title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1117 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Relationship between the average slope in the active commuting to and from school and fitness in adolescents: the mediator role of fatness link: https://peerj.com/articles/8824 last-modified: 2020-06-09 description: Active commuting to and from school (ACS) has been recognized as a potential tool to improve physical fitness. Thus, this study aims to test the relationships between the average slope in the ACS and physical fitness, as well as to verify the mediator role of fatness in the relationship between average slope and physical fitness. A total of 257 participants, 137 boys and 120 girls, from 22 schools belonged to first and second High School grades participated in this study. Based on self-reported measure and Google Earth, participants were grouped into the active commuter (number of trips was ≥5, and the time of the trip was ≥15 min), mixed commuter (number of weekly trips was <5, and the time spent on the trip was <15 min) and passive commuter groups (those who reported traveling regularly by car, motorcycle, or bus). Specifically, in the active commuter group, a positive association between the average slope in the ACS with fatness was found, which in turn was positively related to strength lower limbs and cardiorrespiratory fitness. The average slope was not significantly associated with physical fitness indicators. Furtheremore, fatness did not mediate the relathionship between average slope and physical fitness. This research concluded positive associations between average slope and the body fat in the ACS. The tendency of findings signal that the average slope should be taken into account along with the distance, time and frequency of the active commuting. creator: Pedro Antonio Sánchez Miguel creator: David Sánchez Oliva creator: Mikel Vaquero Solís creator: J. J. Pulido creator: Miguel Angel Tapia Serrano uri: https://doi.org/10.7717/peerj.8824 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sánchez Miguel et al. title: Plastome of the mycoheterotrophic eudicot Exacum paucisquama (Gentianaceae) exhibits extensive gene loss and a highly expanded inverted repeat region link: https://peerj.com/articles/9157 last-modified: 2020-06-09 description: Mycoheterotrophic plants are highly specialized species able to acquire organic carbon from symbiotic fungi, with relaxed dependence on photosynthesis for carbon fixation. The relaxation of the functional constraint of photosynthesis and thereby the relaxed selective pressure on functional photosynthetic genes usually lead to substantial gene loss and a highly degraded plastid genome in heterotrophs. In this study, we sequenced and analyzed the plastome of the eudicot Exacum paucisquama, providing the first plastid genome of a mycoheterotroph in the family Gentianaceae to date. The E. paucisquama plastome was 44,028 bp in length, which is much smaller than the plastomes of autotrophic eudicots. Although the E. paucisquama plastome had a quadripartite structure, a distinct boundary shift was observed in comparison with the plastomes of other eudicots. We detected extensive gene loss and only 21 putative functional genes (15 protein-coding genes, four rRNA genes and two tRNA genes). Our results provide valuable information for comparative evolutionary analyses of plastomes of heterotrophic species belonging to different phylogenetic groups. creator: Zhanghai Li creator: Xiao Ma creator: Yi Wen creator: Sisi Chen creator: Yan Jiang creator: Xiaohua Jin uri: https://doi.org/10.7717/peerj.9157 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Validation of a general subjective well-being factor using Classical Test Theory link: https://peerj.com/articles/9193 last-modified: 2020-06-09 description: BackgroundSubjective Well-Being (SWB) is usually conceptualized in terms of an affective (i.e., judgements of biological emotional reactions and experiences) and a cognitive component (i.e., judgements of life satisfaction in relation to a psychological self-imposed ideal). Recently, researchers have suggested that judgements of harmony in life can replace or at least complement the cognitive component of SWB. Here, however, we go beyond that suggestion and propose that harmony in life should be seen as SWB’s social component since it is the sense of balance between the individual and the world around her—a process that comprises acceptance, adaptation, and balance. By adding judgements of one’s social interactions (i.e., harmony in life) to judgments of one’s life satisfaction (psycho) and judgements of one’s emotional reactions (bio), we propose a tentatively biopsychosocial model of SWB. As a first step, we used different factorial models in order to determine if both a general factor and specific sub-factors contribute to the biopsychosocial model of SWB.MethodA total of 527 participants responded to the Positive Affect Negative Affect Schedule (PANAS; 20 items), the Satisfaction with Life Scale (SWLS; five items), and the Harmony in life Scale (HILS; five items). We conducted exploratory and confirmatory factor analyses to validate the biopsychosocial model of subjective well-being and a general factor (SWBS).ResultsThe 20 PANAS items reflected a mixture of general latent structure saturation and specific latent structure saturation, but contributed to their respective specific latent factor (PA: 48%; NA: 49%) more than to the general latent SWBS factor (positive affect: 25%; negative affect: 32%). The five SWLS items contributed to a larger degree to the general SWBS factor (72%) than to life satisfaction itself (22%), while the five HILS items contributed to even a larger degree to the general SWBS factor (98%) than to harmony in life (0%). The bifactor model was the best model compared with all other models we tested (χ2 = 1,660.78, df = 375, p < 0.001); Satorra Bentler χ2 = 1,265.80, df = 375, p < 0.001; CFI = 0.92; Tucker–Lewis Index = 0.91; RMSEA = 0.067. This model of a general SWBS factor explained about 64% of the total variance in the model, while specific SWBS components together explained 15% of the total variance.ConclusionOur study suggests SWB as a general factor in a multidimensional biopsychosocial model. Indeed, as much as 64% of the variance of SWB was explained by this general factor. The SWB components, however, contributed to a different degree to each corresponding factor in the model. For instance, while the affective and cognitive components seem to be their own constructs and also part of the general SWB factor, the social component tested here contributed 0% to its own variance but 98% to the general factor. creator: Ali Al Nima creator: Kevin M. Cloninger creator: Franco Lucchese creator: Sverker Sikström creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.9193 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Nima et al. title: Silicon induces hormetic dose-response effects on growth and concentrations of chlorophylls, amino acids and sugars in pepper plants during the early developmental stage link: https://peerj.com/articles/9224 last-modified: 2020-06-09 description: BackgroundSilicon (Si) is a beneficial element that has been proven to influence plant responses including growth, development and metabolism in a hormetic manner.MethodsIn the present study, we evaluated the effect of Si on the growth and concentrations of chlorophylls, total amino acids, and total sugars of pepper plants (Capsicum annuum L.) during the early developmental stage in a hydroponic system under conventional (unstressed) conditions. We tested four Si concentrations (applied as calcium silicate): 0, 60, 125 and 250 mg L−1, and growth variables were measured 7, 14, 21 and 28 days after treatment (dat), while biochemical variables were recorded at the end of the experiment, 28 dat.ResultsThe application of 125 mg L−1 Si improved leaf area, fresh and dry biomass weight in leaves and stems, total soluble sugars, and concentrations of chlorophylls a and b in both leaves and stems. The amino acids concentration in leaves and roots, as well as the stem diameter were the highest in plants treated with 60 mg L−1 Si. Nevertheless, Si applications reduced root length, stem diameter and total free amino acids in leaves and stems, especially when applied at the highest concentration (i.e., 250 mg L−1 Si).ConclusionThe application of Si has positive effects on pepper plants during the early developmental stage, including stimulation of growth, as well as increased concentrations of chlorophylls, total free amino acids and total soluble sugars. In general, most benefits from Si applications were observed in the range of 60–125 mg L−1 Si, while some negative effects were observed at the highest concentration applied (i.e., 250 mg L−1 Si). Therefore, pepper is a good candidate crop to benefit from Si application during the early developmental stage under unstressed conditions. creator: Libia Iris Trejo-Téllez creator: Atonaltzin García-Jiménez creator: Hugo Fernando Escobar-Sepúlveda creator: Sara Monzerrat Ramírez-Olvera creator: Jericó Jabín Bello-Bello creator: Fernando Carlos Gómez-Merino uri: https://doi.org/10.7717/peerj.9224 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Trejo-Téllez et al.