employed a flaxseed-derived lignan; secoisolariciresinol (SECO) that acts as an inhibitor of breast cancer resistance protein; another efflux transporter that shares some substrate/inhibitor specificity with P-gp. Molecular dynamics (MD) simulation identified SECO as a possible P-gp inhibitor. Comparing root mean square deviation (RMSD) of P-gp bound with SECO with that bound to its standard inhibitor verapamil showed that fluctuations in RMSD were lower in P-gp bound to SECO demonstrating higher stability of the complex of P-gp with SECO. In addition, the superimposition of P-gp structures after MD simulation showed that the nucleotide-binding domains of P-gp bound to SECO undertook a more central closer position compared with that bound to verapamil. Using rhodamine efflux assay on NCI/ADR-RES cancer cells, SECO was confirmed as a P-gp inhibitor, where cells treated with 25 or 50 µM of SECO showed significantly higher fluorescence intensity compared to control. Using MTT assay, SECO alone showed dose-dependent cytotoxicity, where 25 or 50 µM of SECO caused significantly less NCI/ADR-RES cellular viability compared to control. Furthermore, when 50 µM of SECO was added to doxorubicin (DOX), an anticancer drug, SECO significantly enhanced DOX-induced cytotoxicity compared to DOX alone. The combination index calculated by CompuSyn software indicated synergism between DOX and SECO. Our results suggest SECO as a novel P-gp inhibitor that can re-sensitize cancer cells during DOX chemotherapy. creator: Mohamed A. Morsy creator: Azza A.K. El-Sheikh creator: Ahmed R.N. Ibrahim creator: Katharigatta N. Venugopala creator: Mahmoud Kandeel uri: https://doi.org/10.7717/peerj.9163 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Morsy et al. title: Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region link: https://peerj.com/articles/9240 last-modified: 2020-06-10 description: It has been hypothesised that high-intensity fires prevent fire-dependent fynbos from being replaced by fire-avoiding subtropical thicket on dune landscapes of the Cape Floristic Region (CFR). Recent extensive fires provided an opportunity to test this hypothesis. We posit that (1) fire-related thicket shrub mortality would be size dependent, with smaller individuals suffering higher mortality than larger ones; and (2) that survival and resprouting vigour of thicket shrubs would be negatively correlated with fire severity. We assessed survival and resprouting vigour post-fire in relation to fire severity and pre-fire shrub size at two dune landscapes in the CFR. Fire severity was scored at the base of the shrub and categorised into four levels. Pre-fire size was quantified as an index of lignotuber diameter and stem count of each shrub. Resprouting vigour consisted of two variables; resprouting shoot count and resprouting canopy volume. A total of 29 species were surveyed. Post-fire survival of thicket was high (83–85%). We found that smaller shrubs did have a lower probability of post-fire survival than larger individuals but could detect no consistent relationship between shrub mortality and fire severity. Fire severity had a positive effect on resprouting shoot count but a variable effect on resprouting volume. Pre-fire size was positively related to survival and both measures of resprouting vigour. We conclude that thicket is resilient to high-severity fires but may be vulnerable to frequent fires. Prescribed high-intensity fires in dune landscapes are unlikely to reduce the extent of thicket and promote fynbos expansion. creator: Tiaan Strydom creator: Tineke Kraaij creator: Mark Difford creator: Richard M. Cowling uri: https://doi.org/10.7717/peerj.9240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Strydom et al. title: Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis) link: https://peerj.com/articles/9269 last-modified: 2020-06-10 description: BackgroundDNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention.MethodsTea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea.ResultsWe identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial species, and lay the foundation for further analysis of their functions. creator: Qian Yu creator: Chen Li creator: Jiucheng Zhang creator: Yueyue Tian creator: Hanyue Wang creator: Yue Zhang creator: Zhengqun Zhang creator: Qinzeng Xiang creator: Xiaoyang Han creator: Lixia Zhang uri: https://doi.org/10.7717/peerj.9269 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yu et al. title: DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics link: https://peerj.com/articles/9291 last-modified: 2020-06-10 description: Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets. creator: Jérémy Gauthier creator: Charlotte Mouden creator: Tomasz Suchan creator: Nadir Alvarez creator: Nils Arrigo creator: Chloé Riou creator: Claire Lemaitre creator: Pierre Peterlongo uri: https://doi.org/10.7717/peerj.9291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Gauthier et al. title: Succession of bacterial communities on carrion is independent of vertebrate scavengers link: https://peerj.com/articles/9307 last-modified: 2020-06-10 description: The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging. creator: Cody R. Dangerfield creator: Ethan H. Frehner creator: Evan R. Buechley creator: Çağan H. Şekercioğlu creator: William J. Brazelton uri: https://doi.org/10.7717/peerj.9307 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dangerfield et al. title: Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes link: https://peerj.com/articles/9311 last-modified: 2020-06-10 description: BackgroundDextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol.ResultsComparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis.ConclusionsWe used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii. creator: Zerui Yang creator: Wenli An creator: Shanshan Liu creator: Yuying Huang creator: Chunzhu Xie creator: Song Huang creator: Xiasheng Zheng uri: https://doi.org/10.7717/peerj.9311 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yang et al. title: Plasma membrane proteomic analysis by TMT-PRM provides insight into mechanisms of aluminum resistance in tamba black soybean roots tips link: https://peerj.com/articles/9312 last-modified: 2020-06-10 description: Aluminum (Al) toxicity in acid soil is a worldwide agricultural problem that inhibits crop growth and productivity. However, the signal pathways associated with Al tolerance in plants remain largely unclear. In this study, tandem mass tag (TMT)-based quantitative proteomic methods were used to identify the differentially expressed plasma membrane (PM) proteins in Tamba black soybean (TBS) root tips under Al stress. Data are available via ProteomeXchange with identifier PXD017160. In addition, parallel reaction monitoring (PRM) was used to verify the protein quantitative data. The results showed that 907 PM proteins were identified in Al-treated plants. Among them, compared to untreated plants, 90 proteins were differentially expressed (DEPs) with 46 up-regulated and 44 down-regulated (fold change > 1.3 or < 0.77, p < 0.05). Functional enrichment based on GO, KEGG and protein domain revealed that the DEPs were associated with membrane trafficking and transporters, modifying cell wall composition, defense response and signal transduction. In conclusion, our results highlight the involvement of GmMATE13, GmMATE75, GmMATE87 and H+-ATPase in Al-induced citrate secretion in PM of TBS roots, and ABC transporters and Ca2+ have been implicated in internal detoxification and signaling of Al, respectively. Importantly, our data provides six receptor-like protein kinases (RLKs) as candidate proteins for further investigating Al signal transmembrane mechanisms. creator: Yunmin Wei creator: Caode Jiang creator: Rongrong Han creator: Yonghong Xie creator: Lusheng Liu creator: Yongxiong Yu uri: https://doi.org/10.7717/peerj.9312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wei et al. title: Non-linear responses of net ecosystem productivity to gradient warming in a paddy field in Northeast China link: https://peerj.com/articles/9327 last-modified: 2020-06-10 description: Global warming has a known impact on ecosystems but there is a lack of understanding about its impact on ecosystem processes. Net ecosystem productivity (NEP) and its components play a key part in the global carbon cycle. Analysing the impact of global warming on NEP will improve our understanding of how warming affects ecosystems. In our study, conducted in 2018, five warming treatments were manipulated (0 W, 500 W, 1000 W, 1500 W, and 3000 W) using three repetitions of far infrared open warming over a paddy field in Northeast China. NEP and its two related components, gross primary productivity (GPP) and ecosystem respiration (ER), were measured using the static chamber-infrared gas analyser method to explore the effects of different warming magnitudes on NEP. Results showed that measurement dates, warming treatments, and their interactions significantly affected NEP, ER, and GPP. Warming significantly increased NEP and its components but they showed a non-linear response to different warming magnitudes. The maximum increases in NEP and its components occurred at 1500 W warming. NEP is closely related to its components and the non-linear response of NEP may have primarily resulted from that of GPP. Gradient warming non-linearly increased GPP in the paddy field studied in Northeast China, resulting in the non-linear response of NEP. This study provides a basis for predicting the responses of carbon cycles in future climate events. creator: Yulu Sun creator: Fuyao Qu creator: Xianjin Zhu creator: Bei Sun creator: Guojiao Wang creator: Hong Yin creator: Tao Wan creator: Xiaowen Song creator: Qian Chen uri: https://doi.org/10.7717/peerj.9327 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Sun et al. title: Host transcriptome-guided drug repurposing for COVID-19 treatment: a meta-analysis based approach link: https://peerj.com/articles/9357 last-modified: 2020-06-10 description: BackgroundCoronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization, and the identification of effective therapeutic strategy is a need of the hour to combat SARS-CoV-2 infection. In this scenario, the drug repurposing approach is widely used for the rapid identification of potential drugs against SARS-CoV-2, considering viral and host factors.MethodsWe adopted a host transcriptome-based drug repurposing strategy utilizing the publicly available high throughput gene expression data on SARS-CoV-2 and other respiratory infection viruses. Based on the consistency in expression status of host factors in different cell types and previous evidence reported in the literature, pro-viral factors of SARS-CoV-2 identified and subject to drug repurposing analysis based on DrugBank and Connectivity Map (CMap) using the web tool, CLUE.ResultsThe upregulated pro-viral factors such as TYMP, PTGS2, C1S, CFB, IFI44, XAF1, CXCL2, and CXCL3 were identified in early infection models of SARS-CoV-2. By further analysis of the drug-perturbed expression profiles in the connectivity map, 27 drugs that can reverse the expression of pro-viral factors were identified, and importantly, twelve of them reported to have anti-viral activity. The direct inhibition of the PTGS2 gene product can be considered as another therapeutic strategy for SARS-CoV-2 infection and could suggest six approved PTGS2 inhibitor drugs for the treatment of COVID-19. The computational study could propose candidate repurposable drugs against COVID-19, and further experimental studies are required for validation. creator: Tamizhini Loganathan creator: Srimathy Ramachandran creator: Prakash Shankaran creator: Devipriya Nagarajan creator: Suma Mohan S uri: https://doi.org/10.7717/peerj.9357 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Loganathan et al.