PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Polygamous breeding system identified in the distylous genus Psychotria: P. manillensis in the Ryukyu archipelago, Japan
items: Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata
items: Effect of gender, muscle type and skinfold thickness on myometric parameters in young people
items: Reactions of two xeric-congeneric species of Centaurea (Asteraceae) to soils with different pH values and iron availability
items: Acclimation of liverwort Marchantia polymorpha to physiological drought reveals important roles of antioxidant enzymes, proline and abscisic acid in land plant adaptation to osmotic stress
items: Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders
items: Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations
items: MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla)
items: Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey
items: Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim

Polygamous breeding system identified in the distylous genus Psychotria: P. manillensis in the Ryukyu archipelago, Japan
type: item
type: AcademicArticle
description: Distyly is a genetic polymorphism composed of long-and short-styled flowers in a population. The evolutionary breakdown of distyly has been reported in many taxa, and mainly involves a shift toward monomorphism or dioecism. However, a shift toward monoecism has not been reported in distylous species. Psychotria (Rubiaceae), one of the world largest genera, consists of distylous species and their derivatives. In our preliminary study, however, we identified some monoecious individuals in a population of Psychotria manillensis. To understand the breeding system and reproductive biology of P. manillensis, we investigated floral traits, open fruit set, and flower visitors, and performed hand pollination and bagging experiments in five populations of Okinawa and Iriomote islands, Ryukyu Islands, Japan. The populations of P. manillensis were composed mainly of monoecious individuals (54%), followed by female (30%), male (14%), and hermaphroditic (2%) individuals at the time of flower collection. Of the collected flowers, 93% were functionally unisexual (male or female), whereas only 6.5% were perfect (hermaphroditic). However, some individuals changed sex mainly towards increasing femaleness during the flowering period. Moreover, 35% of the studied plants changed their sexual expression over the years. P. manillensis showed self-compatibility and no agamospermy. The fruit set under open pollination varied among populations and years (1.8–21.9%), but it was significantly higher than that of auto-selfing (0.68–1.56%). Wasps and flies were the main flower visitors and probably the main pollinators of the species. In conclusion, P. manillensis was revealed to be polygamous, involving monoecious, female, male, and hermaphroditic individuals. This is the first report of the polygamous breeding system not only in the genus Psychotria, but also in all heterostylous taxa.
format: application/pdf
format: text/html
creator: Kenta Watanabe
creator: Akira Shimizu
creator: Takashi Sugawara
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.12318
publisher: PeerJ Inc.
rights: © 2021 Watanabe et al.
abstract: Distyly is a genetic polymorphism composed of long-and short-styled flowers in a population. The evolutionary breakdown of distyly has been reported in many taxa, and mainly involves a shift toward monomorphism or dioecism. However, a shift toward monoecism has not been reported in distylous species. Psychotria (Rubiaceae), one of the world largest genera, consists of distylous species and their derivatives. In our preliminary study, however, we identified some monoecious individuals in a population of Psychotria manillensis. To understand the breeding system and reproductive biology of P. manillensis, we investigated floral traits, open fruit set, and flower visitors, and performed hand pollination and bagging experiments in five populations of Okinawa and Iriomote islands, Ryukyu Islands, Japan. The populations of P. manillensis were composed mainly of monoecious individuals (54%), followed by female (30%), male (14%), and hermaphroditic (2%) individuals at the time of flower collection. Of the collected flowers, 93% were functionally unisexual (male or female), whereas only 6.5% were perfect (hermaphroditic). However, some individuals changed sex mainly towards increasing femaleness during the flowering period. Moreover, 35% of the studied plants changed their sexual expression over the years. P. manillensis showed self-compatibility and no agamospermy. The fruit set under open pollination varied among populations and years (1.8–21.9%), but it was significantly higher than that of auto-selfing (0.68–1.56%). Wasps and flies were the main flower visitors and probably the main pollinators of the species. In conclusion, P. manillensis was revealed to be polygamous, involving monoecious, female, male, and hermaphroditic individuals. This is the first report of the polygamous breeding system not only in the genus Psychotria, but also in all heterostylous taxa.
bibliographic citation: Watanabe et al. (2021) Polygamous breeding system identified in the distylous genus Psychotria: P. manillensis in the Ryukyu archipelago, Japan. PeerJ 9:e12318 https://doi.org/10.7717/peerj.12318
date submitted: 2020-10-15
date accepted: 2021-09-25
issued: 2021-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Watanabe
  given name: Kenta
author list: Agent
  family name: Shimizu
  given name: Akira
author list: Agent
  family name: Sugawara
  given name: Takashi
doi: 10.7717/peerj.12318
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-10
copyright: © 2021 Watanabe et al.
attribution name: Watanabe et al.

Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata
type: item
type: AcademicArticle
description: Background Corals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata. Methods M. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions. Results Our results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammoni…
format: application/pdf
format: text/html
creator: Amanda Williams
creator: Jananan S. Pathmanathan
creator: Timothy G. Stephens
creator: Xiaoyang Su
creator: Eric N. Chiles
creator: Dennis Conetta
creator: Hollie M. Putnam
creator: Debashish Bhattacharya
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.12335
publisher: PeerJ Inc.
rights: © 2021 Williams et al.
abstract: Background Corals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata. Methods M. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions. Results Our results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammoni…
bibliographic citation: Williams et al. (2021) Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata. PeerJ 9:e12335 https://doi.org/10.7717/peerj.12335
date submitted: 2021-05-31
date accepted: 2021-09-28
issued: 2021-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Williams
  given name: Amanda
author list: Agent
  family name: Pathmanathan
  given name: Jananan S.
author list: Agent
  family name: Stephens
  given name: Timothy G.
author list: Agent
  family name: Su
  given name: Xiaoyang
author list: Agent
  family name: Chiles
  given name: Eric N.
author list: Agent
  family name: Conetta
  given name: Dennis
author list: Agent
  family name: Putnam
  given name: Hollie M.
author list: Agent
  family name: Bhattacharya
  given name: Debashish
doi: 10.7717/peerj.12335
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-10
copyright: © 2021 Williams et al.
attribution name: Williams et al.

Effect of gender, muscle type and skinfold thickness on myometric parameters in young people
type: item
type: AcademicArticle
description: Background The aim of the study was to compare the mechanical properties of three human skeletal muscles: biceps brachii (BB), rectus femoris (RF), and tibialis anterior (TA) at rest measured by myoton device in males (n = 16, mean age 21.2 ± 0.6 years) and females (n = 16; 21.2 ± 0.9 years) and to investigate the influence of skin and subcutaneous tissue thickness (skinfold thickness, SFT) and gender on myometric parameters of the three skeletal muscles. Methods We measured the following mechanical and viscoelastic muscle properties using MyotonPRO®: frequency (F [Hz]), decrement (D [log]), stiffness (S [N/m]), relaxation time (R [ms]) and creepability (C [De]). The values of SFT for all selected muscles were assessed by caliper. A mixed-design analysis of variance with gender as between subject comparison was used for assessing the differences between gender and muscles in SFT and each of the myometric parameters separately (F, D, S, R and C). Pearson correlation coefficient or Spearman’s rank correlation coefficient between SFT and myometric parameters was conducted for males, females and males and females together. The level of statistical significance was set at α ≤ 0.05 with Bonferroni correction for multiple comparisons. Results The SFT over the RF, TA, and BB muscles in women was statistically significantly larger compared with that of males. In females and males, the SFT over the RF was larger than over the TA and BB, and the SFT over the TA was larger compared with over the BB. The values of F and S recorded for the TA muscle were the highest among the three muscles, while D, C, and R were lowest in TA but highest in the RF muscle in men and women. The values of F and S were smaller in females than in males. Gender comparison of D, C, and R values showed that only D for the RF was significantly lower in females than in males, and C for the RF and TA was significantly larger in females than in males. Some correlation between SFT and myometric parameters wer…
format: application/pdf
format: text/html
creator: Joanna Mencel
creator: Anna Jaskólska
creator: Jaroslaw Marusiak
creator: Katarzyna Kisiel-Sajewicz
creator: Magdalena Siemiatycka
creator: Lukasz Kaminski
creator: Artur Jaskólski
subject: Anatomy and Physiology
subject: Drugs and Devices
subject: Kinesiology
subject: Orthopedics
subject: Pediatrics
description: doi:10.7717/peerj.12367
publisher: PeerJ Inc.
rights: © 2021 Mencel et al.
abstract: Background The aim of the study was to compare the mechanical properties of three human skeletal muscles: biceps brachii (BB), rectus femoris (RF), and tibialis anterior (TA) at rest measured by myoton device in males (n = 16, mean age 21.2 ± 0.6 years) and females (n = 16; 21.2 ± 0.9 years) and to investigate the influence of skin and subcutaneous tissue thickness (skinfold thickness, SFT) and gender on myometric parameters of the three skeletal muscles. Methods We measured the following mechanical and viscoelastic muscle properties using MyotonPRO®: frequency (F [Hz]), decrement (D [log]), stiffness (S [N/m]), relaxation time (R [ms]) and creepability (C [De]). The values of SFT for all selected muscles were assessed by caliper. A mixed-design analysis of variance with gender as between subject comparison was used for assessing the differences between gender and muscles in SFT and each of the myometric parameters separately (F, D, S, R and C). Pearson correlation coefficient or Spearman’s rank correlation coefficient between SFT and myometric parameters was conducted for males, females and males and females together. The level of statistical significance was set at α ≤ 0.05 with Bonferroni correction for multiple comparisons. Results The SFT over the RF, TA, and BB muscles in women was statistically significantly larger compared with that of males. In females and males, the SFT over the RF was larger than over the TA and BB, and the SFT over the TA was larger compared with over the BB. The values of F and S recorded for the TA muscle were the highest among the three muscles, while D, C, and R were lowest in TA but highest in the RF muscle in men and women. The values of F and S were smaller in females than in males. Gender comparison of D, C, and R values showed that only D for the RF was significantly lower in females than in males, and C for the RF and TA was significantly larger in females than in males. Some correlation between SFT and myometric parameters wer…
bibliographic citation: Mencel et al. (2021) Effect of gender, muscle type and skinfold thickness on myometric parameters in young people. PeerJ 9:e12367 https://doi.org/10.7717/peerj.12367
date submitted: 2021-04-13
date accepted: 2021-10-01
issued: 2021-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mencel
  given name: Joanna
author list: Agent
  family name: Jaskólska
  given name: Anna
author list: Agent
  family name: Marusiak
  given name: Jaroslaw
author list: Agent
  family name: Kisiel-Sajewicz
  given name: Katarzyna
author list: Agent
  family name: Siemiatycka
  given name: Magdalena
author list: Agent
  family name: Kaminski
  given name: Lukasz
author list: Agent
  family name: Jaskólski
  given name: Artur
doi: 10.7717/peerj.12367
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-10
copyright: ©2021 Mencel et al.
attribution name: Mencel et al.

Reactions of two xeric-congeneric species of Centaurea (Asteraceae) to soils with different pH values and iron availability
type: item
type: AcademicArticle
description: Centaurea scabiosa L. and C. stoebe Tausch are known to co-exist naturally in two extremely different types of open dry habitats in the temperate zone, alkaline xerothermic grasslands and acidic dry grasslands. However, knowledge about their preferences to edaphic conditions, including soil acidity (pH), and iron (Fe) availability is scarce. Therefore, experimental comparison of soil requirements (acidic Podzol vs alkaline Rendzina) of these species was carried out. The study was designed as a pot experiment and conducted under field conditions. Fe availability was increased by application of Fe-HBED. Reactions of plants to edaphic conditions were determined using growth measurements, leaf morphometric measurements, chlorosis scoring, chlorophyll content and chlorophyll a fluorescence (OJIP) quantification as well as determination of element content (Ca, Mg, Fe, Mn, Zn and Cu). Growth and leaf morphometrical traits of the studied congeneric species were affected similarly by the soil type and differently by the chelate treatment. Increased availability of Fe in Rendzina contrasted the species, as treatment with 25 µmol Fe-HBED kg−1 soil promoted growth only in C. stoebe. Both species turned out to be resistant to Fe-dependent chlorosis which was also reflected in only minor changes in chlorophyll a fluorescence parameters. Both species showed relatively low nutritional demands. Surprisingly, Fe-HBED did not stimulate Fe acquisition in the studied species, nor its translocation along the root:shoot axis. Furthermore, contrary to expectations, C. scabiosa took up less Fe from the acidic than alkaline soil. C. scabiosa not only absorbed more Ca and Zn but also translocated greater amounts of these elements to shoots than C. stoebe. Both species acquired more Mg on Podzol than on Rendzina which suggests adaptation allowing avoidance of aluminum (Al) toxicity on acidic soils. Overall, it seems that C. scabiosa prefers alkaline soils, whilst C. stoebe prefers acidic ones.
format: application/pdf
format: text/html
creator: Mateusz Wala
creator: Jeremi Kołodziejek
creator: Janusz Mazur
creator: Alicja Cienkowska
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biosphere Interactions
description: doi:10.7717/peerj.12417
publisher: PeerJ Inc.
rights: © 2021 Wala et al.
abstract: Centaurea scabiosa L. and C. stoebe Tausch are known to co-exist naturally in two extremely different types of open dry habitats in the temperate zone, alkaline xerothermic grasslands and acidic dry grasslands. However, knowledge about their preferences to edaphic conditions, including soil acidity (pH), and iron (Fe) availability is scarce. Therefore, experimental comparison of soil requirements (acidic Podzol vs alkaline Rendzina) of these species was carried out. The study was designed as a pot experiment and conducted under field conditions. Fe availability was increased by application of Fe-HBED. Reactions of plants to edaphic conditions were determined using growth measurements, leaf morphometric measurements, chlorosis scoring, chlorophyll content and chlorophyll a fluorescence (OJIP) quantification as well as determination of element content (Ca, Mg, Fe, Mn, Zn and Cu). Growth and leaf morphometrical traits of the studied congeneric species were affected similarly by the soil type and differently by the chelate treatment. Increased availability of Fe in Rendzina contrasted the species, as treatment with 25 µmol Fe-HBED kg−1 soil promoted growth only in C. stoebe. Both species turned out to be resistant to Fe-dependent chlorosis which was also reflected in only minor changes in chlorophyll a fluorescence parameters. Both species showed relatively low nutritional demands. Surprisingly, Fe-HBED did not stimulate Fe acquisition in the studied species, nor its translocation along the root:shoot axis. Furthermore, contrary to expectations, C. scabiosa took up less Fe from the acidic than alkaline soil. C. scabiosa not only absorbed more Ca and Zn but also translocated greater amounts of these elements to shoots than C. stoebe. Both species acquired more Mg on Podzol than on Rendzina which suggests adaptation allowing avoidance of aluminum (Al) toxicity on acidic soils. Overall, it seems that C. scabiosa prefers alkaline soils, whilst C. stoebe prefers acidic ones.
bibliographic citation: Wala et al. (2021) Reactions of two xeric-congeneric species of Centaurea (Asteraceae) to soils with different pH values and iron availability. PeerJ 9:e12417 https://doi.org/10.7717/peerj.12417
date submitted: 2021-01-15
date accepted: 2021-10-10
issued: 2021-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wala
  given name: Mateusz
author list: Agent
  family name: Kołodziejek
  given name: Jeremi
author list: Agent
  family name: Mazur
  given name: Janusz
author list: Agent
  family name: Cienkowska
  given name: Alicja
doi: 10.7717/peerj.12417
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-10
copyright: © 2021 Wala et al.
attribution name: Wala et al.

Acclimation of liverwort Marchantia polymorpha to physiological drought reveals important roles of antioxidant enzymes, proline and abscisic acid in land plant adaptation to osmotic stress
type: item
type: AcademicArticle
description: Liverwort Marchantia polymorpha is considered as the key species for addressing a myriad of questions in plant biology. Exploration of drought tolerance mechanism(s) in this group of land plants offers a platform to identify the early adaptive mechanisms involved in drought tolerance. The current study aimed at elucidating the drought acclimation mechanisms in liverwort’s model M. polymorpha. The gemmae, asexual reproductive units of M. polymorpha, were exposed to sucrose (0.2 M), mannitol (0.5 M) and polyethylene glycol (PEG, 10%) for inducing physiological drought to investigate their effects at morphological, physiological and biochemical levels. Our results showed that drought exposure led to extreme growth inhibition, disruption of membrane stability and reduction in photosynthetic pigment contents in M. polymorpha. The increased accumulation of hydrogen peroxide and malondialdehyde, and the rate of electrolyte leakage in the gemmalings of M. polymorpha indicated an evidence of drought-caused oxidative stress. The gemmalings showed significant induction of the activities of key antioxidant enzymes, including superoxide dismutase, catalase, ascorbate peroxidase, dehydroascorbate reductase and glutathione S-transferase, and total antioxidant activity in response to increased oxidative stress under drought. Importantly, to counteract the drought effects, the gemmalings also accumulated a significant amount of proline, which coincided with the evolutionary presence of proline biosynthesis gene Δ1-pyrroline-5-carboxylate synthase 1 (P5CS1) in land plants. Furthermore, the application of exogenous abscisic acid (ABA) reduced drought-induced tissue damage and improved the activities of antioxidant enzymes and accumulation of proline, implying an archetypal role of this phytohormone in M. polymorpha for drought tolerance. We conclude that physiological drought tolerance mechanisms governed by the cellular antioxidants, proline and ABA were adopted in liverwort M. polym…
format: application/pdf
format: text/html
creator: Totan Kumar Ghosh
creator: Naznin Haque Tompa
creator: Md. Mezanur Rahman
creator: Mohammed Mohi-Ud-Din
creator: S. M. Zubair Al-Meraj
creator: Md. Sanaullah Biswas
creator: Mohammad Golam Mostofa
subject: Agricultural Science
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.12419
publisher: PeerJ Inc.
rights: © 2021 Ghosh et al.
abstract: Liverwort Marchantia polymorpha is considered as the key species for addressing a myriad of questions in plant biology. Exploration of drought tolerance mechanism(s) in this group of land plants offers a platform to identify the early adaptive mechanisms involved in drought tolerance. The current study aimed at elucidating the drought acclimation mechanisms in liverwort’s model M. polymorpha. The gemmae, asexual reproductive units of M. polymorpha, were exposed to sucrose (0.2 M), mannitol (0.5 M) and polyethylene glycol (PEG, 10%) for inducing physiological drought to investigate their effects at morphological, physiological and biochemical levels. Our results showed that drought exposure led to extreme growth inhibition, disruption of membrane stability and reduction in photosynthetic pigment contents in M. polymorpha. The increased accumulation of hydrogen peroxide and malondialdehyde, and the rate of electrolyte leakage in the gemmalings of M. polymorpha indicated an evidence of drought-caused oxidative stress. The gemmalings showed significant induction of the activities of key antioxidant enzymes, including superoxide dismutase, catalase, ascorbate peroxidase, dehydroascorbate reductase and glutathione S-transferase, and total antioxidant activity in response to increased oxidative stress under drought. Importantly, to counteract the drought effects, the gemmalings also accumulated a significant amount of proline, which coincided with the evolutionary presence of proline biosynthesis gene Δ1-pyrroline-5-carboxylate synthase 1 (P5CS1) in land plants. Furthermore, the application of exogenous abscisic acid (ABA) reduced drought-induced tissue damage and improved the activities of antioxidant enzymes and accumulation of proline, implying an archetypal role of this phytohormone in M. polymorpha for drought tolerance. We conclude that physiological drought tolerance mechanisms governed by the cellular antioxidants, proline and ABA were adopted in liverwort M. polym…
bibliographic citation: Ghosh et al. (2021) Acclimation of liverwort Marchantia polymorpha to physiological drought reveals important roles of antioxidant enzymes, proline and abscisic acid in land plant adaptation to osmotic stress. PeerJ 9:e12419 https://doi.org/10.7717/peerj.12419
date submitted: 2021-06-17
date accepted: 2021-10-10
issued: 2021-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghosh
  given name: Totan Kumar
author list: Agent
  family name: Tompa
  given name: Naznin Haque
author list: Agent
  family name: Rahman
  given name: Md. Mezanur
author list: Agent
  family name: Mohi-Ud-Din
  given name: Mohammed
author list: Agent
  family name: Al-Meraj
  given name: S. M. Zubair
author list: Agent
  family name: Biswas
  given name: Md. Sanaullah
author list: Agent
  family name: Mostofa
  given name: Mohammad Golam
doi: 10.7717/peerj.12419
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-10
copyright: © 2021 Ghosh et al.
attribution name: Ghosh et al.

Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders
type: item
type: AcademicArticle
description: Background Vaginal lubrication is a crucial physiological response that occurs at the beginning of sexual arousal. However, research on lubrication disorders (LD) is still in its infancy, and the role of long non-coding RNAs (lncRNAs) in LD remains unclear. This study aimed to explore the function of lncRNAs in the pathogenesis of vaginal LD. Methods The expression profiles of LD and normal control (NC) lncRNAs were examined using next-generation sequencing (NGS), and eight selected differentially expressed lncRNAs were verified by quantitative real-time PCR. We conducted GO annotation and KEGG pathway enrichment analyses to determine the principal functions of significantly deregulated genes. LncRNA-mRNA co-expression and protein-protein interaction (PPI) networks were constructed and the lncRNA transcription factors (TFs) were predicted. Results From the results, we identified 181,631 lncRNAs and 145,224 mRNAs in vaginal epithelial tissue. Subsequently, our preliminary judgment revealed a total of 499 up-regulated and 337 down-regulated lncRNAs in LD. The top three enriched GO items of the dysregulated lncRNAs included the following significant terms: “contractile fiber part,” “actin filament-based process,” and “contractile fiber”. The most enriched pathways were “cell-extracellular matrix interactions,” “muscle contraction,” “cell-cell communication,” and “cGMP-PKG signaling pathway”. Our results also showed that the lncRNA-mRNA co-expression network was a powerful platform for predicting lncRNA functions. We determined the three hub genes, ADCY5, CXCL12, and NMU, using PPI network construction and analysis. A total of 231 TFs were predicted with RHOXF1, SNAI2, ZNF354C and TBX15 were suspected to be involved in the mechanism of LD. Conclusion In this study, we constructed the lncRNA-mRNA co-expression network, predicted the lncRNA TFs, and comprehensively analyzed lncRNA expression profiles in LD, providing a basis for future studies on LD clinical biomarkers an…
format: application/pdf
format: text/html
creator: Jingjing Zhang
creator: Jing Zhang
creator: Shengnan Cong
creator: Jingyi Feng
creator: Lianjun Pan
creator: Yuan Zhu
creator: Aixia Zhang
creator: Jiehua Ma
subject: Bioinformatics
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.12485
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background Vaginal lubrication is a crucial physiological response that occurs at the beginning of sexual arousal. However, research on lubrication disorders (LD) is still in its infancy, and the role of long non-coding RNAs (lncRNAs) in LD remains unclear. This study aimed to explore the function of lncRNAs in the pathogenesis of vaginal LD. Methods The expression profiles of LD and normal control (NC) lncRNAs were examined using next-generation sequencing (NGS), and eight selected differentially expressed lncRNAs were verified by quantitative real-time PCR. We conducted GO annotation and KEGG pathway enrichment analyses to determine the principal functions of significantly deregulated genes. LncRNA-mRNA co-expression and protein-protein interaction (PPI) networks were constructed and the lncRNA transcription factors (TFs) were predicted. Results From the results, we identified 181,631 lncRNAs and 145,224 mRNAs in vaginal epithelial tissue. Subsequently, our preliminary judgment revealed a total of 499 up-regulated and 337 down-regulated lncRNAs in LD. The top three enriched GO items of the dysregulated lncRNAs included the following significant terms: “contractile fiber part,” “actin filament-based process,” and “contractile fiber”. The most enriched pathways were “cell-extracellular matrix interactions,” “muscle contraction,” “cell-cell communication,” and “cGMP-PKG signaling pathway”. Our results also showed that the lncRNA-mRNA co-expression network was a powerful platform for predicting lncRNA functions. We determined the three hub genes, ADCY5, CXCL12, and NMU, using PPI network construction and analysis. A total of 231 TFs were predicted with RHOXF1, SNAI2, ZNF354C and TBX15 were suspected to be involved in the mechanism of LD. Conclusion In this study, we constructed the lncRNA-mRNA co-expression network, predicted the lncRNA TFs, and comprehensively analyzed lncRNA expression profiles in LD, providing a basis for future studies on LD clinical biomarkers an…
bibliographic citation: Zhang et al. (2021) Transcriptome profiling of lncRNA and co-expression network in the vaginal epithelial tissue of women with lubrication disorders. PeerJ 9:e12485 https://doi.org/10.7717/peerj.12485
date submitted: 2020-12-16
date accepted: 2021-10-22
issued: 2021-11-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jingjing
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Cong
  given name: Shengnan
author list: Agent
  family name: Feng
  given name: Jingyi
author list: Agent
  family name: Pan
  given name: Lianjun
author list: Agent
  family name: Zhu
  given name: Yuan
author list: Agent
  family name: Zhang
  given name: Aixia
author list: Agent
  family name: Ma
  given name: Jiehua
doi: 10.7717/peerj.12485
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-10
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations
type: item
type: AcademicArticle
description: Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after high-throughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.
format: application/pdf
format: text/html
creator: Ozkan Aydemir
creator: Benedicta Mensah
creator: Patrick W. Marsh
creator: Benjamin Abuaku
creator: James Leslie Myers-Hansen
creator: Jeffrey A. Bailey
creator: Anita Ghansah
subject: Genetics
subject: Molecular Biology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11794
publisher: PeerJ Inc.
rights: © 2021 Aydemir et al.
abstract: Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after high-throughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.
bibliographic citation: Aydemir et al. (2021) Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations. PeerJ 9:e11794 https://doi.org/10.7717/peerj.11794
date submitted: 2020-12-09
date accepted: 2021-06-25
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Aydemir
  given name: Ozkan
author list: Agent
  family name: Mensah
  given name: Benedicta
author list: Agent
  family name: Marsh
  given name: Patrick W.
author list: Agent
  family name: Abuaku
  given name: Benjamin
author list: Agent
  family name: Myers-Hansen
  given name: James Leslie
author list: Agent
  family name: Bailey
  given name: Jeffrey A.
author list: Agent
  family name: Ghansah
  given name: Anita
doi: 10.7717/peerj.11794
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: ©2021 Aydemir et al.
attribution name: Aydemir et al.

MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla)
type: item
type: AcademicArticle
description: Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65–121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25–40% (Lacustris group), 50–87% (Reticulata group, Teleocichla), 68–168% (Saxatilis group), 125–200% (Wallacii group), and 158–241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon.
format: application/pdf
format: text/html
creator: Oldřich Říčan
creator: Klára Dragová
creator: Adriana Almirón
creator: Jorge Casciotta
creator: Jens Gottwald
creator: Lubomír Piálek
subject: Biodiversity
subject: Conservation Biology
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12283
publisher: PeerJ Inc.
rights: © 2021 Říčan et al.
abstract: Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65–121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25–40% (Lacustris group), 50–87% (Reticulata group, Teleocichla), 68–168% (Saxatilis group), 125–200% (Wallacii group), and 158–241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon.
bibliographic citation: Říčan et al. (2021) MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla). PeerJ 9:e12283 https://doi.org/10.7717/peerj.12283
date submitted: 2021-02-24
date accepted: 2021-09-20
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Říčan
  given name: Oldřich
author list: Agent
  family name: Dragová
  given name: Klára
author list: Agent
  family name: Almirón
  given name: Adriana
author list: Agent
  family name: Casciotta
  given name: Jorge
author list: Agent
  family name: Gottwald
  given name: Jens
author list: Agent
  family name: Piálek
  given name: Lubomír
doi: 10.7717/peerj.12283
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: © 2021 Říčan et al.
attribution name: Říčan et al.

Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey
type: item
type: AcademicArticle
description: Tick-borne diseases, such as those transmitted by the blacklegged tick Ixodes scapularis, are a significant and growing public health problem in the US. There is mounting evidence that co-occurring non-pathogenic microbes can also impact tick-borne disease transmission. Shotgun metagenome sequencing enables sampling of the complete tick hologenome—the collective genomes of the tick and all of the microbial species contained therein, whether pathogenic, commensal or symbiotic. This approach simultaneously uncovers taxonomic composition and allows the detection of intraspecific genetic variation, making it a useful tool to compare spatial differences across tick populations. We evaluated this approach by comparing hologenome data from two tick samples (N = 6 ticks per location) collected at a relatively fine spatial scale, approximately 23 km apart, within a single US county. Several intriguing variants in the data between the two sites were detected, including polymorphisms in both in the tick’s own mitochondrial DNA and that of a rickettsial endosymbiont. The two samples were broadly similar in terms of the microbial species present, including multiple known tick-borne pathogens (Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum), filarial nematodes, and Wolbachia and Babesia species. We assembled the complete genome of the rickettsial endosymbiont (most likely Rickettsia buchneri) from both populations. Our results provide further evidence for the use of shotgun metagenome sequencing as a tool to compare tick hologenomes and differentiate tick populations across localized spatial scales.
format: application/pdf
format: text/html
creator: Dana C. Price
creator: Reilly N. Brennan
creator: Nicole E. Wagner
creator: Andrea M. Egizi
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Parasitology
description: doi:10.7717/peerj.12313
publisher: PeerJ Inc.
rights: © 2021 Price et al.
abstract: Tick-borne diseases, such as those transmitted by the blacklegged tick Ixodes scapularis, are a significant and growing public health problem in the US. There is mounting evidence that co-occurring non-pathogenic microbes can also impact tick-borne disease transmission. Shotgun metagenome sequencing enables sampling of the complete tick hologenome—the collective genomes of the tick and all of the microbial species contained therein, whether pathogenic, commensal or symbiotic. This approach simultaneously uncovers taxonomic composition and allows the detection of intraspecific genetic variation, making it a useful tool to compare spatial differences across tick populations. We evaluated this approach by comparing hologenome data from two tick samples (N = 6 ticks per location) collected at a relatively fine spatial scale, approximately 23 km apart, within a single US county. Several intriguing variants in the data between the two sites were detected, including polymorphisms in both in the tick’s own mitochondrial DNA and that of a rickettsial endosymbiont. The two samples were broadly similar in terms of the microbial species present, including multiple known tick-borne pathogens (Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum), filarial nematodes, and Wolbachia and Babesia species. We assembled the complete genome of the rickettsial endosymbiont (most likely Rickettsia buchneri) from both populations. Our results provide further evidence for the use of shotgun metagenome sequencing as a tool to compare tick hologenomes and differentiate tick populations across localized spatial scales.
bibliographic citation: Price et al. (2021) Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey. PeerJ 9:e12313 https://doi.org/10.7717/peerj.12313
date submitted: 2021-03-17
date accepted: 2021-09-24
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Price
  given name: Dana C.
author list: Agent
  family name: Brennan
  given name: Reilly N.
author list: Agent
  family name: Wagner
  given name: Nicole E.
author list: Agent
  family name: Egizi
  given name: Andrea M.
doi: 10.7717/peerj.12313
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: ©2021 Price et al.
attribution name: Price et al.

Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim
type: item
type: AcademicArticle
description: Juglans mandshurica Maxim is a hermaphroditic plant belonging to the genus Juglans in the family Juglandaceae. The pollination period of female flowers is different from the loose powder period of male flowers on the same tree. In several trees, female flowers bloom first, whereas in others, male flowers bloom first. In this study, male and female flower buds of J. mandshurica at the physiological differentiation stage were used. Illumina-based transcriptome sequencing was performed, and the quality of the sequencing results was evaluated and analyzed. A total of 138,138 unigenes with an average length of 788 bp were obtained. There were 8,116 differentially expressed genes (DEGs); 2,840 genes were upregulated, and 5,276 genes were downregulated. The DEGs were classified by Gene Ontology and analyzed by Kyoto Encyclopedia of Genes and Genomes. The signal transduction factors involved in phytohormone synthesis were selected. The results displayed that ARF and SAUR were expressed differently in the auxin signaling pathway. Additionally, DELLA protein (a negative regulator of gibberellin), the cytokinin synthesis pathway, and A-ARR were downregulated. On April 2nd, the contents of IAA, GA, CTK, ETH and SA in male and female flower buds of two types of J. mandshurica were opposite, and there were obvious genes regulating gender differentiation. Overall, we found that the sex differentiation of J. mandshurica was related to various hormone signal transduction pathways, and hormone signal transduction plays a leading role in regulation.
format: application/pdf
format: text/html
creator: Baiting Qin
creator: Xiujun Lu
creator: Xiaomei Sun
creator: Jianguo Cui
creator: Jifeng Deng
creator: Lijie Zhang
subject: Agricultural Science
subject: Cell Biology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12328
publisher: PeerJ Inc.
rights: © 2021 Qin et al.
abstract: Juglans mandshurica Maxim is a hermaphroditic plant belonging to the genus Juglans in the family Juglandaceae. The pollination period of female flowers is different from the loose powder period of male flowers on the same tree. In several trees, female flowers bloom first, whereas in others, male flowers bloom first. In this study, male and female flower buds of J. mandshurica at the physiological differentiation stage were used. Illumina-based transcriptome sequencing was performed, and the quality of the sequencing results was evaluated and analyzed. A total of 138,138 unigenes with an average length of 788 bp were obtained. There were 8,116 differentially expressed genes (DEGs); 2,840 genes were upregulated, and 5,276 genes were downregulated. The DEGs were classified by Gene Ontology and analyzed by Kyoto Encyclopedia of Genes and Genomes. The signal transduction factors involved in phytohormone synthesis were selected. The results displayed that ARF and SAUR were expressed differently in the auxin signaling pathway. Additionally, DELLA protein (a negative regulator of gibberellin), the cytokinin synthesis pathway, and A-ARR were downregulated. On April 2nd, the contents of IAA, GA, CTK, ETH and SA in male and female flower buds of two types of J. mandshurica were opposite, and there were obvious genes regulating gender differentiation. Overall, we found that the sex differentiation of J. mandshurica was related to various hormone signal transduction pathways, and hormone signal transduction plays a leading role in regulation.
bibliographic citation: Qin et al. (2021) Transcriptome-based analysis of the hormone regulation mechanism of gender differentiation in Juglans mandshurica Maxim. PeerJ 9:e12328 https://doi.org/10.7717/peerj.12328
date submitted: 2021-01-26
date accepted: 2021-09-27
issued: 2021-11-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Baiting
author list: Agent
  family name: Lu
  given name: Xiujun
author list: Agent
  family name: Sun
  given name: Xiaomei
author list: Agent
  family name: Cui
  given name: Jianguo
author list: Agent
  family name: Deng
  given name: Jifeng
author list: Agent
  family name: Zhang
  given name: Lijie
doi: 10.7717/peerj.12328
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-09
copyright: © 2021 Qin et al.
attribution name: Qin et al.

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