title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=877 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz) link: https://peerj.com/articles/11780 last-modified: 2021-07-22 description: BackgroundThe YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo.MethodsIn the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments.ResultsBased on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress. creator: Ruifang Ma creator: Bin Huang creator: Zhinuo Huang creator: Zhijun Zhang uri: https://doi.org/10.7717/peerj.11780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ma et al. title: Alterations to arbuscular mycorrhizal fungal community composition is driven by warming at specific elevations link: https://peerj.com/articles/11792 last-modified: 2021-07-22 description: BackgroundGlobal warming can alter plant productivity, and community composition which has consequences for soil-plant associated microorganisms. Arbuscular mycorrhizal fungi (AMF) are distributed widely and form symbiotic relationships with more than 80% of vascular plants and play a key role in nutrient cycling processes at the ecosystem scale.MethodsA simulated warming experiment at multiple elevations (3,000, 3,500, 3,800, and 4,170 m) was conducted utilizing an in-situ open-top chamber (OTC) for exploring the effect of global warming on AMF community structure in the Qinghai-Tibet Plateau (QTP). This region has been identified as one of the most sensitive areas to climatic changes. Soil DNA was extracted and sequenced using next the Mi-Seq platform for diversity profiling.ResultsAMF richness was higher under the simulated warming chamber, however this only occurred in the elevation of 3,500 m. Warming did not alter other AMF alpha diversity indices (e.g. Shannon, Ace, and Simpson evenness index). Glomus and Acaulospora were the dominate AMF genera as assessed through their relative abundance and occurrence in control and warming treatments at the different elevations.ConclusionWarming changed significantly AMF community. The effects of warming on AMF community structure varied depend on elevations. Moreover, the occurrences of AMF in different genera were also presented the different responses to warming in four elevations. creator: Mei Yang creator: Zhaoyong Shi creator: Bede S. Mickan creator: Mengge Zhang creator: Libing Cao uri: https://doi.org/10.7717/peerj.11792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Yang et al. title: Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression link: https://peerj.com/articles/11806 last-modified: 2021-07-22 description: Turkey respiratory and gut microbiota play important roles in promoting health and production performance. Loss of microbiota homeostasis due to pathogen infection can worsen the disease or predispose the bird to infection by other pathogens. While turkeys are highly susceptible to influenza viruses of different origins, the impact of influenza virus infection on turkey gut and respiratory microbiota has not been demonstrated. In this study, we investigated the relationships between low pathogenicity avian influenza (LPAI) virus replication, cytokine gene expression, and respiratory and gut microbiota disruption in specific-pathogen-free turkeys. Differential replication of two LPAI H5N2 viruses paralleled the levels of clinical signs and cytokine gene expression. During active virus shedding, there was significant increase of ileal and nasal bacterial contents, which inversely corresponded with bacterial species diversity. Spearman’s correlation tests between bacterial abundance and local viral titers revealed that LPAI virus-induced dysbiosis was strongest in the nasal cavity followed by trachea, and weakest in the gut. Significant correlations were also observed between cytokine gene expression levels and relative abundances of several bacteria in tracheas of infected turkeys. For example, interferon γ/λ and interleukin-6 gene expression levels were correlated positively with Staphylococcus and Pseudomonas abundances, and negatively with Lactobacillus abundance. Overall, our data suggest a potential relationship where bacterial community diversity and enrichment or depletion of several bacterial genera in the gut and respiratory tract are dependent on the level of LPAI virus replication. Further work is needed to establish whether respiratory and enteric dysbiosis in LPAI virus-infected turkeys is a result of host immunological responses or other causes such as changes in nutritional uptake. creator: John M. Ngunjiri creator: Kara J.M. Taylor creator: Hana Ji creator: Michael C. Abundo creator: Amir Ghorbani creator: Mahesh KC creator: Chang-Won Lee uri: https://doi.org/10.7717/peerj.11806 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ngunjiri et al. title: Predicted distribution of a rare and understudied forest carnivore: Humboldt marten (Martes caurina humboldtensis) link: https://peerj.com/articles/11670 last-modified: 2021-07-21 description: BackgroundMany mammalian species have experienced range contractions. Following a reduction in distribution that has resulted in apparently small and disjunct populations, the Humboldt marten (Martes caurina humboldtensis) was recently designated as federally Threatened and state Endangered. This subspecies of Pacific marten occurring in coastal Oregon and northern California, also known as coastal martens, appear unlike martens that occur in snow-associated regions in that vegetation associations appear to differ widely between Humboldt marten populations. We expected current distributions represent realized niches, but estimating factors associated with long-term occurrence was challenging for this rare and little-known species. Here, we assessed the predicted contemporary distribution of Humboldt martens and interpret our findings as hypotheses correlated with the subspecies’ niche to inform strategic conservation actions.MethodsWe modeled Humboldt marten distribution using a maximum entropy (Maxent) approach. We spatially-thinned 10,229 marten locations collected from 1996–2020 by applying a minimum distance of 500-m between locations, resulting in 384 locations used to assess correlations of marten occurrence with biotic and abiotic variables. We independently optimized the spatial scale of each variable and focused development of model variables on biotic associations (e.g., hypothesized relationships with forest conditions), given that abiotic factors such as precipitation are largely static and not alterable within a management context.ResultsHumboldt marten locations were positively associated with increased shrub cover (salal (Gautheria shallon)), mast producing trees (e.g., tanoak, Notholithocarpus densiflorus), increased pine (Pinus sp.) proportion of total basal area, annual precipitation at home-range spatial scales, low and high amounts of canopy cover and slope, and cooler August temperatures. Unlike other recent literature, we found little evidence that Humboldt martens were associated with old-growth structural indices. This case study provides an example of how limited information on rare or lesser-known species can lead to differing interpretations, emphasizing the need for study-level replication in ecology. Humboldt marten conservation would benefit from continued survey effort to clarify range extent, population sizes, and fine-scale habitat use. creator: Katie M. Moriarty creator: Joel Thompson creator: Matthew Delheimer creator: Brent R. Barry creator: Mark Linnell creator: Taal Levi creator: Keith Hamm creator: Desiree Early creator: Holly Gamblin creator: Micaela Szykman Gunther creator: Jordan Ellison creator: Janet S. Prevéy creator: Jennifer Hartman creator: Raymond Davis uri: https://doi.org/10.7717/peerj.11670 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2021 Moriarty et al. title: Morphological observation and protein expression of fertile and abortive ovules in Castanea mollissima link: https://peerj.com/articles/11756 last-modified: 2021-07-21 description: Chinese chestnuts (Castanea mollissima Blume.) contain 12–18 ovules in one ovary, but only one ovule develops into a seed, indicating a high ovule abortion rate. In this study, the Chinese chestnut ‘Huaihuang’ was used to explore the possible mechanisms of ovule abortion with respect to morphology and proteomics. The morphology and microstructure of abortive ovules were found to be considerably different from those of fertile ovules at 20 days after anthesis (20 DAA). The fertile ovules had completely formed tissues, such as the embryo sac, embryo and endosperm. By contrast, in the abortive ovules, there were no embryo sacs, and wide spaces between the integuments were observed, with few nucelli. Fluorescence labelling of the nuclei and transmission electron microscopy (TEM) observations showed that cells of abortive ovules were abnormally shaped and had thickened cell walls, folded cell membranes, condensed cytoplasm, ruptured nuclear membranes, degraded nucleoli and reduced mitochondria. The iTRAQ (isobaric tag for relative and absolute quantitation) results showed that in the abortive ovules, low levels of soluble protein with small molecular weights were found, and most of differently expressed proteins (DEPs) were related to protein synthesis, accumulation of active oxygen free radical, energy synthesis and so on. These DEPs might be associated with abnormal ovules formation. creator: Bingshuai Du creator: Qing Zhang creator: Qingqin Cao creator: Yu Xing creator: Ling Qin creator: Kefeng Fang uri: https://doi.org/10.7717/peerj.11756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Du et al. title: The effects of genetic drift and genomic selection on differentiation and local adaptation of the introduced populations of Aedes albopictus in southern Russia link: https://peerj.com/articles/11776 last-modified: 2021-07-21 description: BackgroundAsian tiger mosquito Aedes albopictus is an arbovirus vector that has spread from its native habitation areal in Southeast Asia throughout North and South Americas, Europe, and Africa. Ae. albopictus was first detected in the Southern Federal District of the Russian Federation in the subtropical town of Sochi in 2011. In subsequent years, this species has been described in the continental areas with more severe climate and lower winter temperatures.MethodsGenomic analysis of pooled Ae. albopictus samples collected in the mosquito populations in the coastal and continental regions of the Krasnodar Krai was conducted to look for the genetic changes associated with the spread and potential cold adaptation in Ae. albopictus.ResultsThe results of the phylogenetic analysis based on mitochondrial genomes corresponded well with the hypothesis that Ae. albopictus haplotype A1a2a1 was introduced into the region from a single source. Population analysis revealed the role of dispersal and genetic drift in the local adaptation of the Asian tiger mosquito. The absence of shared haplotypes between the samples and high fixation indices suggest that gene flow between samples was heavily restricted. Mitochondrial and genomic differentiation together with different distances between dispersal routes, natural and anthropogenic barriers and local effective population size reduction could lead to difficulties in local climatic adaptations due to reduced selection effectiveness. We have found genomic regions with selective sweep patterns which can be considered as having been affected by recent selection events. The genes located in these regions participate in neural protection, lipid conservation, and cuticle formation during diapause. These processes were shown to be important for cold adaptation in the previous transcriptomic and proteomic studies. However, the population history and relatively low coverage obtained in the present article could have negatively affect sweep detection. creator: Evgenii A. Konorov creator: Vyacheslav Yurchenko creator: Ivan Patraman creator: Alexander Lukashev creator: Nadezhda Oyun uri: https://doi.org/10.7717/peerj.11776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Konorov et al. title: Leveraging the potential of nature to meet net zero greenhouse gas emissions in Washington State link: https://peerj.com/articles/11802 last-modified: 2021-07-21 description: The State of Washington, USA, has set a goal to reach net zero greenhouse gas emissions by 2050, the year around which the Intergovernmental Panel on Climate Change (IPCC) recommended we must limit global warming to 1.5 °C above that of pre-industrial times or face catastrophic changes. We employed existing approaches to calculate the potential for a suite of Natural Climate Solution (NCS) pathways to reduce Washington’s net emissions under three implementation scenarios: Limited, Moderate, and Ambitious. We found that NCS could reduce emissions between 4.3 and 8.8 MMT CO2eyr−1 in thirty-one years, accounting for 4% to 9% of the State’s net zero goal. These potential reductions largely rely on changing forest management practices on portions of private and public timber lands. We also mapped the distribution of each pathway’s Ambitious potential emissions reductions by county, revealing spatial clustering of high potential reductions in three regions closely tied to major business sectors: private industrial forestry in southwestern coastal forests, cropland agriculture in the Columbia Basin, and urban and rural development in the Puget Trough. Overall, potential emissions reductions are provided largely by a single pathway, Extended Timber Harvest Rotations, which mostly clusters in southwestern counties. However, mapping distribution of each of the other pathways reveals wider distribution of each pathway’s unique geographic relevance to support fair, just, and efficient deployment. Although the relative potential for a single pathway to contribute to statewide emissions reductions may be small, they could provide co-benefits to people, communities, economies, and nature for adaptation and resiliency across the state. creator: James C. Robertson creator: Kristina V. Randrup creator: Emily R. Howe creator: Michael J. Case creator: Phillip S. Levin uri: https://doi.org/10.7717/peerj.11802 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Robertson et al. title: Co-expression network and comparative transcriptome analysis for fiber initiation and elongation reveal genetic differences in two lines from upland cotton CCRI70 RIL population link: https://peerj.com/articles/11812 last-modified: 2021-07-21 description: Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω, TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development. creator: Xiao Jiang creator: Liqiang Fan creator: Pengtao Li creator: Xianyan Zou creator: Zhen Zhang creator: Senmiao Fan creator: Juwu Gong creator: Youlu Yuan creator: Haihong Shang uri: https://doi.org/10.7717/peerj.11812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Jiang et al. title: The predatory bug Orius strigicollis shows a preference for egg-laying sites based on plant topography link: https://peerj.com/articles/11818 last-modified: 2021-07-21 description: BackgroundOviposition site selection is an important factor in determining the success of insect populations. Orius spp. are widely used in the biological control of a wide range of soft-bodied insect pests such as thrips, aphids, and mites. Orius strigicollis (Heteroptera: Anthocoridae) is the dominant Orius species in southern China; however, what factor drives its selection of an oviposition site after mating currently remains unknown.MethodsHere, kidney bean pods (KBPs) were chosen as the oviposition substrate, and choice and nonchoice experiments were conducted to determine the preferences concerning oviposition sites on the KBPs of O. strigicollis. The mechanism of oviposition behavior was revealed through observation and measurement of oviposition action, the egg hatching rate, and the oviposition time.ResultsWe found that O. strigicollis preferred the seams of the pods for oviposition, especially the seams at the tips of the KBPs. Choice and nonchoice experiments showed that females did not lay eggs when the KBP tail parts were unavailable. The rates of egg hatching on different KBP parts were not significantly different, but the time required for females to lay eggs on the tip seam was significantly lower. Decreased oviposition time is achieved on the tip seam because the insect can exploit support points found there and gain leverage for insertion of the ovipositor.DiscussionThe preferences for oviposition sites of O. strigicollis are significantly influenced by the topography of the KBP surface. Revealing such behavior and mechanisms will provide an important scientific basis for the mass rearing of predatory bugs. creator: Chendi Yu creator: Jun Huang creator: Xiaoyun Ren creator: G Mandela Fernández-Grandon creator: Xiaowei Li creator: Muhammad Hafeez creator: Yaobin Lu uri: https://doi.org/10.7717/peerj.11818 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yu et al. title: A simple mechanistic model of the invasive species Heracleum sosnowskyi propagule dispersal by wind link: https://peerj.com/articles/11821 last-modified: 2021-07-21 description: BackgroundInvasive species are one of the key elements of human-mediated ecosystem degradation and ecosystem services impairment worldwide. Dispersal of propagules is the first stage of plant species spread and strongly influences the dynamics of biological invasion. Therefore, distance prediction for invasive species spread is critical for invasion management. Heracleum sosnowskyi is one of the most dangerous invasive species with wind-dispersed propagules (seeds) across Eastern Europe. This study developed a simple mechanistic model for H. sosnowskyi propagule dispersal and their distances with an accuracy comparable to that of empirical measurements.MethodsWe measured and compared the propagule traits (terminal velocity, mass, area, and wing loading) and release height for H. sosnowskyi populations from two geographically distant regions of European Russia. We tested two simple mechanistic models: a ballistic model and a wind gradient model using identical artificial propagules. The artificial propagules were made of colored paper with a mass, area, wing loading, and terminal velocity close to those of natural H. sosnowskyi mericarps.ResultsThe wind gradient model produced the best results. The first calculations of maximum possible propagule transfer distance by wind using the model and data from weather stations showed that the role of wind as a vector of long-distance dispersal for invasive Heracleum species was strongly underestimated. The published dataset with H. sosnowskyi propagule traits and release heights allows for modeling of the propagules’ dispersal distances by wind at any geographical point within their entire invasion range using data from the closest weather stations. The proposed simple model for the prediction of H. sosnowskyi propagule dispersal by wind may be included in planning processes for managing invasion of this species. creator: Ivan Chadin creator: Igor Dalke creator: Denis Tishin creator: Ilya Zakhozhiy creator: Ruslan Malyshev uri: https://doi.org/10.7717/peerj.11821 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chadin et al.