PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: DAXX mediates high phosphate-induced endothelial cell apoptosis in vitro through activating ERK signaling
items: Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)
items: Profiling tear proteomes of patients with unilateral relapsed Behcet’s disease-associated uveitis using data-independent acquisition proteomics
items: Salmo salar fish waste oil: Fatty acids composition and antibacterial activity
items: Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing
items: Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots
items: Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees
items: Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs
items: Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia
items: Response of arbuscular mycorrhizal fungal community in soil and roots to grazing differs in a wetland on the Qinghai-Tibet plateau

DAXX mediates high phosphate-induced endothelial cell apoptosis in vitro through activating ERK signaling
type: item
type: AcademicArticle
description: Backgroud and Purpose Hyperphosphatemia, which is a high inorganic phosphate (Pi) level in the serum, promotes endothelial cells dysfunction and is associated with cardiovascular diseases in patients with chronic kidney diseases (CKD). However, the underlying mechanism of high Pi-induced endothelia cell apoptosis remains unclear. Methods Human umbilical vein endothelial cells (HUVECs) were treated with normal Pi (1.0 mM) and high Pi (3.0 mM), and then cell apoptosis, abnormal gene expression and potential signaling pathway involvement in simulated hyperphosphatemia were examined using flow cytometry, quantitative PCR (qPCR) and western blot analysis. A two-step 5/6 nephrectomy was carried out to induce CKD and biochemical measurements were taken. Results The rat model of CKD revealed that hyperphosphatemia is correlated with an increased death-domain associated protein (DAXX) expression in endothelial cells. In vitro, high Pi increased the mRNA and protein expression level of DAXX in HUVECs, effects that were reversed by additional phosphonoformic acid treatment. Functionally, high Pi resulted in a significantly increased apoptosis in HUVECs, whereas DAXX knockdown markedly repressed high Pi-induced cell apoptosis, indicating that DAXX mediated high Pi-induced endothelial cell apoptosis. High Pi treatment and DAXX overexpression induced the activation of extracellular regulated protein kinases (ERKs), while DAXX knockdown inhibited high Pi-induced ERKs activation. Finally, we demonstrated that DAXX overexpression induced HUVECs apoptosis in the presence of normal Pi, whereas additional treatment with U0126 (a specific ERK inhibitor) reversed that effect. Conclusion Upregulated DAXX promoted high Pi-induced HUVECs apoptosis by activating ERK signaling and indicated that the DAXX/ERK signaling axis may be served as a potential target for CKD therapy.
format: application/pdf
format: text/html
creator: Shu Wang
creator: Mingyu Wu
creator: Ling Qin
creator: Yaxiang Song
creator: Ai Peng
subject: Cell Biology
subject: Nephrology
description: doi:10.7717/peerj.9203
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Backgroud and Purpose Hyperphosphatemia, which is a high inorganic phosphate (Pi) level in the serum, promotes endothelial cells dysfunction and is associated with cardiovascular diseases in patients with chronic kidney diseases (CKD). However, the underlying mechanism of high Pi-induced endothelia cell apoptosis remains unclear. Methods Human umbilical vein endothelial cells (HUVECs) were treated with normal Pi (1.0 mM) and high Pi (3.0 mM), and then cell apoptosis, abnormal gene expression and potential signaling pathway involvement in simulated hyperphosphatemia were examined using flow cytometry, quantitative PCR (qPCR) and western blot analysis. A two-step 5/6 nephrectomy was carried out to induce CKD and biochemical measurements were taken. Results The rat model of CKD revealed that hyperphosphatemia is correlated with an increased death-domain associated protein (DAXX) expression in endothelial cells. In vitro, high Pi increased the mRNA and protein expression level of DAXX in HUVECs, effects that were reversed by additional phosphonoformic acid treatment. Functionally, high Pi resulted in a significantly increased apoptosis in HUVECs, whereas DAXX knockdown markedly repressed high Pi-induced cell apoptosis, indicating that DAXX mediated high Pi-induced endothelial cell apoptosis. High Pi treatment and DAXX overexpression induced the activation of extracellular regulated protein kinases (ERKs), while DAXX knockdown inhibited high Pi-induced ERKs activation. Finally, we demonstrated that DAXX overexpression induced HUVECs apoptosis in the presence of normal Pi, whereas additional treatment with U0126 (a specific ERK inhibitor) reversed that effect. Conclusion Upregulated DAXX promoted high Pi-induced HUVECs apoptosis by activating ERK signaling and indicated that the DAXX/ERK signaling axis may be served as a potential target for CKD therapy.
bibliographic citation: Wang et al. (2020) DAXX mediates high phosphate-induced endothelial cell apoptosis in vitro through activating ERK signaling. PeerJ 8:e9203 https://doi.org/10.7717/peerj.9203
date submitted: 2019-09-27
date accepted: 2020-04-24
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shu
author list: Agent
  family name: Wu
  given name: Mingyu
author list: Agent
  family name: Qin
  given name: Ling
author list: Agent
  family name: Song
  given name: Yaxiang
author list: Agent
  family name: Peng
  given name: Ai
doi: 10.7717/peerj.9203
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae)
type: item
type: AcademicArticle
description: The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.
format: application/pdf
format: text/html
creator: Carla Cicero
creator: Nicholas A. Mason
creator: Lauryn Benedict
creator: James D. Rising
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.9249
publisher: PeerJ Inc.
rights: © 2020 Cicero et al.
abstract: The New World sparrows (Passerellidae) are a large, diverse group of songbirds that vary in morphology, behavior, and ecology. Thus, they are excellent for studying trait evolution in a phylogenetic framework. We examined lability versus conservatism in morphological and behavioral traits in two related clades of sparrows (Aimophila, Peucaea), and assessed whether habitat has played an important role in trait evolution. We first inferred a multi-locus phylogeny which we used to reconstruct ancestral states, and then quantified phylogenetic signal among morphological and behavioral traits in these clades and in New World sparrows more broadly. Behavioral traits have a stronger phylogenetic signal than morphological traits. Specifically, vocal duets and song structure are the most highly conserved traits, and nesting behavior appears to be maintained within clades. Furthermore, we found a strong correlation between open habitat and unpatterned plumage, complex song, and ground nesting. However, even within lineages that share the same habitat type, species vary in nesting, plumage pattern, song complexity, and duetting. Our findings highlight trade-offs between behavior, morphology, and ecology in sparrow diversification.
bibliographic citation: Cicero et al. (2020) Behavioral, morphological, and ecological trait evolution in two clades of New World Sparrows (Aimophila and Peucaea, Passerellidae). PeerJ 8:e9249 https://doi.org/10.7717/peerj.9249
date submitted: 2019-11-22
date accepted: 2020-05-07
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cicero
  given name: Carla
author list: Agent
  family name: Mason
  given name: Nicholas A.
author list: Agent
  family name: Benedict
  given name: Lauryn
author list: Agent
  family name: Rising
  given name: James D.
doi: 10.7717/peerj.9249
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Cicero et al.
attribution name: Cicero et al.

Profiling tear proteomes of patients with unilateral relapsed Behcet’s disease-associated uveitis using data-independent acquisition proteomics
type: item
type: AcademicArticle
description: Purpose To explore whether unilateral relapse of Bechet’s disease-associated uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye and potential tear biomarkers for uveitis recurrence and disease monitoring. Method To minimize interindividual variations, bilateral tear samples were collected from the same patient (n = 15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identify proteins that differed between active and quiescent eyes. Results A total of 1,797 confident proteins were identified in the tear samples, of which 381 (21.2%) were also highly expressed in various tissues and organs. Fifty-one (2.8%) proteins differed in terms of expression between tears in active and quiescent eyes, 9 (17.6%) of which were functionally related to immunity or inflammation. Alpha-1-acid glycoprotein 1 (fold change = 3.2, p = 0.007) was increased and Annexin A1 (fold change = −1.7, p < 0.001) was decreased in the tears of the active BDU eye compared to the contralateral quiescent eye. Conclusions A substantial amount of confident proteins were detected in the tears of BDU patients, including proteins that were deferentially expressed in the uveitis-relapsed eyes and the contralateral quiescent eyes. Some of these identified tear proteins play important roles in immune and inflammatory processes. Tear proteome might be a good source of biomarkers for uveitis.
format: application/pdf
format: text/html
creator: Anyi Liang
creator: Weiwei Qin
creator: Meifen Zhang
creator: Fei Gao
creator: Chan Zhao
creator: Youhe Gao
subject: Biochemistry
subject: Immunology
subject: Ophthalmology
subject: Rheumatology
description: doi:10.7717/peerj.9250
publisher: PeerJ Inc.
rights: © 2020 Liang et al.
abstract: Purpose To explore whether unilateral relapse of Bechet’s disease-associated uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye and potential tear biomarkers for uveitis recurrence and disease monitoring. Method To minimize interindividual variations, bilateral tear samples were collected from the same patient (n = 15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identify proteins that differed between active and quiescent eyes. Results A total of 1,797 confident proteins were identified in the tear samples, of which 381 (21.2%) were also highly expressed in various tissues and organs. Fifty-one (2.8%) proteins differed in terms of expression between tears in active and quiescent eyes, 9 (17.6%) of which were functionally related to immunity or inflammation. Alpha-1-acid glycoprotein 1 (fold change = 3.2, p = 0.007) was increased and Annexin A1 (fold change = −1.7, p < 0.001) was decreased in the tears of the active BDU eye compared to the contralateral quiescent eye. Conclusions A substantial amount of confident proteins were detected in the tears of BDU patients, including proteins that were deferentially expressed in the uveitis-relapsed eyes and the contralateral quiescent eyes. Some of these identified tear proteins play important roles in immune and inflammatory processes. Tear proteome might be a good source of biomarkers for uveitis.
bibliographic citation: Liang et al. (2020) Profiling tear proteomes of patients with unilateral relapsed Behcet’s disease-associated uveitis using data-independent acquisition proteomics. PeerJ 8:e9250 https://doi.org/10.7717/peerj.9250
date submitted: 2019-11-10
date accepted: 2020-05-07
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Anyi
author list: Agent
  family name: Qin
  given name: Weiwei
author list: Agent
  family name: Zhang
  given name: Meifen
author list: Agent
  family name: Gao
  given name: Fei
author list: Agent
  family name: Zhao
  given name: Chan
author list: Agent
  family name: Gao
  given name: Youhe
doi: 10.7717/peerj.9250
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: © 2020 Liang et al.
attribution name: Liang et al.

Salmo salar fish waste oil: Fatty acids composition and antibacterial activity
type: item
type: AcademicArticle
description: Background and aims Fish by-products are generally used to produce fishmeal or fertilizers, with fish oil as a by-product. Despite their importance, fish wastes are still poorly explored and characterized and more studies are needed to reveal their potentiality. The goal of the present study was to qualitatively characterize and investigate the antimicrobial effects of the fish oil extracted from Salmo salar waste samples and to evaluate the potential use of these compounds for treating pathogen infections. Methods Salmo salar waste samples were divided in two groups: heads and soft tissues. Fatty acids composition, and in particular the content in saturated (SAFAs), mono-unsaturated (MUFAs) and Polyunsaturated (PUFAs) fatty acids, was characterized through GC/MS Thermo Focus GC-DSQ II equipped with a ZB-5 fused silica capillary tubes column. The antimicrobial activity of the salmon waste oils was evaluated through the Minimum Inhibitory Concentration assay and the antibiotics contamination was determined by Liquid Chromatography with tandem Mass Spectrometry (LC-MS/MS) analysis. All experiments were done at least in triplicate. Results GC/MS analysis has shown the specific fatty acid composition of the salmon waste oils and their enrichment in MUFAs and PUFAs, with special reference to omega-3, -6, -7, -9 fatty acids. Furthermore, our study has highlighted the antimicrobial activity of the fish waste oil samples against two Gram+ and Gram- bacterial strains. Conclusions These data confirm that the fish waste is still quantitatively and qualitatively an important source of available biological properties that could be extracted and utilized representing an important strategy to counteract infective diseases in the context of the circular economy.
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format: text/html
creator: Luigi Inguglia
creator: Marco Chiaramonte
creator: Vita Di Stefano
creator: Domenico Schillaci
creator: Gaetano Cammilleri
creator: Licia Pantano
creator: Manuela Mauro
creator: Mirella Vazzana
creator: Vincenzo Ferrantelli
creator: Rosalia Nicolosi
creator: Vincenzo Arizza
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.9299
publisher: PeerJ Inc.
rights: © 2020 Inguglia et al.
abstract: Background and aims Fish by-products are generally used to produce fishmeal or fertilizers, with fish oil as a by-product. Despite their importance, fish wastes are still poorly explored and characterized and more studies are needed to reveal their potentiality. The goal of the present study was to qualitatively characterize and investigate the antimicrobial effects of the fish oil extracted from Salmo salar waste samples and to evaluate the potential use of these compounds for treating pathogen infections. Methods Salmo salar waste samples were divided in two groups: heads and soft tissues. Fatty acids composition, and in particular the content in saturated (SAFAs), mono-unsaturated (MUFAs) and Polyunsaturated (PUFAs) fatty acids, was characterized through GC/MS Thermo Focus GC-DSQ II equipped with a ZB-5 fused silica capillary tubes column. The antimicrobial activity of the salmon waste oils was evaluated through the Minimum Inhibitory Concentration assay and the antibiotics contamination was determined by Liquid Chromatography with tandem Mass Spectrometry (LC-MS/MS) analysis. All experiments were done at least in triplicate. Results GC/MS analysis has shown the specific fatty acid composition of the salmon waste oils and their enrichment in MUFAs and PUFAs, with special reference to omega-3, -6, -7, -9 fatty acids. Furthermore, our study has highlighted the antimicrobial activity of the fish waste oil samples against two Gram+ and Gram- bacterial strains. Conclusions These data confirm that the fish waste is still quantitatively and qualitatively an important source of available biological properties that could be extracted and utilized representing an important strategy to counteract infective diseases in the context of the circular economy.
bibliographic citation: Inguglia et al. (2020) Salmo salar fish waste oil: Fatty acids composition and antibacterial activity. PeerJ 8:e9299 https://doi.org/10.7717/peerj.9299
date submitted: 2020-01-08
date accepted: 2020-05-14
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Inguglia
  given name: Luigi
author list: Agent
  family name: Chiaramonte
  given name: Marco
author list: Agent
  family name: Di Stefano
  given name: Vita
author list: Agent
  family name: Schillaci
  given name: Domenico
author list: Agent
  family name: Cammilleri
  given name: Gaetano
author list: Agent
  family name: Pantano
  given name: Licia
author list: Agent
  family name: Mauro
  given name: Manuela
author list: Agent
  family name: Vazzana
  given name: Mirella
author list: Agent
  family name: Ferrantelli
  given name: Vincenzo
author list: Agent
  family name: Nicolosi
  given name: Rosalia
author list: Agent
  family name: Arizza
  given name: Vincenzo
doi: 10.7717/peerj.9299
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Inguglia et al.
attribution name: Inguglia et al.

Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing
type: item
type: AcademicArticle
description: Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.
format: application/pdf
format: text/html
creator: Viktoria Yu Shtratnikova
creator: Mikhail I. Schelkunov
creator: Aleksey A. Penin
creator: Maria D. Logacheva
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9309
publisher: PeerJ Inc.
rights: © 2020 Shtratnikova et al.
abstract: Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.
bibliographic citation: Shtratnikova et al. (2020) Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing. PeerJ 8:e9309 https://doi.org/10.7717/peerj.9309
date submitted: 2019-06-13
date accepted: 2020-05-17
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shtratnikova
  given name: Viktoria Yu
author list: Agent
  family name: Schelkunov
  given name: Mikhail I.
author list: Agent
  family name: Penin
  given name: Aleksey A.
author list: Agent
  family name: Logacheva
  given name: Maria D.
doi: 10.7717/peerj.9309
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: © 2020 Shtratnikova et al.
attribution name: Shtratnikova et al.

Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots
type: item
type: AcademicArticle
description: Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.
format: application/pdf
format: text/html
creator: Girma Eshetu Teshome
creator: Yeshitila Mekbib
creator: Guangwan Hu
creator: Zhi-Zhong Li
creator: Jinming Chen
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.9314
publisher: PeerJ Inc.
rights: © 2020 Teshome et al.
abstract: Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.
bibliographic citation: Teshome et al. (2020) Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. PeerJ 8:e9314 https://doi.org/10.7717/peerj.9314
date submitted: 2020-01-03
date accepted: 2020-05-17
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Teshome
  given name: Girma Eshetu
author list: Agent
  family name: Mekbib
  given name: Yeshitila
author list: Agent
  family name: Hu
  given name: Guangwan
author list: Agent
  family name: Li
  given name: Zhi-Zhong
author list: Agent
  family name: Chen
  given name: Jinming
doi: 10.7717/peerj.9314
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Teshome et al.
attribution name: Teshome et al.

Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees
type: item
type: AcademicArticle
description: Spiders (Araneae) form abundant and diverse assemblages in agroecosystems such as fruit orchards, and thus might have an important role as natural enemies of orchard pests. Although spiders are polyphagous and opportunistic predators in general, limited information exists on their natural prey at both species and community levels. Thus, the aim of this study was to assess the natural prey (realized trophic niche) of arboreal hunting spiders, their role in trophic webs and their biological control potential with direct observation of predation events in apple orchards. Hunting spiders with prey in their chelicerae were collected in the canopy of apple trees in organic apple orchards in Hungary during the growing seasons between 2013 and 2019 and both spiders and their prey were identified and measured. Among others, the composition of the actual (captured by spiders) and the potential (available in the canopy) prey was compared, trophic niche and food web metrics were calculated, and some morphological, dimensional data of the spider-prey pairs were analyzed. Species-specific differences in prey composition or pest control ability were also discussed. By analyzing a total of 878 prey items captured by spiders, we concluded that arboreal hunting spiders forage selectively and consume a large number of apple pests; however, spiders’ beneficial effects are greatly reduced by their high levels of intraguild predation and by a propensity to switch from pests to alternative prey. In this study, arboreal hunting spiders showed negative selectivity for pests, no selectivity for natural enemies and positive selectivity for neutral species. In the trophic web, the dominant hunting spider taxa/groups (Carrhotus xanthogramma, Philodromus cespitum, Clubiona spp., Ebrechtella tricuspidata, Xysticus spp. and ‘Other salticids’) exhibit different levels of predation on different prey groups and the trophic web’s structure changes depending on the time of year. Hunting spiders show a …
format: application/pdf
format: text/html
creator: László Mezőfi
creator: Gábor Markó
creator: Csaba Nagy
creator: Dávid Korányi
creator: Viktor Markó
subject: Agricultural Science
subject: Ecology
description: doi:10.7717/peerj.9334
publisher: PeerJ Inc.
rights: © 2020 Mezőfi et al.
abstract: Spiders (Araneae) form abundant and diverse assemblages in agroecosystems such as fruit orchards, and thus might have an important role as natural enemies of orchard pests. Although spiders are polyphagous and opportunistic predators in general, limited information exists on their natural prey at both species and community levels. Thus, the aim of this study was to assess the natural prey (realized trophic niche) of arboreal hunting spiders, their role in trophic webs and their biological control potential with direct observation of predation events in apple orchards. Hunting spiders with prey in their chelicerae were collected in the canopy of apple trees in organic apple orchards in Hungary during the growing seasons between 2013 and 2019 and both spiders and their prey were identified and measured. Among others, the composition of the actual (captured by spiders) and the potential (available in the canopy) prey was compared, trophic niche and food web metrics were calculated, and some morphological, dimensional data of the spider-prey pairs were analyzed. Species-specific differences in prey composition or pest control ability were also discussed. By analyzing a total of 878 prey items captured by spiders, we concluded that arboreal hunting spiders forage selectively and consume a large number of apple pests; however, spiders’ beneficial effects are greatly reduced by their high levels of intraguild predation and by a propensity to switch from pests to alternative prey. In this study, arboreal hunting spiders showed negative selectivity for pests, no selectivity for natural enemies and positive selectivity for neutral species. In the trophic web, the dominant hunting spider taxa/groups (Carrhotus xanthogramma, Philodromus cespitum, Clubiona spp., Ebrechtella tricuspidata, Xysticus spp. and ‘Other salticids’) exhibit different levels of predation on different prey groups and the trophic web’s structure changes depending on the time of year. Hunting spiders show a …
bibliographic citation: Mezőfi et al. (2020) Beyond polyphagy and opportunism: natural prey of hunting spiders in the canopy of apple trees. PeerJ 8:e9334 https://doi.org/10.7717/peerj.9334
date submitted: 2020-01-20
date accepted: 2020-05-19
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mezőfi
  given name: László
author list: Agent
  family name: Markó
  given name: Gábor
author list: Agent
  family name: Nagy
  given name: Csaba
author list: Agent
  family name: Korányi
  given name: Dávid
author list: Agent
  family name: Markó
  given name: Viktor
doi: 10.7717/peerj.9334
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: © 2020 Mezőfi et al.
attribution name: Mezőfi et al.

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs
type: item
type: AcademicArticle
description: Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes corre…
format: application/pdf
format: text/html
creator: Feng Lv
creator: Xiaojuan Wang
creator: Xin Pang
creator: Guohua Liu
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.9353
publisher: PeerJ Inc.
rights: © 2020 Lv et al.
abstract: Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes corre…
bibliographic citation: Lv et al. (2020) Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs. PeerJ 8:e9353 https://doi.org/10.7717/peerj.9353
date submitted: 2019-12-04
date accepted: 2020-05-23
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Feng
author list: Agent
  family name: Wang
  given name: Xiaojuan
author list: Agent
  family name: Pang
  given name: Xin
author list: Agent
  family name: Liu
  given name: Guohua
doi: 10.7717/peerj.9353
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Lv et al.
attribution name: Lv et al.

Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia
type: item
type: AcademicArticle
description: Reef-building corals can harbour high abundances of diverse invertebrate epifauna. Coral characteristics and environmental conditions are important drivers of community structure of coral-associated invertebrates; however, our current understanding of drivers of epifaunal distributions is still unclear. This study tests the relative importance of the physical environment (current flow speed) and host quality (e.g., colony height, surface area, distance between branches, penetration depth among branches, and background partial mortality) in structuring epifaunal communities living within branching Pocillopora colonies on a back reef in Moorea, French Polynesia. A total of 470 individuals belonging to four phyla, 16 families and 39 genera were extracted from 36 Pocillopora spp. colonies. Decapods were the most abundant epifaunal organisms (accounting for 84% of individuals) found living in Pocillopora spp. While coral host characteristics and flow regime are very important, these parameters were not correlated with epifaunal assemblages at the time of the study. Epifaunal assemblages associated with Pocillopora spp. were consistent and minimally affected by differences in host characteristics and flow regime. The consistency in abundance and taxon richness among colonies (regardless of habitat characteristics) highlighted the importance of total habitat availability. With escalating effects of climate change and other localized disturbances, it is critical to preserve branching corals to support epifaunal communities.
format: application/pdf
format: text/html
creator: Chiara Pisapia
creator: Jessica Stella
creator: Nyssa J. Silbiger
creator: Robert Carpenter
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.9364
publisher: PeerJ Inc.
rights: © 2020 Pisapia et al.
abstract: Reef-building corals can harbour high abundances of diverse invertebrate epifauna. Coral characteristics and environmental conditions are important drivers of community structure of coral-associated invertebrates; however, our current understanding of drivers of epifaunal distributions is still unclear. This study tests the relative importance of the physical environment (current flow speed) and host quality (e.g., colony height, surface area, distance between branches, penetration depth among branches, and background partial mortality) in structuring epifaunal communities living within branching Pocillopora colonies on a back reef in Moorea, French Polynesia. A total of 470 individuals belonging to four phyla, 16 families and 39 genera were extracted from 36 Pocillopora spp. colonies. Decapods were the most abundant epifaunal organisms (accounting for 84% of individuals) found living in Pocillopora spp. While coral host characteristics and flow regime are very important, these parameters were not correlated with epifaunal assemblages at the time of the study. Epifaunal assemblages associated with Pocillopora spp. were consistent and minimally affected by differences in host characteristics and flow regime. The consistency in abundance and taxon richness among colonies (regardless of habitat characteristics) highlighted the importance of total habitat availability. With escalating effects of climate change and other localized disturbances, it is critical to preserve branching corals to support epifaunal communities.
bibliographic citation: Pisapia et al. (2020) Epifaunal invertebrate assemblages associated with branching Pocilloporids in Moorea, French Polynesia. PeerJ 8:e9364 https://doi.org/10.7717/peerj.9364
date submitted: 2020-01-20
date accepted: 2020-05-26
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pisapia
  given name: Chiara
author list: Agent
  family name: Stella
  given name: Jessica
author list: Agent
  family name: Silbiger
  given name: Nyssa J.
author list: Agent
  family name: Carpenter
  given name: Robert
doi: 10.7717/peerj.9364
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: © 2020 Pisapia et al.
attribution name: Pisapia et al.

Response of arbuscular mycorrhizal fungal community in soil and roots to grazing differs in a wetland on the Qinghai-Tibet plateau
type: item
type: AcademicArticle
description: Grazing as one of the most important disturbances affects the abundance, diversity and community composition of arbuscular mycorrhizal (AM) fungi in ecosystems, but the AM fungi in response to grazing in wetland ecosystems remain poorly documented. Here, we examined AM fungi in roots and soil in grazing and non-grazing plots in Zoige wetland on the Qinghai-Tibet plateau. Grazing significantly increased AM fungal spore density and glomalin-related soil proteins, but had no significant effect on the extra radical hyphal density of AM fungi. While AM fungal richness and community composition differed between roots and soil, grazing was found to influence only the community composition in soil. This study shows that moderate grazing can increase the biomass of AM fungi and soil carbon sequestration, and maintain the AM fungal diversity in the wetland ecosystem. This finding may enhance our understanding of the AM fungi in response to grazing in the wetland on the Qinghai-Tibet plateau.
format: application/pdf
format: text/html
creator: Zhong-Feng Li
creator: Peng-Peng Lü
creator: Yong-Long Wang
creator: Hui Yao
creator: Pulak Maitra
creator: Xiang Sun
creator: Yong Zheng
creator: Liang-Dong Guo
subject: Ecology
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.9375
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Grazing as one of the most important disturbances affects the abundance, diversity and community composition of arbuscular mycorrhizal (AM) fungi in ecosystems, but the AM fungi in response to grazing in wetland ecosystems remain poorly documented. Here, we examined AM fungi in roots and soil in grazing and non-grazing plots in Zoige wetland on the Qinghai-Tibet plateau. Grazing significantly increased AM fungal spore density and glomalin-related soil proteins, but had no significant effect on the extra radical hyphal density of AM fungi. While AM fungal richness and community composition differed between roots and soil, grazing was found to influence only the community composition in soil. This study shows that moderate grazing can increase the biomass of AM fungi and soil carbon sequestration, and maintain the AM fungal diversity in the wetland ecosystem. This finding may enhance our understanding of the AM fungi in response to grazing in the wetland on the Qinghai-Tibet plateau.
bibliographic citation: Li et al. (2020) Response of arbuscular mycorrhizal fungal community in soil and roots to grazing differs in a wetland on the Qinghai-Tibet plateau. PeerJ 8:e9375 https://doi.org/10.7717/peerj.9375
date submitted: 2020-01-14
date accepted: 2020-05-27
issued: 2020-06-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhong-Feng
author list: Agent
  family name: Lü
  given name: Peng-Peng
author list: Agent
  family name: Wang
  given name: Yong-Long
author list: Agent
  family name: Yao
  given name: Hui
author list: Agent
  family name: Maitra
  given name: Pulak
author list: Agent
  family name: Sun
  given name: Xiang
author list: Agent
  family name: Zheng
  given name: Yong
author list: Agent
  family name: Guo
  given name: Liang-Dong
doi: 10.7717/peerj.9375
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-19
copyright: ©2020 Li et al.
attribution name: Li et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359