PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: SEPALLATA­-like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs
items: Alterations of gut fungal microbiota in patients with rheumatoid arthritis
items: Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis
items: Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy
items: Analysis and comparison of protein secondary structures in the rachis of avian flight feathers
items: Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)
items: Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)
items: Response of bacterial community structure to different ecological niches and their functions in Korean pine forests
items: Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China
items: Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants

SEPALLATA­-like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs
type: item
type: AcademicArticle
description: Background The architecture of inflorescence and the development of floral organs can influence the yield of seeds and have a significant impact on plant propagation. E-class floral homeotic MADS-box genes exhibit important roles in regulation of floral transition and differentiation of floral organs. Woad (Isatis indigotica) possesses unique inflorescence, floral organs and fruit. However, very little research has been carried out to determine the function of MADS-box genes in this medicinal cruciferous plant species. Results SEPALLATA orthologs in I. indigotica were cloned by degenerate PCR. The sequence possessing the highest identity with SEP2 and SEP4 of Arabidopsis were named as IiSEP2 and IiSEP4, respectively. Constitutive expression of IiSEP2 in Columbia (Col-0) ecotype of Arabidopsis led to early flowering, and the number of the flowers and the lateral branches was reduced, indicating an alteration in architecture of the inflorescences. Moreover, the number of the floral organs was declined, the sepals were turned into carpelloid tissues bearing stigmatic papillae and ovules, and secondary flower could be produced in apetalous terminal flowers. In 35S::IiSEP4-GFP transgenic Arabidopsis plants in Landsberg erecta (Ler) genetic background, the number of the floral organs was decreased, sepals were converted into curly carpelloid structures, accompanied by generation of ovules. Simultaneously, the size of petals, stamens and siliques was diminished. In 35S::IiSEP4-GFP transgenic plants of apetalous ap1 cal double mutant in Ler genetic background, the cauliflower phenotype was attenuated significantly, and the petal formation could be rescued. Occasionally, chimeric organs composed of petaloid and sepaloid tissues, or petaloid and stamineous tissues, were produced in IiSEP4 transgenic plants of apl cal double mutant. It suggested that overexpression of IiSEP4 could restore the capacity in petal differentiation. Silencing of IiSEP4 by Virus-Induced Gene Silencin…
format: application/pdf
format: text/html
creator: Yan-Qin Ma
creator: Zuo-Qian Pu
creator: Xiao-Min Tan
creator: Qi Meng
creator: Kai-Li Zhang
creator: Liu Yang
creator: Ye-Ye Ma
creator: Xuan Huang
creator: Zi-Qin Xu
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13034
publisher: PeerJ Inc.
rights: © 2022 Ma et al.
abstract: Background The architecture of inflorescence and the development of floral organs can influence the yield of seeds and have a significant impact on plant propagation. E-class floral homeotic MADS-box genes exhibit important roles in regulation of floral transition and differentiation of floral organs. Woad (Isatis indigotica) possesses unique inflorescence, floral organs and fruit. However, very little research has been carried out to determine the function of MADS-box genes in this medicinal cruciferous plant species. Results SEPALLATA orthologs in I. indigotica were cloned by degenerate PCR. The sequence possessing the highest identity with SEP2 and SEP4 of Arabidopsis were named as IiSEP2 and IiSEP4, respectively. Constitutive expression of IiSEP2 in Columbia (Col-0) ecotype of Arabidopsis led to early flowering, and the number of the flowers and the lateral branches was reduced, indicating an alteration in architecture of the inflorescences. Moreover, the number of the floral organs was declined, the sepals were turned into carpelloid tissues bearing stigmatic papillae and ovules, and secondary flower could be produced in apetalous terminal flowers. In 35S::IiSEP4-GFP transgenic Arabidopsis plants in Landsberg erecta (Ler) genetic background, the number of the floral organs was decreased, sepals were converted into curly carpelloid structures, accompanied by generation of ovules. Simultaneously, the size of petals, stamens and siliques was diminished. In 35S::IiSEP4-GFP transgenic plants of apetalous ap1 cal double mutant in Ler genetic background, the cauliflower phenotype was attenuated significantly, and the petal formation could be rescued. Occasionally, chimeric organs composed of petaloid and sepaloid tissues, or petaloid and stamineous tissues, were produced in IiSEP4 transgenic plants of apl cal double mutant. It suggested that overexpression of IiSEP4 could restore the capacity in petal differentiation. Silencing of IiSEP4 by Virus-Induced Gene Silencin…
bibliographic citation: Ma et al. (2022) SEPALLATA­-like genes of Isatis indigotica can affect the architecture of the inflorescences and the development of the floral organs. PeerJ 10:e13034 https://doi.org/10.7717/peerj.13034
date submitted: 2021-09-06
date accepted: 2022-02-08
issued: 2022-03-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Yan-Qin
author list: Agent
  family name: Pu
  given name: Zuo-Qian
author list: Agent
  family name: Tan
  given name: Xiao-Min
author list: Agent
  family name: Meng
  given name: Qi
author list: Agent
  family name: Zhang
  given name: Kai-Li
author list: Agent
  family name: Yang
  given name: Liu
author list: Agent
  family name: Ma
  given name: Ye-Ye
author list: Agent
  family name: Huang
  given name: Xuan
author list: Agent
  family name: Xu
  given name: Zi-Qin
doi: 10.7717/peerj.13034
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-01
copyright: © 2022 Ma et al.
attribution name: Ma et al.

Alterations of gut fungal microbiota in patients with rheumatoid arthritis
type: item
type: AcademicArticle
description: Background Rheumatoid arthritis (RA) is a systemic autoimmune disease, in addition, gut microbiota plays an important role in the etiology of RA. However, our understanding of alterations to the gut fungal microbiota in Chinese population with RA is still limited. Methods Serum samples were obtained from 62 patients with RA, and 39 age- and gender-matched healthy controls (HCs). Fecal samples were obtained from 42 RA patients and 39 HCs. Fecal fungal microbiota targeting internal transcribed spacer region 2 (ITS2) rRNA genes was investigated using MiSeq sequencing, as well as their associations with some diagnostic biomarkers for RA. Results Our results showed that the fungal diversity did not alter in RA patients but taxonomic composition of the fecal fungal microbiota did. The gut mycobiota of RA patients was characterized by decreased abundance of Pholiota, Scedosporium, and Trichosporon. The linear discriminant analysis (LDA) effect size analysis (LEfSe) analysis identified several RA-enriched fungal genera, which were positively correlated with most RA biomarkers. Furthermore, since RA is an age- and gende-related disease, we classified RA patients into subgroups with age and gender and analyzed the sequencing results. Our data demonstrated that Wallemia and Irpex were the most discriminatory against RA patients over 60 years old, while Pseudeurotiaceae was the most discriminatory against female RA patients. Conclusions The case-control study presented here confirmed the alterations of gut fungal microbiota in Chinese patients with RA, and we speculated that the fungal dysbiosis may contribute to RA development.
format: application/pdf
format: text/html
creator: Xiaoyu Sun
creator: Yushuang Wang
creator: Xinke Li
creator: Meiling Wang
creator: Jianyi Dong
creator: Wei Tang
creator: Zengjie Lei
creator: Yuling Guo
creator: Ming Li
creator: Yuyuan Li
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Gastroenterology and Hepatology
subject: Rheumatology
description: doi:10.7717/peerj.13037
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Background Rheumatoid arthritis (RA) is a systemic autoimmune disease, in addition, gut microbiota plays an important role in the etiology of RA. However, our understanding of alterations to the gut fungal microbiota in Chinese population with RA is still limited. Methods Serum samples were obtained from 62 patients with RA, and 39 age- and gender-matched healthy controls (HCs). Fecal samples were obtained from 42 RA patients and 39 HCs. Fecal fungal microbiota targeting internal transcribed spacer region 2 (ITS2) rRNA genes was investigated using MiSeq sequencing, as well as their associations with some diagnostic biomarkers for RA. Results Our results showed that the fungal diversity did not alter in RA patients but taxonomic composition of the fecal fungal microbiota did. The gut mycobiota of RA patients was characterized by decreased abundance of Pholiota, Scedosporium, and Trichosporon. The linear discriminant analysis (LDA) effect size analysis (LEfSe) analysis identified several RA-enriched fungal genera, which were positively correlated with most RA biomarkers. Furthermore, since RA is an age- and gende-related disease, we classified RA patients into subgroups with age and gender and analyzed the sequencing results. Our data demonstrated that Wallemia and Irpex were the most discriminatory against RA patients over 60 years old, while Pseudeurotiaceae was the most discriminatory against female RA patients. Conclusions The case-control study presented here confirmed the alterations of gut fungal microbiota in Chinese patients with RA, and we speculated that the fungal dysbiosis may contribute to RA development.
bibliographic citation: Sun et al. (2022) Alterations of gut fungal microbiota in patients with rheumatoid arthritis. PeerJ 10:e13037 https://doi.org/10.7717/peerj.13037
date submitted: 2021-07-21
date accepted: 2022-02-09
issued: 2022-03-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xiaoyu
author list: Agent
  family name: Wang
  given name: Yushuang
author list: Agent
  family name: Li
  given name: Xinke
author list: Agent
  family name: Wang
  given name: Meiling
author list: Agent
  family name: Dong
  given name: Jianyi
author list: Agent
  family name: Tang
  given name: Wei
author list: Agent
  family name: Lei
  given name: Zengjie
author list: Agent
  family name: Guo
  given name: Yuling
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Li
  given name: Yuyuan
doi: 10.7717/peerj.13037
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-01
copyright: © 2022 Sun et al.
attribution name: Sun et al.

Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis
type: item
type: AcademicArticle
description: Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
format: application/pdf
format: text/html
creator: John Geoffrey Gill
creator: Kristina M. Hill-Spanik
creator: Kerry A. Whittaker
creator: Martin L. Jones
creator: Craig Plante
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.12835
publisher: PeerJ Inc.
rights: © 2022 Gill et al.
abstract: Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
bibliographic citation: Gill et al. (2022) Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 10:e12835 https://doi.org/10.7717/peerj.12835
date submitted: 2021-08-17
date accepted: 2022-01-04
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gill
  given name: John Geoffrey
author list: Agent
  family name: Hill-Spanik
  given name: Kristina M.
author list: Agent
  family name: Whittaker
  given name: Kerry A.
author list: Agent
  family name: Jones
  given name: Martin L.
author list: Agent
  family name: Plante
  given name: Craig
doi: 10.7717/peerj.12835
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Gill et al.
attribution name: Gill et al.

Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy
type: item
type: AcademicArticle
description: Iberian natural steppes have traditionally been used for extensive sheep grazing, which has been noted to be positively associated with steppe bird abundance and diversity. Sheep numbers in Spain, which harbors the largest European populations of many steppe bird species, decreased by 9.2 million (37.3%) between 1992 and 2020. Steppe birds in Spain have faced dramatic declines during the same period, but there is a lack of knowledge about the potential association between sheep and open-habitat bird declines. We used sheep data from the Spanish Ministry of Agriculture and bird data (1998–2018) from the Spanish Common Bird Monitoring Program to assess the association at the Spanish scale between sheep decline and the Farmland Bird Index (FBI) and the Natural Shrub-steppe Bird Index (SBI). We also used an independent dataset on population trends of the Dupont’s Lark (Chersophilus duponti) to assess the relationship between sheep numbers and the decline of this threatened steppe specialist passerine in Spain, whose European population is restricted to Iberian natural steppes. To test for a spurious relationship between temporal series, variables were tested for cointegration. After confirming cointegration, we found a strong positive relationship between sheep abundance and the trends of the FBI and SBI indices during the period 1998–2018. The association between sheep abundance and trends of the Dupont’s Lark (2004–2015) was positive although it was not statistically significant. Although the main causes of decline of farmland and steppe birds are mainly related to agricultural intensification and land use changes, the correlation found, using two independent cointegrated datasets, between the reduction in farmland and shrub-steppe birds and sheep numbers at the country scale suggests that the decline of steppe birds in Spain may be also associated with the decline in sheep numbers. This agrees with previous studies that found a positive relationship between intermedi…
format: application/pdf
format: text/html
creator: Juan Traba
creator: Cristian Pérez-Granados
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12870
publisher: PeerJ Inc.
rights: © 2022 Traba and Pérez-Granados
abstract: Iberian natural steppes have traditionally been used for extensive sheep grazing, which has been noted to be positively associated with steppe bird abundance and diversity. Sheep numbers in Spain, which harbors the largest European populations of many steppe bird species, decreased by 9.2 million (37.3%) between 1992 and 2020. Steppe birds in Spain have faced dramatic declines during the same period, but there is a lack of knowledge about the potential association between sheep and open-habitat bird declines. We used sheep data from the Spanish Ministry of Agriculture and bird data (1998–2018) from the Spanish Common Bird Monitoring Program to assess the association at the Spanish scale between sheep decline and the Farmland Bird Index (FBI) and the Natural Shrub-steppe Bird Index (SBI). We also used an independent dataset on population trends of the Dupont’s Lark (Chersophilus duponti) to assess the relationship between sheep numbers and the decline of this threatened steppe specialist passerine in Spain, whose European population is restricted to Iberian natural steppes. To test for a spurious relationship between temporal series, variables were tested for cointegration. After confirming cointegration, we found a strong positive relationship between sheep abundance and the trends of the FBI and SBI indices during the period 1998–2018. The association between sheep abundance and trends of the Dupont’s Lark (2004–2015) was positive although it was not statistically significant. Although the main causes of decline of farmland and steppe birds are mainly related to agricultural intensification and land use changes, the correlation found, using two independent cointegrated datasets, between the reduction in farmland and shrub-steppe birds and sheep numbers at the country scale suggests that the decline of steppe birds in Spain may be also associated with the decline in sheep numbers. This agrees with previous studies that found a positive relationship between intermedi…
bibliographic citation: Traba et al. (2022) Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy. PeerJ 10:e12870 https://doi.org/10.7717/peerj.12870
date submitted: 2021-10-12
date accepted: 2022-01-11
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Traba
  given name: Juan
author list: Agent
  family name: Pérez-Granados
  given name: Cristian
doi: 10.7717/peerj.12870
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Traba and Pérez-Granados
attribution name: Traba and Pérez-Granados

Analysis and comparison of protein secondary structures in the rachis of avian flight feathers
type: item
type: AcademicArticle
description: Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.
format: application/pdf
format: text/html
creator: Pin-Yen Lin
creator: Pei-Yu Huang
creator: Yao-Chang Lee
creator: Chen Siang Ng
subject: Biochemistry
subject: Biophysics
subject: Zoology
description: doi:10.7717/peerj.12919
publisher: PeerJ Inc.
rights: © 2022 Lin et al.
abstract: Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.
bibliographic citation: Lin et al. (2022) Analysis and comparison of protein secondary structures in the rachis of avian flight feathers. PeerJ 10:e12919 https://doi.org/10.7717/peerj.12919
date submitted: 2021-10-29
date accepted: 2022-01-20
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Pin-Yen
author list: Agent
  family name: Huang
  given name: Pei-Yu
author list: Agent
  family name: Lee
  given name: Yao-Chang
author list: Agent
  family name: Ng
  given name: Chen Siang
doi: 10.7717/peerj.12919
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Lin et al.
attribution name: Lin et al.

Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)
type: item
type: AcademicArticle
description: Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to decipher the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found high abundance proteins related to nitrate and amino acids metabolismsin the salt-tolerant cultivars. The significant increase in abundance of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. Moreover, the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including sterol side chain reductase, gamma aminobutyrate transaminase and starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future.
format: application/pdf
format: text/html
creator: Qiang Wang
creator: Baike Wang
creator: Huifang Liu
creator: Hongwei Han
creator: Hongmei Zhuang
creator: Juan Wang
creator: Tao Yang
creator: Hao Wang
creator: Yong Qin
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12955
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to decipher the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found high abundance proteins related to nitrate and amino acids metabolismsin the salt-tolerant cultivars. The significant increase in abundance of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. Moreover, the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including sterol side chain reductase, gamma aminobutyrate transaminase and starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future.
bibliographic citation: Wang et al. (2022) Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium). PeerJ 10:e12955 https://doi.org/10.7717/peerj.12955
date submitted: 2021-07-29
date accepted: 2022-01-27
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Wang
  given name: Baike
author list: Agent
  family name: Liu
  given name: Huifang
author list: Agent
  family name: Han
  given name: Hongwei
author list: Agent
  family name: Zhuang
  given name: Hongmei
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Yang
  given name: Tao
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.12955
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)
type: item
type: AcademicArticle
description: Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful i…
format: application/pdf
format: text/html
creator: Yaqi Wang
creator: Maoning Zhang
creator: Pei Du
creator: Hua Liu
creator: Zhongxin Zhang
creator: Jing Xu
creator: Li Qin
creator: Bingyan Huang
creator: Zheng Zheng
creator: Wenzhao Dong
creator: Xinyou Zhang
creator: Suoyi Han
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12965
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful i…
bibliographic citation: Wang et al. (2022) Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.). PeerJ 10:e12965 https://doi.org/10.7717/peerj.12965
date submitted: 2021-10-01
date accepted: 2022-01-28
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yaqi
author list: Agent
  family name: Zhang
  given name: Maoning
author list: Agent
  family name: Du
  given name: Pei
author list: Agent
  family name: Liu
  given name: Hua
author list: Agent
  family name: Zhang
  given name: Zhongxin
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Qin
  given name: Li
author list: Agent
  family name: Huang
  given name: Bingyan
author list: Agent
  family name: Zheng
  given name: Zheng
author list: Agent
  family name: Dong
  given name: Wenzhao
author list: Agent
  family name: Zhang
  given name: Xinyou
author list: Agent
  family name: Han
  given name: Suoyi
doi: 10.7717/peerj.12965
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Response of bacterial community structure to different ecological niches and their functions in Korean pine forests
type: item
type: AcademicArticle
description: A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemo…
format: application/pdf
format: text/html
creator: Rui-Qing Ji
creator: Meng-Le Xie
creator: Guan-Lin Li
creator: Yang Xu
creator: Ting-Ting Gao
creator: Peng-Jie Xing
creator: Li-Peng Meng
creator: Shu-Yan Liu
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12978
publisher: PeerJ Inc.
rights: © 2022 Ji et al.
abstract: A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemo…
bibliographic citation: Ji et al. (2022) Response of bacterial community structure to different ecological niches and their functions in Korean pine forests. PeerJ 10:e12978 https://doi.org/10.7717/peerj.12978
date submitted: 2021-07-05
date accepted: 2022-01-31
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Rui-Qing
author list: Agent
  family name: Xie
  given name: Meng-Le
author list: Agent
  family name: Li
  given name: Guan-Lin
author list: Agent
  family name: Xu
  given name: Yang
author list: Agent
  family name: Gao
  given name: Ting-Ting
author list: Agent
  family name: Xing
  given name: Peng-Jie
author list: Agent
  family name: Meng
  given name: Li-Peng
author list: Agent
  family name: Liu
  given name: Shu-Yan
doi: 10.7717/peerj.12978
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Ji et al.
attribution name: Ji et al.

Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China
type: item
type: AcademicArticle
description: Background With the exacerbating effects of the global climate change and the more and more attention to the study of plant carbon sink, an increasing number of researches on plant carbon sinks has grown. Although many studies exist on shrub vegetation, soil and litters, most studies focus on the community structure, biomass, surface soil of single plant and shrub layer vegetation, and lack the studies which included the potential relationships between climate change and ecological stoichiometric elements, comprehensive research on main species, even herb and litter layer. In order to provide relevant theoretical basis and data support, it is necessary to take the main terrestrial shrub ecosystem in Central Yunnan as the starting point to analyze and explore its carbon sink distribution characteristics, formation causes, the correlation between climatic factors (temperature and precipitation) and stoichiometric elements, which from community and species levels. Methods Plants which originated from 12 main shrub species, litter and soil samples which collected in 69 plots were from 23 plots (Q1–Q23) of 11 cities (countries) in the central Yunnan, China. The biomass and carbon density distribution pattern of each shrub ecosystem and the potential correlations with main climate factors was explored and identified. Some indexes were analyzed such as biomass and carbon density of each part of the shrub ecosystem distribution pattern, correlation, significant changes, formation reasons with the mean value (±standard deviation: SD). Through the redundancy analysis(RDA) of carbon (c), nitrogen (n), phosphorus (P) and main climate factors (precipitation and temperature), the distribution pattern of stoichiometric elements in shrub ecosystem can be judged. Results (1) The above-ground biomass (AGB), under-ground biomass (UGB) and root-shoot ratio (R/S) were between 1.13–2.03 t/hm2, 0.62–1.49 t/hm2, and 0.38–0.84, the carbon element was distributed in herb layer under-ground p…
format: application/pdf
format: text/html
creator: Zihao Guo
creator: Wei Chen
creator: Qianwei Chen
creator: Xingyue Liu
creator: Sisi Hong
creator: Xiuwen Zhu
creator: Hede Gong
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.13005
publisher: PeerJ Inc.
rights: © 2022 Guo et al.
abstract: Background With the exacerbating effects of the global climate change and the more and more attention to the study of plant carbon sink, an increasing number of researches on plant carbon sinks has grown. Although many studies exist on shrub vegetation, soil and litters, most studies focus on the community structure, biomass, surface soil of single plant and shrub layer vegetation, and lack the studies which included the potential relationships between climate change and ecological stoichiometric elements, comprehensive research on main species, even herb and litter layer. In order to provide relevant theoretical basis and data support, it is necessary to take the main terrestrial shrub ecosystem in Central Yunnan as the starting point to analyze and explore its carbon sink distribution characteristics, formation causes, the correlation between climatic factors (temperature and precipitation) and stoichiometric elements, which from community and species levels. Methods Plants which originated from 12 main shrub species, litter and soil samples which collected in 69 plots were from 23 plots (Q1–Q23) of 11 cities (countries) in the central Yunnan, China. The biomass and carbon density distribution pattern of each shrub ecosystem and the potential correlations with main climate factors was explored and identified. Some indexes were analyzed such as biomass and carbon density of each part of the shrub ecosystem distribution pattern, correlation, significant changes, formation reasons with the mean value (±standard deviation: SD). Through the redundancy analysis(RDA) of carbon (c), nitrogen (n), phosphorus (P) and main climate factors (precipitation and temperature), the distribution pattern of stoichiometric elements in shrub ecosystem can be judged. Results (1) The above-ground biomass (AGB), under-ground biomass (UGB) and root-shoot ratio (R/S) were between 1.13–2.03 t/hm2, 0.62–1.49 t/hm2, and 0.38–0.84, the carbon element was distributed in herb layer under-ground p…
bibliographic citation: Guo et al. (2022) Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China. PeerJ 10:e13005 https://doi.org/10.7717/peerj.13005
date submitted: 2021-10-11
date accepted: 2022-02-03
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Zihao
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Chen
  given name: Qianwei
author list: Agent
  family name: Liu
  given name: Xingyue
author list: Agent
  family name: Hong
  given name: Sisi
author list: Agent
  family name: Zhu
  given name: Xiuwen
author list: Agent
  family name: Gong
  given name: Hede
doi: 10.7717/peerj.13005
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Guo et al.
attribution name: Guo et al.

Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants
type: item
type: AcademicArticle
description: Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.
format: application/pdf
format: text/html
creator: Yu-Xuan Li
creator: Xing-Fan Dong
creator: Ai-Ling Yang
creator: Han-Bo Zhang
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13012
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.
bibliographic citation: Li et al. (2022) Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants. PeerJ 10:e13012 https://doi.org/10.7717/peerj.13012
date submitted: 2021-10-26
date accepted: 2022-02-04
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yu-Xuan
author list: Agent
  family name: Dong
  given name: Xing-Fan
author list: Agent
  family name: Yang
  given name: Ai-Ling
author list: Agent
  family name: Zhang
  given name: Han-Bo
doi: 10.7717/peerj.13012
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Li et al.
attribution name: Li et al.

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