title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1279 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics link: https://peerj.com/articles/7558 last-modified: 2019-09-24 description: BackgroundChloroplast genomes provide insufficient phylogenetic information to distinguish between closely related sugarcane cultivars, due to the recent origin of many cultivars and the conserved sequence of the chloroplast. In comparison, the mitochondrial genome of plants is much larger and more plastic and could contain increased phylogenetic signals. We assembled a consensus reference mitochondrion with Illumina TruSeq synthetic long reads and Oxford Nanopore Technologies MinION long reads. Based on this assembly we also analyzed the mitochondrial transcriptomes of sugarcane and sorghum and improved the annotation of the sugarcane mitochondrion as compared with other species.MethodsMitochondrial genomes were assembled from genomic read pools using a bait and assemble methodology. The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.ResultsThe sugarcane mitochondrion is comprised of two independent chromosomes, for which there is no evidence of recombination. Based on the reference assembly from the sugarcane cultivar SP80-3280 the mitogenomes of four additional cultivars (R570, LCP85-384, RB72343 and SP70-1143) were assembled (with the SP70-1143 assembly utilizing both genomic and transcriptomic data). We demonstrate that the sugarcane plastome is completely transcribed and we assembled the chloroplast genome of SP80-3280 using transcriptomic data only. Phylogenomic analysis using mitogenomes allow closely related sugarcane cultivars to be distinguished and supports the discrimination between Saccharum officinarum and Saccharum cultum as modern sugarcane’s female parent. From whole chloroplast comparisons, we demonstrate that modern sugarcane arose from a limited number of Saccharum cultum female founders. Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding regions than without. We reveal one confirmed and one potential cytoplasmic male sterility (CMS) factor in the sugarcane mitochondrion, both of which are transcribed.ConclusionTranscript processing in the sugarcane mitochondrion is highly complex with diverse splice events, the majority of which span the two chromosomes. PolyA baited transcripts are consistent with the use of polyadenylation for transcript degradation. For the first time we annotate two CMS factors within the sugarcane mitochondrion and demonstrate that sugarcane possesses all the molecular machinery required for CMS and rescue. A mechanism of cross-chromosomal splicing based on guide RNAs is proposed. We also demonstrate that mitogenomes can be used to perform phylogenomic studies on sugarcane cultivars. creator: Dyfed Lloyd Evans creator: Thandekile Thandiwe Hlongwane creator: Shailesh V. Joshi creator: Diego M. Riaño Pachón uri: https://doi.org/10.7717/peerj.7558 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lloyd Evans et al. title: Tanaella quintanai, a new deep-water tanaellid (Crustacea: Peracarida: Tanaidacea) from the Colombian Caribbean Coast, with a key to the species of the genus Tanaella Norman & Stebbing, 1886 link: https://peerj.com/articles/7571 last-modified: 2019-09-24 description: A new tanaidacean, Tanaella quintanai sp. nov., is described based on specimens collected from depths of 1,598 to 2,853 m during 2014–2015. The new species appears to be most closely related to the western Atlantic species, T. kroyeri and T. mclellandi. Tanaella quintanai can be separated from the two former, as well as from the other members of the genus by a combination of characters, including (1) a labium with apical lobe bearing one blunt seta (2) a cheliped with the inner margin of the dactylus bearing a sub-proximal bipinnate seta, (3) pereopods 1−3 with basis having sub-dorsoproximal and sub-ventroproximal margins setulose, (4) pereopods 4−6 with basis having ventroproximal margin setulose, (5) pereopods 4−6 with unguis bearing two parallel rows of small setules, and (6) a pleotelson as long as pleonites 1–5 combined. A key separating the currently recognized species of Tanaella is presented. creator: Andrés G. Morales-Núñez creator: Néstor E. Ardila uri: https://doi.org/10.7717/peerj.7571 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Morales-Núñez and Ardila title: In situ growth and bioerosion rates of Lophelia pertusa in a Norwegian fjord and open shelf cold-water coral habitat link: https://peerj.com/articles/7586 last-modified: 2019-09-24 description: Coral reef resilience depends on the balance between carbonate precipitation, leading to reef growth, and carbonate degradation, for example, through bioerosion. Changes in environmental conditions are likely to affect the two processes differently, thereby shifting the balance between reef growth and degradation. In cold-water corals estimates of accretion-erosion processes in their natural habitat are scarce and solely live coral growth rates were studied with regard to future environmental changes in the laboratory so far, limiting our ability to assess the potential of cold-water coral reef ecosystems to cope with environmental changes. In the present study, growth rates of the two predominant colour morphotypes of live Lophelia pertusa as well as bioerosion rates of dead coral framework were assessed in different environmental settings in Norwegian cold-water coral reefs in a 1-year in situ experiment. Net growth (in weight gain and linear extension) of live L. pertusa was in the lower range of previous estimates and did not significantly differ between inshore (fjord) and offshore (open shelf) habitats. However, slightly higher net growth rates were obtained inshore. Bioerosion rates were significantly higher on-reef in the fjord compared to off-reef deployments in- and offshore. Besides, on-reef coral fragments yielded a broader range of individual growth and bioerosion rates, indicating higher turnover in live reef structures than off-reef with regard to accretion–bioerosion processes. Moreover, if the higher variation in growth rates represents a greater variance in (genetic) adaptations to natural environmental variability in the fjord, inshore reefs could possibly benefit under future ocean change compared to offshore reefs. Although not significantly different due to high variances between replicates, growth rates of orange branches were consistently higher at all sites, while mortality was statistically significantly lower, potentially indicating higher stress-resistance than the less pigmented white phenotype. Comparing the here measured rates of net accretion of live corals (regardless of colour morphotype) with net erosion of dead coral framework gives a first estimate of the dimensions of both processes in natural cold-water coral habitats, indicating that calcium carbonate loss through bioerosion amounts to one fifth to one sixth of the production rates by coral calcification (disregarding accretion processes of other organisms and proportion of live and dead coral framework in a reef). With regard to likely accelerating bioerosion and diminishing growth rates of corals under ocean acidification, the balance of reef accretion and degradation may be shifted towards higher biogenic dissolution in the future. creator: Janina V. Büscher creator: Max Wisshak creator: Armin U. Form creator: Jürgen Titschack creator: Kerstin Nachtigall creator: Ulf Riebesell uri: https://doi.org/10.7717/peerj.7586 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Büscher et al. title: Estimating flowering transition dates from status-based phenological observations: a test of methods link: https://peerj.com/articles/7720 last-modified: 2019-09-24 description: The scale of phenological research has expanded due to the digitization of herbarium specimens and volunteer based contributions. These data are status-based, representing the presence or absence of a specific phenophase. Modelling the progress of plant dormancy to growth and reproduction and back to dormancy requires estimating the transition dates from these status-based observations. There are several methods available for this ranging from statistical moments using the day of year to newly introduced methods using concepts from other fields. Comparing the proficiency of different estimators is difficult since true transition dates are rarely known. Here I use a recently released dataset of in-situ flowering observations of the perennial forb Echinacea angustifolia. In this dataset, due to high sampling frequency and unique physiology, the transition dates of onset, peak, and end of flowering are known to within 3 days. I used a Monte Carlo analysis to test eight different estimators across two scales using a range of sample sizes and proportion of flowering presence observations. I evaluated the estimators accuracy in predicting the onset, peak, and end of flowering at the population level, and predicting onset and end of flowering for individual plants. Overall, a method using a Weibull distribution performed the best for population level onset and end estimates, but other estimators may be more appropriate when there is a large amount of absence observations relative to presence observations. For individual estimates a method using the midway point between the first flower presence and most prior flower absence, within 7 days, is the best option as long as the restriction does not limit the final sample size. Otherwise, the Weibull method is adequate for individual estimates as well. These methods allow practitioners to effectively utilize the large amount of status-based phenological observations currently available. creator: Shawn D. Taylor uri: https://doi.org/10.7717/peerj.7720 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Taylor title: ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics link: https://peerj.com/articles/7729 last-modified: 2019-09-24 description: Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user’s needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed. creator: Marco Cacciabue creator: Anabella Currá creator: Maria I. Gismondi uri: https://doi.org/10.7717/peerj.7729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cacciabue et al. title: Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats link: https://peerj.com/articles/7743 last-modified: 2019-09-24 description: The hypothalamus has an integral role in energy homeostasis regulation, and its dysfunctions lead to the development of type 2 diabetes (T2D). Physical activity positively affects the prevention and treatment of T2D. However, there is not much information on the adaptive mechanisms of the hypothalamus. In this study, RNA sequencing was used to determine how acute exercise affects hypothalamic transcriptome from both type 2 diabetic Goto-Kakizaki (GK) and control Wistar rats with or without a single session of running (15 m/min for 60 min). Through pairwise comparisons, we identified 957 differentially expressed genes (DEGs), of which 726, 197, and 98 genes were found between GK and Wistar, exercised GK and GK, and exercised Wistar and Wistar, respectively. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that lipid metabolism-related terms and pathways were enriched in GK and exercised GK rats, and nervous system related terms and pathways were enriched in exercised GK and Wistar rats. Furthermore, 45 DEGs were associated with T2D and related phenotypes according to the annotations in the Rat Genome Database. Among these 45 DEGs, several genes (Plin2, Cd36, Lpl, Wfs1, Cck) related to lipid metabolism or the nervous system are associated with the exercise-induced benefits in the hypothalamus of GK rats. Our findings might assist in identifying potential therapeutic targets for T2D prevention and treatment. creator: Shuying Fu creator: Yuhuan Meng creator: Shudai Lin creator: Wenlu Zhang creator: Yuting He creator: Lizhen Huang creator: Hongli Du uri: https://doi.org/10.7717/peerj.7743 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Fu et al. title: Characterizing gene tree conflict in plastome-inferred phylogenies link: https://peerj.com/articles/7747 last-modified: 2019-09-24 description: Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes. creator: Joseph F. Walker creator: Nathanael Walker-Hale creator: Oscar M. Vargas creator: Drew A. Larson creator: Gregory W. Stull uri: https://doi.org/10.7717/peerj.7747 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Walker et al. title: Efficacy of Paclitaxel plus TS1 against previously treated EGFR mutated non-small cell lung cancer link: https://peerj.com/articles/7767 last-modified: 2019-09-24 description: BackgroundLater line chemotherapy (≥2nd lines) such as Docetaxel or immunotherapy is frequently used. As the life expectancy of lung cancer patients is getting longer, we need to provide more treatment options. Other treatment options are not well documented except for Doxetaxel and immunotherapy. Therefore, the efficacy of paclitaxel plus TS1 (TTS1) is warranted.MethodsWe retrospectively reviewed the chart records of our non-small cell lung cancer patients who were treated between 2010 and 2013. Clinical characteristics, type of tumor, EGFR mutation status, and treatment response to first-line EGFR-TKI therapy and efficacy of TTS1, were collected.ResultsTwenty eight patients were enrolled in this study. No patients archived complete response and seven patients had partial response (ORR: 25%). The disease control rate was 60.7% (17/28). The progression free survival (PFS) was 4.0 months and overall survival (OS) was 15.8 months. Of them, 17 had EGFR mutations, eight EGFR wild type, and three were unknown EGFR status. After TTS1 treatment, patients with EGFR mutations had better PFS (4.9 months vs. 1.8 months) and OS (15.5 months vs. 7.2 months) compared with those of EGFR wild type.ConclusionsTTS1 are effective later line chemotherapy, especially in tumor EGFR mutated patients. Paclitaxel plus TS1 is another treatment of choice for NSCLC patients before a more effective treatment strategy is found. creator: Yen-Han Tseng creator: Jen-Fu Shih creator: Heng-Sheng Chao creator: Yuh-Min Chen uri: https://doi.org/10.7717/peerj.7767 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tseng et al. title: Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth link: https://peerj.com/articles/7445 last-modified: 2019-09-23 description: Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N2-fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N2-fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N2-fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis, Fusarium graminearum, Gibberella zeae, Fusarium solani, Colletotrichum gossypii and Alternaria longipes. 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture. creator: Xiaomeng Liu creator: Qin Li creator: Yongbin Li creator: Guohua Guan creator: Sanfeng Chen uri: https://doi.org/10.7717/peerj.7445 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Evaluation of the effects of the green nanoparticles zinc oxide on monosodium glutamate-induced toxicity in the brain of rats link: https://peerj.com/articles/7460 last-modified: 2019-09-23 description: BackgroundMonosodium glutamate (MSG) is used extensively as a food additive in the diets of many countries around the world.Aim of the studyOur aim was to determine the effects of green zinc oxide nanoparticles on MSG-induced oxidative damage, neurotransmitter changes, and histopathological alternation in the cerebral cortexes of rats.MethodsMSG was administered orally at two doses of 6 and 17.5 mg/kg body weight. The higher dose was associated with a significant decline in the activities of superoxide dismutase, catalase, and glutathione peroxidase, as well as the levels of brain-derived neurotrophic factor (BDNF) and glutathione (GSH) in the cerebral cortex of rats.ResultsThe administration of zinc oxide nanoparticles/green tea extract (ZnO NPs/GTE) to 17.5 mg/kg MSG-treated rats was associated with significant improvements in all parameters previously shown to be altered by MSG. The higher dose of MSG induced significant histopathological variation in brain tissue. Co-treatment of rats with ZnO NPs/GTE and MSG-HD inhibited the reduction of neurotransmitters and acetylcholinesterase by MSG.ConclusionsZnO NPs/GTE have the potential to protect against oxidative stress and neuronal necrosis induced by MSG-HD. ZnO NPs/GTE conferred a greater benefit than the control treatment or ZnO NPs or GTE administered separately. creator: Reham Z. Hamza creator: Fawziah A. Al-Salmi creator: Nahla S. El-Shenawy uri: https://doi.org/10.7717/peerj.7460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hamza et al.