title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1277 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of genes encoding ALMT and MATE transporters as candidate aluminum tolerance genes from a typical acid soil plant, Psychotria rubra (Rubiaceae) link: https://peerj.com/articles/7739 last-modified: 2019-09-25 description: To understand how tropical plants have adapted to acid soils, we analyzed the transcriptome of seedlings of Psychotria rubra, a typical species found on acid soils. Using RNA-seq, we identified 22,798 genes, including several encoding proteins of the Al3+-activated malate transporter (ALMT) and multidrug and toxic compound extrusion (MATE) families. Molecular phylogenetic analysis of ALMTs and MATEs revealed the grouping of those from P. rubra, which may be useful to select targets for elucidating the molecular basis of P. rubra adaptation to acid soils in the future. The transcriptome datasets obtained in this study would help us to further understand the physiological and ecological aspects of soil adaptation of Psychotria species. creator: Akira Iguchi creator: Kazutsuka Sanmiya creator: Kenta Watanabe uri: https://doi.org/10.7717/peerj.7739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Iguchi et al. title: Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.) link: https://peerj.com/articles/7750 last-modified: 2019-09-25 description: BackgroundStarch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism, determining amylopectin structure.MethodsFull length coding sequences (CDS) of SBE genes were cloned using reverse transcription PCR (RT-PCR) technology, and neighbor-joining (NJ) tree was used for phylogenetic analysis. Single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyze the spatial and temporal expression of NnSBE genes. The effect of NnSBE genes on amylopectin’s fine structures was explored using affinity and the enzyme activity analysis of two isoforms in amylopectin and amylose.ResultsIn this study, two SBE family genes, NnSBEI and NnSBEIII, were identified in lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis sorted NnSBEI into SBE family B and NnSBEIII into SBE family A. UPGMA phylogenetic tree divided 45 individuals of lotus into three classes. The homozygous haplotype (A G G A G) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in the middle of the development stage, while NnSBEI increased in the mid-late developmental stage. The different affinity activity of the two isozymes binding amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity.DiscussionGenetic diversity showed that NnSBE genes received artificial selection during the process of cultivation and domestication in lotus seeds. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes were related to the chain length of amylopectin. creator: Fenglin Zhu creator: Han Sun creator: Ying Diao creator: Xingwen Zheng creator: Keqiang Xie creator: Zhongli Hu uri: https://doi.org/10.7717/peerj.7750 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhu et al. title: Cloning expression and immunogenicity analysis of inhibin gene in Ye Mule Aries sheep link: https://peerj.com/articles/7761 last-modified: 2019-09-25 description: BackgroundYe Mule Aries sheep is one of the most important sheep breeds in Xinjiang, China. This breed is well adapted to harsh environmental conditions and displays strong disease resistance, fast growth, and high cold tolerance. To analyze the clonal expression and immunogenicity of the Ye Mule Aries sheep inhibin gene, total RNA was extracted from sheep ovarian tissue and used as a template to generate a eukaryotic expression vector and study inhibin immunogenicity.MethodsPrimers were designed to amplify the inhibin A gene via polymerase chain reaction and the amplified product was cloned between the ScalI and EcoRI restriction sites of the expression vector pEGFP-N1 to construct a recombinant plasmid, pEGFP-INHα. Following the validation of successful cloning, the pEGFP-INHα plasmid was transfected into BHK cells to verify expression in eukaryotes and subsequently utilized as an antigen in rabbits. Rabbits were tested for anti-inhibin antibodies and serum follicle-stimulating hormone (FSH) concentrations.ResultsThe analysis of the INHα gene sequence revealed that INHα is 1109 bp long and is translated to an approximately 40 KDa protein. Bioinformatics approach indicated that the INHα gene is highly conserved between organisms. Immunization with the eukaryotic expression vector, pEGFP-INHα, which expresses the INHα gene elicited immune response and generatigeneration on of anti-INHα antibody. The antibody had a significant regulatory effect on the serum concentration of FSH in rabbits and led to higher levels of FSH, indicating increased ovary function.ConclusionsThe present work resulted in a successful construction of eukaryotic expression plasmid pEGFP-INHα and verified the immunogenicity of this highly conserved protein. Further, the expression of pEGFP-INHα was shown to have a significant impact on the secretion of FSH, indicating a potential regulatory role in ovarian function. In conclusion, our current findings can serve as a working model for studying the effect of INHα on the breeding performance of Ye Mule Aries sheep, providing a novel strategy to improve their reproduction rates. creator: Zengwen Huang creator: Juan Zhang creator: WuReliHazi Hazihan creator: Zhengyun Cai creator: Guosheng Xin creator: Xiaofang Feng creator: Yaling Gu uri: https://doi.org/10.7717/peerj.7761 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huang et al. title: Human disturbance caused stronger influences on global vegetation change than climate change link: https://peerj.com/articles/7763 last-modified: 2019-09-25 description: Global vegetation distribution has been influenced by human disturbance and climate change. The past vegetation changes were studied in numerous studies while few studies had addressed the relative contributions of human disturbance and climate change on vegetation change. To separate the influences of human disturbance and climate change on the vegetation changes, we compared the existing vegetation which indicates the vegetation distribution under human influences with the potential vegetation which reflects the vegetation distribution without human influences. The results showed that climate-induced vegetation changes only occurred in a few grid cells from the period 1982–1996 to the period 1997–2013. Human-induced vegetation changes occurred worldwide, except in the polar and desert regions. About 3% of total vegetation distribution was transformed by human activities from the period 1982–1996 to the period 1997–2013. Human disturbances caused stronger damage to global vegetation change than climate change. Our results indicated that the regions where vegetation experienced both human disturbance and climate change are eco-fragile regions. creator: Xianliang Zhang creator: Xuanrui Huang uri: https://doi.org/10.7717/peerj.7763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang and Huang title: Development of a highly sensitive magneto-enzyme lateral flow immunoassay for dengue NS1 detection link: https://peerj.com/articles/7779 last-modified: 2019-09-25 description: BackgroundDengue infection represents a global health issue of growing importance. Dengue non-structural protein 1 (NS1) plays a central role in the early detection of the disease. The most common method for NS1 detection is testing by lateral flow immunoassays (LFIAs) with varying sensitivity. In this study, we present a highly sensitive magneto-enzyme LFIA for prompt diagnosis of dengue.MethodsWe have demonstrated the development of a magneto-enzyme LFIA combining super-paramagnetic nanoparticles as labels and Biotin–Streptavidin signal amplification strategy to detect dengue NS1. Factors affecting the test performance including antibody pair, super-paramagnetic nanoparticle size, nitrocellulose membrane type, amounts of detection and capture antibodies, and amounts of Streptavidin-polyHRP were optimized. Analytical sensitivity and cross-reactivity were determined. Clinical performance of the novel assay was evaluated using a panel of 120 clinical sera.ResultsThis newly developed assay could detect NS1 of all four serotypes of dengue virus (DENV). The limit of detection (LOD) was found to be as low as 0.25 ng ml−1 for DENV-1 and DENV-3, 0.1 ng ml−1 for DENV-2, and 1.0 ng ml−1 for DENV-4. The LOD for DENV-2 was a 50-fold improvement over the best values previously reported. There was an absence of cross-reactivity with Zika NS1, Hepatitis B virus, Hepatitis C virus, and Japanese encephalitis virus. The sensitivity and specificity of the novel assay were 100% when tested on clinical samples.ConclusionsWe have successfully developed a magneto-enzyme LFIA, allowing rapid and highly sensitive detection of dengue NS1, which is essential for proper management of patients infected with DENV. creator: Tien V. Tran creator: Ba V. Nguyen creator: Thao T.P. Nguyen creator: Tung T. Tran creator: Khanh G. Pham creator: Quang B. Le creator: Binh N. Do creator: Hung N. Pham creator: Chuyen V. Nguyen creator: Duong P.H. Dinh creator: Van T. Ha creator: Trang H.T. Doan creator: Hoa Q. Le uri: https://doi.org/10.7717/peerj.7779 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tran et al. 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.