title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=809 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications link: https://peerj.com/articles/12465 last-modified: 2021-11-16 description: Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini. creator: Nian Gong creator: Lin Yang creator: Xiangsheng Chen uri: https://doi.org/10.7717/peerj.12465 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Gong et al. title: Interleukin 20 receptor A expression in colorectal cancer and its clinical significance link: https://peerj.com/articles/12467 last-modified: 2021-11-16 description: BackgroundInterleukin 20 receptor A (IL20RA) has been shown to play a role in the establishment and progression of multiple tumors. However, the expression of this protein in colorectal cancer (CRC) and its correlation with the clinicopathological parameters of CRC have remained unclear.MethodsA total of 323 paraffin sections including CRC tissues and adjacent normal tissues after surgery were collected. IL20RA protein expression was detected by immunohistochemical staining. The difference expression of IL20RA mRNA between CRC and normal tissues was also explored in the Oncomine and GEO databases. In addition, the IL20RA-related differentially expressed genes were analyzed in TCGA database and enrichment analysis was conducted to explore the cell functions and pathways related to IL20RA expression.ResultsThere was increased IL20RA expression in CRC compared with that in normal tissues. High IL20RA expression was associated with greater tumor diameter, lymph node metastasis, and poor TNM stage in CRC, while also being suggestive of poor prognosis. The main pathways of IL20RA-related differentially expressed genes in TCGA were protein heterodimerization activity, oxygen binding, oxygen transporter activity, hormone activity, and lipid transporter activity. Meanwhile, IL20RA-related differentially expressed genes were mainly enriched in peroxidase, nucleotide stimulant repair, fatty acid metabolism, basal transcription factor, and RNA degradation.ConclusionsIL20RA might have a role as a biomarker for CRC. Its upregulation might contribute to an aggressive phenotype in CRC. IL20RA’s involvement in the development and progression of CRC might occur through it affecting fatty acid metabolism, oxygen binding, oxygen transport, and hormone activity. creator: Rui Liu creator: Honghao Yin creator: Xin Sun creator: Songyi Liu creator: Ang Wang creator: Ying Wu creator: Yuan Yuan creator: Yuehua Gong creator: Chengzhong Xing uri: https://doi.org/10.7717/peerj.12467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: A workflow for low-cost automated image analysis of myxomycete spore numbers, size and shape link: https://peerj.com/articles/12471 last-modified: 2021-11-16 description: Measuring spore size is a standard method for the description of fungal taxa, but in manual microscopic analyses the number of spores that can be measured and information on their morphological traits are typically limited. To overcome this weakness we present a method to analyze the size and shape of large numbers of spherical bodies, such as spores or pollen, by using inexpensive equipment. A spore suspension mounted on a slide is treated with a low-cost, high-vibration device to distribute spores uniformly in a single layer without overlap. Subsequently, 10,000 to 50,000 objects per slide are measured by automated image analysis. The workflow involves (1) slide preparation, (2) automated image acquisition by light microscopy, (3) filtering to separate high-density clusters, (4) image segmentation by applying a machine learning software, Waikato Environment for Knowledge Analysis (WEKA), and (5) statistical evaluation of the results. The technique produced consistent results and compared favorably with manual measurements in terms of precision. Moreover, measuring spore size distribution yields information not obtained by manual microscopic analyses, as shown for the myxomycete Physarum albescens. The exact size distribution of spores revealed irregularities in spore formation resulting from the influence of environmental conditions on spore maturation. A comparison of the spore size distribution within and between sporocarp colonies showed large environmental and likely genetic variation. In addition, the comparison identified specimens with spores roughly twice the normal size. The successful implementation of the presented method for analyzing myxomycete spores also suggests potential for other applications. creator: Jan Woyzichovski creator: Oleg Shchepin creator: Nikki Heherson Dagamac creator: Martin Schnittler uri: https://doi.org/10.7717/peerj.12471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Woyzichovski et al. title: Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum link: https://peerj.com/articles/12484 last-modified: 2021-11-16 description: BackgroundGolden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response.MethodsIn this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments.ResultsHerein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton. creator: Zilin Zhao creator: Jiaran Shuang creator: Zhaoguo Li creator: Huimin Xiao creator: Yuling Liu creator: Tao Wang creator: Yangyang Wei creator: Shoulin Hu creator: Sumei Wan creator: Renhai Peng uri: https://doi.org/10.7717/peerj.12484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhao et al. title: Construction of an AI-2 quorum sensing induced heterologous protein expression system in Escherichia coli link: https://peerj.com/articles/12497 last-modified: 2021-11-16 description: BackgroundThe pET expression system based on T7 promoter which is induced by isopropyl-β-D-1-thiogalactopyranoside (IPTG) is by far the most commonly used system for production of heterogeneous proteins in Escherichia coli. However, this system was limited by obvious drawbacks including the host toxicity and metabolic burden imposed by the presence of IPTG.MethodsIn this study, we incorporated the autoinducer-2 (AI-2) quorum sensing system to realize autoinduction of the pET expression system. The autoinduction expression vector pXWZ1 was constructed by inserting the lsr promoter regions into the pET28a(+) vector. The expression efficiency of the reporter genes gfpuv and lacZ by the pXWZ1 and pET28a(+) vectors were compared.ResultsThe results showed that the expression levels of the both report genes in the cells transformed with pXWZ1 without any addition of exogenous inducer were higher than that transformed with pET28a(+) vectors by the induction of IPTG.ConclusionThis new auto-induction system will exclude the limitations of the IPTG induction including toxic to host and increasing formation of inclusion body and will become a more economical and convenient tool for recombinant protein expression. creator: Fei Shang creator: Hui Wang creator: Dan Zhang creator: Wenhui Wang creator: Jiangliu Yu creator: Ting Xue uri: https://doi.org/10.7717/peerj.12497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shang et al. title: Exotic predators are not better biocontrol agents: the harlequin ladybird is not the most voracious in Mexico link: https://peerj.com/articles/12503 last-modified: 2021-11-16 description: The use of exotic species for pest biocontrol has been a common pathway for introduction and dispersal of invasive species that may have undesired outcomes. Biocontrol agents are believed to be a less damaging alternative than pesticides, but some species may also prey on or parasitize native species or outcompete them for resources. The harlequin ladybird (Harmonia axyridis) is a well-known biocontrol agent originally from Asia that has established invasive populations in 59 countries around the globe. Harlequin ladybirds are generalist predators that in addition to pests prey on an array of different species including other coccinelids’ eggs and larvae. In Mexico, native ladybirds that share ecological requirements with harlequin ladybirds are at risk of being outcompeted and predated upon. The aim of our study was to compare the foraging efficiency of harlequin ladybirds against three species of native coccinelids when preying on aphids. We investigated the foraging behaviour of ladybirds alone and in pairs with a conspecific, a native heterospecific or an exotic heterospecific. We found that the native Cycloneda sanguinea was the species that consumed the most aphids, while Hippodamia convergens was the fastest to find and consume each aphid. Harlequin ladybirds and H. convergens consumed the same number of aphids while P. vittigera consumed less. Conspecific competition was stronger than heterospecific competition. We discuss the suitability of using the exotic invasive harlequin ladybird for aphid biocontrol in comparison with native coccinelids. creator: Morelia Camacho-Cervantes creator: Wendy Mendoza-Arroyo creator: Daniela Arellano-Sánchez creator: Ek del-Val uri: https://doi.org/10.7717/peerj.12503 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Camacho-Cervantes et al. title: Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris: possible influence of the rearing water and more link: https://peerj.com/articles/12241 last-modified: 2021-11-15 description: BackgroundMicrobial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management.MethodIn light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method.ResultsWe found a core microbiota made of taxa related to Aestuariibacter, Alteromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process. creator: Carolane Giraud creator: Nolwenn Callac creator: Maxime Beauvais creator: Jean-René Mailliez creator: Dominique Ansquer creator: Nazha Selmaoui-Folcher creator: Dominique Pham creator: Nelly Wabete creator: Viviane Boulo uri: https://doi.org/10.7717/peerj.12241 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Giraud et al. title: Preliminary placement and new records of an overlooked Amazonian tree, Christiana mennegae (Malvaceae) link: https://peerj.com/articles/12244 last-modified: 2021-11-15 description: Christiana mennegae is a phylogenetically enigmatic taxon and represents a case in point of a species whose presence escaped the radar of the Amazon lists and the Brazilian Flora project. Here we expand its distribution by adding new records from Peru and overlooked ones from Brazil. To investigate its phylogenetic placement in the Brownlowioideae, part of the rbcL gene of the plastid and the intergenic ITS2 region were sequenced. Macro- and micro-morphological investigation of features of C. mennegae using SEM of foliar, flower, fruit and seed structures are presented. A lectotype for the name is designated here. The morphology of trichomes revealed five types of trichomes ranging from glandular to branched and unbranched and we also report stomata on the seed surface for the first time in Brownlowioideae. Christiana mennegae and C. africana were recovered as sister species in the phylogenetic analysis, albeit with low to moderate support, and more species of this and closely related genera must be sampled and analyzed in order to obtain a clearer picture of the group’s affinities and relationships. We provide an update of its conservation status from Vulnerable to Least Concern. We also highlight the need for investment in the digitization of biological collections, botanical capacity building at the local level and the importance of the availability of online literature to speed the study of Amazonian plant diversity. creator: Rafael G. Barbosa-Silva creator: Thales Silva Coutinho creator: Santelmo Vasconcelos creator: Delmo Fonseca da Silva creator: Guilherme Oliveira creator: Daniela C. Zappi uri: https://doi.org/10.7717/peerj.12244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Barbosa-Silva et al. title: Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya link: https://peerj.com/articles/12290 last-modified: 2021-11-15 description: Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world’s most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance. creator: Sijun Liu creator: Si-Ming Zhang creator: Sarah K. Buddenborg creator: Eric S. Loker creator: Bryony C. Bonning uri: https://doi.org/10.7717/peerj.12290 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Liu et al. title: Fighting SARS-CoV-2 with green seaweed Ulva sp. extract: extraction protocol predetermines crude ulvan extract anti-SARS-CoV-2 inhibition properties in in vitro Vero-E6 cells assay link: https://peerj.com/articles/12398 last-modified: 2021-11-15 description: Due to the global COVID-19 pandemic, there is a need to screen for novel compounds with antiviral activity against SARS-COV-2. Here we compared chemical composition and the in vitro anti- SARS-COV-2 activity of two different Ulva sp. crude ulvan extracts: one obtained by an HCl-based and another one by ammonium oxalate-based (AOx) extraction protocols. The composition of the crude extracts was analyzed and their antiviral activity was assessed in a cytopathic effect reduction assay using Vero E6 cells. We show that the extraction protocols have a significant impact on the chemical composition, anti- SARS-COV-2 activity, and cytotoxicity of these ulvan extracts. The ulvan extract based on the AOx protocol had a higher average molecular weight, higher charge, and 11.3-fold higher antiviral activity than HCl-based extract. Our results strongly suggest that further bioassay-guided investigation into bioactivity of compounds found in Ulva sp. ulvan extracts could lead to the discovery of novel anti-SARS-CoV-2 antivirals. creator: Shai Shefer creator: Arthur Robin creator: Alexander Chemodanov creator: Mario Lebendiker creator: Robert Bostwick creator: Lynn Rasmussen creator: Michael Lishner creator: Michael Gozin creator: Alexander Golberg uri: https://doi.org/10.7717/peerj.12398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Shefer et al.