PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new and very spiny lizard (Gymnophthalmidae: Echinosaura) from the Andes in northwestern Ecuador
items: Current freezing and thawing scenarios employed by North Atlantic fisheries: their potential role in Newfoundland and Labrador’s northern cod (Gadus morhua) fishery
items: CRYAB predicts clinical prognosis and is associated with immunocyte infiltration in colorectal cancer
items: Identification of Theileria spp. in sheep and goats from Jeddah, Saudi Arabia, using molecular techniques
items: A fresh look at Cladarosymblema narrienense, a tetrapodomorph fish (Sarcopterygii: Megalichthyidae) from the Carboniferous of Australia, illuminated via X-ray tomography
items: Transcriptome atlas of Phalaenopsis equestris
items: Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
items: Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea)
items: Description and ontogeny of a 40-million-year-old parasitic isopodan crustacean: Parvucymoides dvorakorum gen. et sp. nov.
items: Origin of the X-chromosome influences the development and treatment outcomes of Turner syndrome

A new and very spiny lizard (Gymnophthalmidae: Echinosaura) from the Andes in northwestern Ecuador
type: item
type: AcademicArticle
description: We describe a new species of Neotropical spiny-lizard of the genus Echinosaura from the Imbabura and Carchi Provinces on the western slopes of the Andes in northwestern Ecuador. The new species mostly resembles E. horrida. However, it can be distinguished from all congeners by having keeled enlarged dorsal scales forming a paired vertebral row, two paravertebral series of short oblique rows of projecting scales, and a pair of spine-like scales on temporal and nuchal regions. We also provide a detailed description of the osteology of the skull and pectoral girdle of the new species and present a phylogenetic hypothesis for Echinosaura based on three mitochondrial genes (12S, 16S, ND4) and one nuclear gene (c-mos).
format: application/pdf
format: text/html
creator: Mario H. Yánez-Muñoz
creator: Omar Torres-Carvajal
creator: Juan P. Reyes-Puig
creator: Miguel A. Urgiles-Merchán
creator: Claudia Koch
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12523
publisher: PeerJ Inc.
rights: © 2021 Yánez-Muñoz et al.
abstract: We describe a new species of Neotropical spiny-lizard of the genus Echinosaura from the Imbabura and Carchi Provinces on the western slopes of the Andes in northwestern Ecuador. The new species mostly resembles E. horrida. However, it can be distinguished from all congeners by having keeled enlarged dorsal scales forming a paired vertebral row, two paravertebral series of short oblique rows of projecting scales, and a pair of spine-like scales on temporal and nuchal regions. We also provide a detailed description of the osteology of the skull and pectoral girdle of the new species and present a phylogenetic hypothesis for Echinosaura based on three mitochondrial genes (12S, 16S, ND4) and one nuclear gene (c-mos).
bibliographic citation: Yánez-Muñoz et al. (2021) A new and very spiny lizard (Gymnophthalmidae: Echinosaura) from the Andes in northwestern Ecuador. PeerJ 9:e12523 https://doi.org/10.7717/peerj.12523
date submitted: 2021-09-06
date accepted: 2021-10-29
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yánez-Muñoz
  given name: Mario H.
author list: Agent
  family name: Torres-Carvajal
  given name: Omar
author list: Agent
  family name: Reyes-Puig
  given name: Juan P.
author list: Agent
  family name: Urgiles-Merchán
  given name: Miguel A.
author list: Agent
  family name: Koch
  given name: Claudia
doi: 10.7717/peerj.12523
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: ©2021 Yánez-Muñoz et al.
attribution name: Yánez-Muñoz et al.

Current freezing and thawing scenarios employed by North Atlantic fisheries: their potential role in Newfoundland and Labrador’s northern cod (Gadus morhua) fishery
type: item
type: AcademicArticle
description: Seafood is very perishable and can quickly spoil due to three mechanisms: autolysis, microbial degradation, and oxidation. Primary commercial sectors within the North Atlantic fisheries include demersal, pelagic, and shellfish fisheries. The preservation techniques employed across each sector can be relatively consistent; however, some key differences exist across species and regions to maintain product freshness. Freezing has long been employed as a preservation technique to maintain product quality for extended periods. Freezing allows seafood to be held until demand improves and shipped long distances using lower-cost ground transportation while maintaining organoleptic properties and product quality. Thawing is the opposite of freezing and can be applied before additional processing or the final sale point. However, all preservation techniques have limitations, and a properly frozen and thawed fish will still suffer from drip loss. This review summarizes the general introduction of spoilage and seafood spoilage mechanisms and the latest preservation techniques in the seafood industry, focusing on freezing and thawing processes and technologies. This review also considers the concept of global value chains (GVC) and the points to freeze and thaw seafood along the GVC to improve its quality with the intention of helping Newfoundland and Labrador’s emerging Northern cod (Gadus morhua) fisheries enhance product quality, meet market demands and increase stakeholder value.
format: application/pdf
format: text/html
creator: Pete Brown
creator: Deepika Dave
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Food Science and Technology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12526
publisher: PeerJ Inc.
rights: © 2021 Brown and Dave
abstract: Seafood is very perishable and can quickly spoil due to three mechanisms: autolysis, microbial degradation, and oxidation. Primary commercial sectors within the North Atlantic fisheries include demersal, pelagic, and shellfish fisheries. The preservation techniques employed across each sector can be relatively consistent; however, some key differences exist across species and regions to maintain product freshness. Freezing has long been employed as a preservation technique to maintain product quality for extended periods. Freezing allows seafood to be held until demand improves and shipped long distances using lower-cost ground transportation while maintaining organoleptic properties and product quality. Thawing is the opposite of freezing and can be applied before additional processing or the final sale point. However, all preservation techniques have limitations, and a properly frozen and thawed fish will still suffer from drip loss. This review summarizes the general introduction of spoilage and seafood spoilage mechanisms and the latest preservation techniques in the seafood industry, focusing on freezing and thawing processes and technologies. This review also considers the concept of global value chains (GVC) and the points to freeze and thaw seafood along the GVC to improve its quality with the intention of helping Newfoundland and Labrador’s emerging Northern cod (Gadus morhua) fisheries enhance product quality, meet market demands and increase stakeholder value.
bibliographic citation: Brown et al. (2021) Current freezing and thawing scenarios employed by North Atlantic fisheries: their potential role in Newfoundland and Labrador’s northern cod (Gadus morhua) fishery. PeerJ 9:e12526 https://doi.org/10.7717/peerj.12526
date submitted: 2021-07-16
date accepted: 2021-10-30
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Pete
author list: Agent
  family name: Dave
  given name: Deepika
doi: 10.7717/peerj.12526
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: ©2021 Brown and Dave
attribution name: Brown and Dave

CRYAB predicts clinical prognosis and is associated with immunocyte infiltration in colorectal cancer
type: item
type: AcademicArticle
description: Background αB-Crystallin (CRYAB) is differentially expressed in various tumors. However, the correlation between CRYAB and immune cell infiltration in colorectal cancer (CRC) remains unclear. Materials & Methods Kaplan–Meier survival curves in The Cancer Genome Atlas (TCGA) were used to evaluate the relationship between CRYAB expression and both overall survival and progression-free survival. The relationships between CRYAB expression and infiltrating immune cells and their corresponding gene marker sets were examined using the TIMER database. Results The expression of CRYAB was lower in CRC tumor tissues than in normal tissues (P < 0.05). High CRYAB gene expression and high levels of CRYAB gene methylation were correlated with high-grade malignant tumors and more advanced tumor, nodes and metastasis (TNM) cancer stages. In addition, in colorectal cancer, there was a positive correlation between CRYAB expression and immune infiltrating cells including neutrophils, macrophages, CD8 + T cells, and CD4 + T cells, as well as immune-related genes including CD2, CD3D, and CD3E. Methylation sites such as cg13084335, cg15545878, cg13210534, and cg15318568 were positively correlated with low expression of CRYAB. Conclusion Because CRYAB likely plays an important role in immune cell infiltration, it may be a potential tumor-suppressor gene in CRC and a potential novel therapeutic target and predictive biomarker for colorectal cancer (CRC).
format: application/pdf
format: text/html
creator: Junsheng Deng
creator: Xiaoli Chen
creator: Ting Zhan
creator: Mengge Chen
creator: Xisheng Yan
creator: Xiaodong Huang
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12578
publisher: PeerJ Inc.
rights: © 2021 Deng et al.
abstract: Background αB-Crystallin (CRYAB) is differentially expressed in various tumors. However, the correlation between CRYAB and immune cell infiltration in colorectal cancer (CRC) remains unclear. Materials & Methods Kaplan–Meier survival curves in The Cancer Genome Atlas (TCGA) were used to evaluate the relationship between CRYAB expression and both overall survival and progression-free survival. The relationships between CRYAB expression and infiltrating immune cells and their corresponding gene marker sets were examined using the TIMER database. Results The expression of CRYAB was lower in CRC tumor tissues than in normal tissues (P < 0.05). High CRYAB gene expression and high levels of CRYAB gene methylation were correlated with high-grade malignant tumors and more advanced tumor, nodes and metastasis (TNM) cancer stages. In addition, in colorectal cancer, there was a positive correlation between CRYAB expression and immune infiltrating cells including neutrophils, macrophages, CD8 + T cells, and CD4 + T cells, as well as immune-related genes including CD2, CD3D, and CD3E. Methylation sites such as cg13084335, cg15545878, cg13210534, and cg15318568 were positively correlated with low expression of CRYAB. Conclusion Because CRYAB likely plays an important role in immune cell infiltration, it may be a potential tumor-suppressor gene in CRC and a potential novel therapeutic target and predictive biomarker for colorectal cancer (CRC).
bibliographic citation: Deng et al. (2021) CRYAB predicts clinical prognosis and is associated with immunocyte infiltration in colorectal cancer. PeerJ 9:e12578 https://doi.org/10.7717/peerj.12578
date submitted: 2021-03-29
date accepted: 2021-11-09
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Deng
  given name: Junsheng
author list: Agent
  family name: Chen
  given name: Xiaoli
author list: Agent
  family name: Zhan
  given name: Ting
author list: Agent
  family name: Chen
  given name: Mengge
author list: Agent
  family name: Yan
  given name: Xisheng
author list: Agent
  family name: Huang
  given name: Xiaodong
doi: 10.7717/peerj.12578
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: ©2021 Deng et al.
attribution name: Deng et al.

Identification of Theileria spp. in sheep and goats from Jeddah, Saudi Arabia, using molecular techniques
type: item
type: AcademicArticle
description: Background Thileriosis is a tick -born disease caused by hemoprotozoan parasites which has global veterinary and economic implications. Methods Blood samples were collected from 216 sheep and 83 goats from Jeddah, Saudi Arabia, were analyzed to determine whether the animals were infected with Theileria spp. parasites. The parasites were detected using a polymerase chain reaction (PCR) targeting the gene of 18S rRNA followed by sequencing. Results According to obtained findings, Theileria spp. were detected in sheep (57.8%, 48/83) and goats (51.9%, 112/216). Phylogenetic analysis to sequence data showed that T. ovis identified in this study were found to be closely connected to an isolate from Turkey, with 84.4–99.8% pairwise identity and 52.35–99.79% coverage.
format: application/pdf
format: text/html
creator: Dina M. Metwally
creator: Reem Alajmi
creator: Muslimah N. Alsulami
creator: Isra M. Al-Turaiki
creator: Rewaida Abdel-Gaber
creator: Afrah F. Alkhuriji
creator: Haleema H. Albohiri
creator: Khalil Mohamed
creator: Hanadi B. Baghdadi
creator: Manal F. El-Khadragy
creator: Guillermo T. Isaias
creator: Saeed El-Ashram
subject: Bioinformatics
subject: Parasitology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.12596
publisher: PeerJ Inc.
rights: © 2021 Metwally et al.
abstract: Background Thileriosis is a tick -born disease caused by hemoprotozoan parasites which has global veterinary and economic implications. Methods Blood samples were collected from 216 sheep and 83 goats from Jeddah, Saudi Arabia, were analyzed to determine whether the animals were infected with Theileria spp. parasites. The parasites were detected using a polymerase chain reaction (PCR) targeting the gene of 18S rRNA followed by sequencing. Results According to obtained findings, Theileria spp. were detected in sheep (57.8%, 48/83) and goats (51.9%, 112/216). Phylogenetic analysis to sequence data showed that T. ovis identified in this study were found to be closely connected to an isolate from Turkey, with 84.4–99.8% pairwise identity and 52.35–99.79% coverage.
bibliographic citation: Metwally et al. (2021) Identification of Theileria spp. in sheep and goats from Jeddah, Saudi Arabia, using molecular techniques. PeerJ 9:e12596 https://doi.org/10.7717/peerj.12596
date submitted: 2021-07-06
date accepted: 2021-11-14
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Metwally
  given name: Dina M.
author list: Agent
  family name: Alajmi
  given name: Reem
author list: Agent
  family name: Alsulami
  given name: Muslimah N.
author list: Agent
  family name: Al-Turaiki
  given name: Isra M.
author list: Agent
  family name: Abdel-Gaber
  given name: Rewaida
author list: Agent
  family name: Alkhuriji
  given name: Afrah F.
author list: Agent
  family name: Albohiri
  given name: Haleema H.
author list: Agent
  family name: Mohamed
  given name: Khalil
author list: Agent
  family name: Baghdadi
  given name: Hanadi B.
author list: Agent
  family name: El-Khadragy
  given name: Manal F.
author list: Agent
  family name: Isaias
  given name: Guillermo T.
author list: Agent
  family name: El-Ashram
  given name: Saeed
doi: 10.7717/peerj.12596
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: ©2021 Metwally et al.
attribution name: Metwally et al.

A fresh look at Cladarosymblema narrienense, a tetrapodomorph fish (Sarcopterygii: Megalichthyidae) from the Carboniferous of Australia, illuminated via X-ray tomography
type: item
type: AcademicArticle
description: Background The megalichthyids are one of several clades of extinct tetrapodomorph fish that lived throughout the Devonian–Permian periods. They are advanced “osteolepidid-grade” fishes that lived in freshwater swamp and lake environments, with some taxa growing to very large sizes. They bear cosmine-covered bones and a large premaxillary tusk that lies lingually to a row of small teeth. Diagnosis of the family remains controversial with various authors revising it several times in recent works. There are fewer than 10 genera known globally, and only one member definitively identified from Gondwana. Cladarosymblema narrienense Fox et al. 1995 was described from the Lower Carboniferous Raymond Formation in Queensland, Australia, on the basis of several well-preserved specimens. Despite this detailed work, several aspects of its anatomy remain undescribed. Methods Two especially well-preserved 3D fossils of Cladarosymblema narrienense, including the holotype specimen, are scanned using synchrotron or micro-computed tomography (µCT), and 3D modelled using specialist segmentation and visualisation software. New anatomical detail, in particular internal anatomy, is revealed for the first time in this taxon. A novel phylogenetic matrix, adapted from other recent work on tetrapodomorphs, is used to clarify the interrelationships of the megalichthyids and confirm the phylogenetic position of C. narrienense. Results Never before seen morphological details of the palate, hyoid arch, basibranchial skeleton, pectoral girdle and axial skeleton are revealed and described. Several additional features are confirmed or updated from the original description. Moreover, the first full, virtual cranial endocast of any tetrapodomorph fish is presented and described, giving insight into the early neural adaptations in this group. Phylogenetic analysis confirms the monophyly of the Megalichthyidae with seven genera included (Askerichthys, Cladarosymblema, Ectosteorhachis, Mahalalepis, Megal…
format: application/pdf
format: text/html
creator: Alice M. Clement
creator: Richard Cloutier
creator: Jing Lu
creator: Egon Perilli
creator: Anton Maksimenko
creator: John Long
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12597
publisher: PeerJ Inc.
rights: © 2021 Clement et al.
abstract: Background The megalichthyids are one of several clades of extinct tetrapodomorph fish that lived throughout the Devonian–Permian periods. They are advanced “osteolepidid-grade” fishes that lived in freshwater swamp and lake environments, with some taxa growing to very large sizes. They bear cosmine-covered bones and a large premaxillary tusk that lies lingually to a row of small teeth. Diagnosis of the family remains controversial with various authors revising it several times in recent works. There are fewer than 10 genera known globally, and only one member definitively identified from Gondwana. Cladarosymblema narrienense Fox et al. 1995 was described from the Lower Carboniferous Raymond Formation in Queensland, Australia, on the basis of several well-preserved specimens. Despite this detailed work, several aspects of its anatomy remain undescribed. Methods Two especially well-preserved 3D fossils of Cladarosymblema narrienense, including the holotype specimen, are scanned using synchrotron or micro-computed tomography (µCT), and 3D modelled using specialist segmentation and visualisation software. New anatomical detail, in particular internal anatomy, is revealed for the first time in this taxon. A novel phylogenetic matrix, adapted from other recent work on tetrapodomorphs, is used to clarify the interrelationships of the megalichthyids and confirm the phylogenetic position of C. narrienense. Results Never before seen morphological details of the palate, hyoid arch, basibranchial skeleton, pectoral girdle and axial skeleton are revealed and described. Several additional features are confirmed or updated from the original description. Moreover, the first full, virtual cranial endocast of any tetrapodomorph fish is presented and described, giving insight into the early neural adaptations in this group. Phylogenetic analysis confirms the monophyly of the Megalichthyidae with seven genera included (Askerichthys, Cladarosymblema, Ectosteorhachis, Mahalalepis, Megal…
bibliographic citation: Clement et al. (2021) A fresh look at Cladarosymblema narrienense, a tetrapodomorph fish (Sarcopterygii: Megalichthyidae) from the Carboniferous of Australia, illuminated via X-ray tomography. PeerJ 9:e12597 https://doi.org/10.7717/peerj.12597
date submitted: 2021-09-28
date accepted: 2021-11-14
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clement
  given name: Alice M.
author list: Agent
  family name: Cloutier
  given name: Richard
author list: Agent
  family name: Lu
  given name: Jing
author list: Agent
  family name: Perilli
  given name: Egon
author list: Agent
  family name: Maksimenko
  given name: Anton
author list: Agent
  family name: Long
  given name: John
doi: 10.7717/peerj.12597
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: ©2021 Clement et al.
attribution name: Clement et al.

Transcriptome atlas of Phalaenopsis equestris
type: item
type: AcademicArticle
description: The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here, we present an RNA-seq-based transcriptome map of P. equestris that covers 19 organs of the plant, including leaves, roots, floral organs and the shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of the P. equestris transcriptome map with the gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) for visualizing gene expression profiles. As an example of the application, we analyzed the expression of Phalaenopsis “orphan” genes–those that do not have recognizable similarity with the genes of other plants. We found that approximately half of these genes were not expressed; the ones that were expressed were predominantly expressed in reproductive structures.
format: application/pdf
format: text/html
creator: Anna V. Klepikova
creator: Artem S. Kasianov
creator: Margarita A. Ezhova
creator: Aleksey A. Penin
creator: Maria D. Logacheva
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12600
publisher: PeerJ Inc.
rights: © 2021 Klepikova et al.
abstract: The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here, we present an RNA-seq-based transcriptome map of P. equestris that covers 19 organs of the plant, including leaves, roots, floral organs and the shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of the P. equestris transcriptome map with the gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) for visualizing gene expression profiles. As an example of the application, we analyzed the expression of Phalaenopsis “orphan” genes–those that do not have recognizable similarity with the genes of other plants. We found that approximately half of these genes were not expressed; the ones that were expressed were predominantly expressed in reproductive structures.
bibliographic citation: Klepikova et al. (2021) Transcriptome atlas of Phalaenopsis equestris. PeerJ 9:e12600 https://doi.org/10.7717/peerj.12600
date submitted: 2020-11-26
date accepted: 2021-11-15
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klepikova
  given name: Anna V.
author list: Agent
  family name: Kasianov
  given name: Artem S.
author list: Agent
  family name: Ezhova
  given name: Margarita A.
author list: Agent
  family name: Penin
  given name: Aleksey A.
author list: Agent
  family name: Logacheva
  given name: Maria D.
doi: 10.7717/peerj.12600
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: ©2021 Klepikova et al.
attribution name: Klepikova et al.

Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank
type: item
type: AcademicArticle
description: Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank.
format: application/pdf
format: text/html
creator: Yoonhee Cho
creator: Ji Seon Kim
creator: Yu-Cheng Dai
creator: Yusufjon Gafforov
creator: Young Woon Lim
subject: Bioinformatics
subject: Ecology
subject: Mycology
subject: Taxonomy
description: doi:10.7717/peerj.12625
publisher: PeerJ Inc.
rights: © 2021 Cho et al.
abstract: Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank.
bibliographic citation: Cho et al. (2021) Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank. PeerJ 9:e12625 https://doi.org/10.7717/peerj.12625
date submitted: 2021-08-26
date accepted: 2021-11-19
issued: 2021-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cho
  given name: Yoonhee
author list: Agent
  family name: Kim
  given name: Ji Seon
author list: Agent
  family name: Dai
  given name: Yu-Cheng
author list: Agent
  family name: Gafforov
  given name: Yusufjon
author list: Agent
  family name: Lim
  given name: Young Woon
doi: 10.7717/peerj.12625
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-10
copyright: © 2021 Cho et al.
attribution name: Cho et al.

Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea)
type: item
type: AcademicArticle
description: The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.
format: application/pdf
format: text/html
creator: Xinghao Li
creator: Nan Song
creator: Heng Zhang
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12169
publisher: PeerJ Inc.
rights: © 2021 Xinghao et al.
abstract: The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.
bibliographic citation: Li et al. (2021) Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea). PeerJ 9:e12169 https://doi.org/10.7717/peerj.12169
date submitted: 2021-03-18
date accepted: 2021-08-26
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xinghao
author list: Agent
  family name: Song
  given name: Nan
author list: Agent
  family name: Zhang
  given name: Heng
doi: 10.7717/peerj.12169
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: ©2021 Xinghao et al.
attribution name: Xinghao et al.

Description and ontogeny of a 40-million-year-old parasitic isopodan crustacean: Parvucymoides dvorakorum gen. et sp. nov.
type: item
type: AcademicArticle
description: A collection of exceptionally well-preserved fossil specimens of crustaceans, clearly representatives of Isopoda, is presented here. Excavated from the late Eocene (approximately 40 million years ago) freshwater sediments of the Trupelník hill field site near Kučlín, Czech Republic, these specimens are preserved with many details of the appendages. The morphological characteristics of the fossils were documented using macro-photography with polarised light, as well as stereo imaging. These characteristics, especially including the trunk appendage morphology, were compared to those of related extant groups from different ontogenetic stages. All specimens are conspecific, representing a single species Parvucymoides dvorakorum gen. et sp. nov. Morphometric analysis of body shapes and sizes of the reconstructed fossils and related extant species were performed. These analyses provided insight into the ontogenetic stages of each reconstructed fossil specimen. In combination with the morphological assessment, the results indicate that the fossils represent at least two (possibly three) developmental stages, including immatures. The morphology of the appendages suggests that these fossils were parasites. The fossils are interpreted as either representatives of Cymothoidae or at least closely related to this group.
format: application/pdf
format: text/html
creator: Serita Van der Wal
creator: Mario Schädel
creator: Boris Ekrt
creator: Joachim T. Haug
subject: Biodiversity
subject: Environmental Sciences
subject: Paleontology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.12317
publisher: PeerJ Inc.
rights: © 2021 Van der Wal et al.
abstract: A collection of exceptionally well-preserved fossil specimens of crustaceans, clearly representatives of Isopoda, is presented here. Excavated from the late Eocene (approximately 40 million years ago) freshwater sediments of the Trupelník hill field site near Kučlín, Czech Republic, these specimens are preserved with many details of the appendages. The morphological characteristics of the fossils were documented using macro-photography with polarised light, as well as stereo imaging. These characteristics, especially including the trunk appendage morphology, were compared to those of related extant groups from different ontogenetic stages. All specimens are conspecific, representing a single species Parvucymoides dvorakorum gen. et sp. nov. Morphometric analysis of body shapes and sizes of the reconstructed fossils and related extant species were performed. These analyses provided insight into the ontogenetic stages of each reconstructed fossil specimen. In combination with the morphological assessment, the results indicate that the fossils represent at least two (possibly three) developmental stages, including immatures. The morphology of the appendages suggests that these fossils were parasites. The fossils are interpreted as either representatives of Cymothoidae or at least closely related to this group.
bibliographic citation: Van der Wal et al. (2021) Description and ontogeny of a 40-million-year-old parasitic isopodan crustacean: Parvucymoides dvorakorum gen. et sp. nov.. PeerJ 9:e12317 https://doi.org/10.7717/peerj.12317
date submitted: 2021-02-18
date accepted: 2021-09-25
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Van der Wal
  given name: Serita
author list: Agent
  family name: Schädel
  given name: Mario
author list: Agent
  family name: Ekrt
  given name: Boris
author list: Agent
  family name: Haug
  given name: Joachim T.
doi: 10.7717/peerj.12317
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Van der Wal et al.
attribution name: Van der Wal et al.

Origin of the X-chromosome influences the development and treatment outcomes of Turner syndrome
type: item
type: AcademicArticle
description: Turner syndrome (TS) affects 1/2,500 live-born female infants. In the present study, we attempted to clarify the relationship between genetic factors (especially the X-chromosome origin), clinical features, body/sexual development, and treatment outcomes. We enrolled 39 female infants aged between 3 and 14 years. General demographic and clinical features were documented, and laboratory analysis of blood samples was performed. Subject karyotype was determined by G-banding of 50 peripheral white blood cells, and the parenteral origin of the retained X-chromosome was determined. Next, growth hormone (GH) treatment was prescribed for 12 months, with follow-ups performed as determined. For patient groups separated according to X-chromosome origin, the basal height, bone age, insulin-like growth factor (IGF)-1, and insulin-like growth factor binding protein-3 (IGFBP-3) levels were comparable; however, after the 12-month treatment, significant differences in the height increase and IGF-1 levels were observed. If the X-chromosome (or chromosomes) originated from both parents, the increase in height was less substantial, with lower serum IGF-1 levels. The uterine size, prolactin level, increased weight after treatment, and bone age difference after treatment negatively correlated with the mother’s age at the time of birth. The mother’s height at the time of birth demonstrated a negative correlation with the basal bone age difference and a positive correlation with the IGF-1 level. In summary, the retained X-chromosome derived from both parents is associated with poorer response to GH therapy. The mother’s age and height at the time of birth can strongly impact the patient’s body/sexual development and the response to GH treatment. Thus, the mother’s age and height at the time of birth and the parental origin of the X-chromosome should be carefully considered before developing a treatment plan for TS.
format: application/pdf
format: text/html
creator: Ying Zhang
creator: Yongchen Yang
creator: Pin Li
creator: Sheng Guo
subject: Pediatrics
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.12354
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Turner syndrome (TS) affects 1/2,500 live-born female infants. In the present study, we attempted to clarify the relationship between genetic factors (especially the X-chromosome origin), clinical features, body/sexual development, and treatment outcomes. We enrolled 39 female infants aged between 3 and 14 years. General demographic and clinical features were documented, and laboratory analysis of blood samples was performed. Subject karyotype was determined by G-banding of 50 peripheral white blood cells, and the parenteral origin of the retained X-chromosome was determined. Next, growth hormone (GH) treatment was prescribed for 12 months, with follow-ups performed as determined. For patient groups separated according to X-chromosome origin, the basal height, bone age, insulin-like growth factor (IGF)-1, and insulin-like growth factor binding protein-3 (IGFBP-3) levels were comparable; however, after the 12-month treatment, significant differences in the height increase and IGF-1 levels were observed. If the X-chromosome (or chromosomes) originated from both parents, the increase in height was less substantial, with lower serum IGF-1 levels. The uterine size, prolactin level, increased weight after treatment, and bone age difference after treatment negatively correlated with the mother’s age at the time of birth. The mother’s height at the time of birth demonstrated a negative correlation with the basal bone age difference and a positive correlation with the IGF-1 level. In summary, the retained X-chromosome derived from both parents is associated with poorer response to GH therapy. The mother’s age and height at the time of birth can strongly impact the patient’s body/sexual development and the response to GH treatment. Thus, the mother’s age and height at the time of birth and the parental origin of the X-chromosome should be carefully considered before developing a treatment plan for TS.
bibliographic citation: Zhang et al. (2021) Origin of the X-chromosome influences the development and treatment outcomes of Turner syndrome. PeerJ 9:e12354 https://doi.org/10.7717/peerj.12354
date submitted: 2020-12-10
date accepted: 2021-09-29
issued: 2021-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ying
author list: Agent
  family name: Yang
  given name: Yongchen
author list: Agent
  family name: Li
  given name: Pin
author list: Agent
  family name: Guo
  given name: Sheng
doi: 10.7717/peerj.12354
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-09
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

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